diff options
| author | Alexander_Kabui | 2024-01-02 13:21:07 +0300 |
|---|---|---|
| committer | Alexander_Kabui | 2024-01-02 13:21:07 +0300 |
| commit | 70c4201b332e0e2c0d958428086512f291469b87 (patch) | |
| tree | aea4fac8782c110fc233c589c3f0f7bd34bada6c /gn2/wqflask/static | |
| parent | 5092eb42f062b1695c4e39619f0bd74a876cfac2 (diff) | |
| parent | 965ce5114d585624d5edb082c710b83d83a3be40 (diff) | |
| download | genenetwork2-70c4201b332e0e2c0d958428086512f291469b87.tar.gz | |
merge changes
Diffstat (limited to 'gn2/wqflask/static')
164 files changed, 22431 insertions, 0 deletions
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00000000..1501e280 --- /dev/null +++ b/gn2/wqflask/static/new/css/autocomplete.css @@ -0,0 +1,85 @@ +.autocomplete { + /*the container must be positioned relative:*/ + position: relative; + display: inline-block; + + +} + +input.autocomplete { + border: 1px solid transparent; + background-color: #f1f1f1; + padding: 10px; + font-size: 16px; +} + +input[type=text].autocomplete { + background-color: #f1f1f1; + width: 100%; +} + +input[type=submit].autocomplete { + background-color: DodgerBlue; + color: #fff; +} + +.autocomplete-items { + position: absolute; + border: 1px solid #d4d4d4; + border-bottom: none; + border-top: none; + z-index: 99; + /*position the autocomplete items to be the same width as the container:*/ + top: 100%; + left: 0; + right: 0; + border:1px solid black; + border-top:none; + box-shadow: rgba(0, 0, 0, 0.25) 0px 54px 55px, rgba(0, 0, 0, 0.12) 0px -12px 30px, rgba(0, 0, 0, 0.12) 0px 4px 6px, rgba(0, 0, 0, 0.17) 0px 12px 13px, rgba(0, 0, 0, 0.09) 0px -3px 5px; + +} + +.autocomplete-items div { + padding: 10px; + cursor: pointer; + background-color: #fff; + border-bottom: 1px dotted #d4d4d4; +} + +.autocomplete-items div:hover { + /*when hovering an item:*/ + background-color: #e9e9e9; +} + +.autocomplete-active { + /*when navigating through the items using the arrow keys:*/ + background-color: DodgerBlue !important; + color: #ffffff; +} + +.recent-search-title { + display: -webkit-box; + display: -moz-box; + display: -ms-flexbox; + display: -webkit-flex; + display: flex; +} + +.recent-search-title * { + -webkit-box-flex: 1 1 auto; + -moz-box-flex: 1 1 auto; + -webkit-flex: 1 1 auto; + -ms-flex: 1 1 auto; + flex: 1 1 auto; +} + + +.recent-search-title input[type="button"] { + border: none; + background: none; + cursor: pointer; + margin: 0; + padding: 0; + color: blue; + +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/bar_chart.css b/gn2/wqflask/static/new/css/bar_chart.css new file mode 100644 index 00000000..20730c2f --- /dev/null +++ b/gn2/wqflask/static/new/css/bar_chart.css @@ -0,0 +1,23 @@ +.barchart .axis path, +.barchart .axis line { + fill: none; + stroke: #000; + shape-rendering: crispEdges; +} + +.bar { + fill: steelblue; + shape-rendering: crispEdges; +} + +#legend-left, #legend-right { + font-size: 20px; +} + +.nvd3 .nv-group { + fill-opacity: .9 !important; +} + +.nvtooltip table td.legend-color-guide div { + display: none; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/bootstrap-custom.css b/gn2/wqflask/static/new/css/bootstrap-custom.css new file mode 100644 index 00000000..007dcc44 --- /dev/null +++ b/gn2/wqflask/static/new/css/bootstrap-custom.css @@ -0,0 +1,7560 @@ +/*! + * Bootstrap v3.3.0 (http://getbootstrap.com) + * Copyright 2011-2014 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + */ + +/*! normalize.css v3.0.2 | MIT License | git.io/normalize */ +html { + font-family: sans-serif; + -webkit-text-size-adjust: 100%; + -ms-text-size-adjust: 100%; +} + +body { + margin: 0; +} + +article, +aside, +details, +figcaption, +figure, +footer, +header, +hgroup, +main, +menu, +nav, +section, +summary { + display: block; +} + +audio, +canvas, +progress, +video { + display: inline-block; + vertical-align: baseline; +} + +audio:not([controls]) { + display: none; + height: 0; +} + +[hidden], +template { + display: none; +} + +a { + background-color: transparent; +} + +a:active, +a:hover { + outline: 0; +} + +abbr[title] { + border-bottom: 1px dotted; +} + +b, +strong { + font-weight: bold; +} + +dfn { + font-style: italic; +} + +h1 { + margin: .67em 0; + font-size: 2em; +} + +mark { + color: #000; + background: #ff0; +} + +small { + font-size: 80%; +} + +sub, +sup { + position: relative; + font-size: 75%; + line-height: 0; + vertical-align: baseline; +} + +sup { + top: -.5em; +} + +sub { + bottom: -.25em; +} + +img { + border: 0; +} + +svg:not(:root) { + overflow: hidden; +} + +figure { + margin: 1em 40px; +} + +hr { + height: 0; + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; +} + +pre { + overflow: auto; +} + +code, +kbd, +pre, +samp { + font-family: monospace, monospace; + font-size: 1em; +} + +button, +input, +optgroup, +select, +textarea { + margin: 0; + font: inherit; + color: inherit; +} + +button { + overflow: visible; +} + +button, +select { + text-transform: none; +} + +button, +html input[type="button"], +input[type="reset"], +input[type="submit"] { + -webkit-appearance: button; + cursor: pointer; +} + +button[disabled], +html input[disabled] { + cursor: default; +} + +button::-moz-focus-inner, +input::-moz-focus-inner { + padding: 0; + border: 0; +} + +input { + line-height: normal; +} + +input[type="checkbox"], +input[type="radio"] { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; + padding: 0; +} + +input[type="number"]::-webkit-inner-spin-button, +input[type="number"]::-webkit-outer-spin-button { + height: auto; +} + +input[type="search"] { + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; + -webkit-appearance: textfield; +} + +input[type="search"]::-webkit-search-cancel-button, +input[type="search"]::-webkit-search-decoration { + -webkit-appearance: none; +} + +fieldset { + padding: .35em .625em .75em; + margin: 0 2px; + border: 1px solid #c0c0c0; +} + +legend { + padding: 0; + border: 0; +} + +textarea { + overflow: auto; +} + +optgroup { + font-weight: bold; +} + +table { + border-spacing: 0; + border-collapse: collapse; +} + +td, +th { + padding: 0; +} + +/*! Source: https://github.com/h5bp/html5-boilerplate/blob/master/src/css/main.css */ +@media print { + + *, + *:before, + *:after { + color: #000 !important; + text-shadow: none !important; + background: transparent !important; + -webkit-box-shadow: none !important; + box-shadow: none !important; + } + + a, + a:visited { + text-decoration: underline; + } + + a[href]:after { + content: " ("attr(href) ")"; + } + + abbr[title]:after { + content: " ("attr(title) ")"; + } + + a[href^="#"]:after, + a[href^="javascript:"]:after { + content: ""; + } + + pre, + blockquote { + border: 1px solid #999; + + page-break-inside: avoid; + } + + thead { + display: table-header-group; + } + + tr, + img { + page-break-inside: avoid; + } + + img { + max-width: 100% !important; + } + + p, + h2, + h3 { + orphans: 3; + widows: 3; + } + + h2, + h3 { + page-break-after: avoid; + } + + select { + background: #fff !important; + } + + .navbar { + display: none; + } + + .btn>.caret, + .dropup>.btn>.caret { + border-top-color: #000 !important; + } + + .label { + border: 1px solid #000; + } + + .table { + border-collapse: collapse !important; + } + + .table td, + .table th { + background-color: #fff !important; + } + + .table-bordered th, + .table-bordered td { + border: 1px solid #000 !important; + } +} + +@font-face { + font-family: 'Glyphicons Halflings'; + + src: url('../fonts/glyphicons-halflings-regular.eot'); + src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg'); +} + +.glyphicon { + position: relative; + top: 1px; + display: inline-block; + font-family: 'Glyphicons Halflings'; + font-style: normal; + font-weight: normal; + line-height: 1; + + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} + +.glyphicon-asterisk:before { + content: "\2a"; +} + +.glyphicon-plus:before { + content: "\2b"; +} + +.glyphicon-euro:before, +.glyphicon-eur:before { + content: "\20ac"; +} + +.glyphicon-minus:before { + content: "\2212"; +} + +.glyphicon-cloud:before { + content: "\2601"; +} + +.glyphicon-envelope:before { + content: "\2709"; +} + +.glyphicon-pencil:before { + content: "\270f"; +} + +.glyphicon-glass:before { + content: "\e001"; +} + +.glyphicon-music:before { + content: "\e002"; +} + +.glyphicon-search:before { + content: "\e003"; +} + +.glyphicon-heart:before { + content: "\e005"; +} + +.glyphicon-star:before { + content: "\e006"; +} + +.glyphicon-star-empty:before { + content: "\e007"; +} + +.glyphicon-user:before { + content: "\e008"; +} + +.glyphicon-film:before { + content: "\e009"; +} + +.glyphicon-th-large:before { + content: "\e010"; +} + +.glyphicon-th:before { + content: "\e011"; +} + +.glyphicon-th-list:before { + content: "\e012"; +} + +.glyphicon-ok:before { + content: "\e013"; +} + +.glyphicon-remove:before { + content: "\e014"; +} + +.glyphicon-zoom-in:before { + content: "\e015"; +} + +.glyphicon-zoom-out:before { + content: "\e016"; +} + +.glyphicon-off:before { + content: "\e017"; +} + +.glyphicon-signal:before { + content: "\e018"; +} + +.glyphicon-cog:before { + content: "\e019"; +} + +.glyphicon-trash:before { + content: "\e020"; +} + +.glyphicon-home:before { + content: "\e021"; +} + +.glyphicon-file:before { + content: "\e022"; +} + +.glyphicon-time:before { + content: "\e023"; +} + +.glyphicon-road:before { + content: "\e024"; +} + +.glyphicon-download-alt:before { + content: "\e025"; +} + +.glyphicon-download:before { + content: "\e026"; +} + +.glyphicon-upload:before { + content: "\e027"; +} + +.glyphicon-inbox:before { + content: "\e028"; +} + +.glyphicon-play-circle:before { + content: "\e029"; +} + +.glyphicon-repeat:before { + content: "\e030"; +} + +.glyphicon-refresh:before { + content: "\e031"; +} + +.glyphicon-list-alt:before { + content: "\e032"; +} + +.glyphicon-lock:before { + content: "\e033"; +} + +.glyphicon-flag:before { + content: "\e034"; +} + +.glyphicon-headphones:before { + content: "\e035"; +} + +.glyphicon-volume-off:before { + content: "\e036"; +} + +.glyphicon-volume-down:before { + content: "\e037"; +} + +.glyphicon-volume-up:before { + content: "\e038"; +} + +.glyphicon-qrcode:before { + content: "\e039"; +} + +.glyphicon-barcode:before { + content: "\e040"; +} + +.glyphicon-tag:before { + content: "\e041"; +} + +.glyphicon-tags:before { + content: "\e042"; +} + +.glyphicon-book:before { + content: "\e043"; +} + +.glyphicon-bookmark:before { + content: "\e044"; +} + +.glyphicon-print:before { + content: "\e045"; +} + +.glyphicon-camera:before { + content: "\e046"; +} + +.glyphicon-font:before { + content: "\e047"; +} + +.glyphicon-bold:before { + content: "\e048"; +} + +.glyphicon-italic:before { + content: "\e049"; +} + +.glyphicon-text-height:before { + content: "\e050"; +} + +.glyphicon-text-width:before { + content: "\e051"; +} + +.glyphicon-align-left:before { + content: "\e052"; +} + +.glyphicon-align-center:before { + content: "\e053"; +} + +.glyphicon-align-right:before { + content: "\e054"; +} + +.glyphicon-align-justify:before { + content: "\e055"; +} + +.glyphicon-list:before { + content: "\e056"; +} + +.glyphicon-indent-left:before { + content: "\e057"; +} + +.glyphicon-indent-right:before { + content: "\e058"; +} + +.glyphicon-facetime-video:before { + content: "\e059"; +} + +.glyphicon-picture:before { + content: "\e060"; +} + +.glyphicon-map-marker:before { + content: "\e062"; +} + +.glyphicon-adjust:before { + content: "\e063"; +} + +.glyphicon-tint:before { + content: "\e064"; +} + +.glyphicon-edit:before { + content: "\e065"; +} + +.glyphicon-share:before { + content: "\e066"; +} + +.glyphicon-check:before { + content: "\e067"; +} + +.glyphicon-move:before { + content: "\e068"; +} + +.glyphicon-step-backward:before { + content: "\e069"; +} + +.glyphicon-fast-backward:before { + content: "\e070"; +} + +.glyphicon-backward:before { + content: "\e071"; +} + +.glyphicon-play:before { + content: "\e072"; +} + +.glyphicon-pause:before { + content: "\e073"; +} + +.glyphicon-stop:before { + content: "\e074"; +} + +.glyphicon-forward:before { + content: "\e075"; +} + +.glyphicon-fast-forward:before { + content: "\e076"; +} + +.glyphicon-step-forward:before { + content: "\e077"; +} + +.glyphicon-eject:before { + content: "\e078"; +} + +.glyphicon-chevron-left:before { + content: "\e079"; +} + +.glyphicon-chevron-right:before { + content: "\e080"; +} + +.glyphicon-plus-sign:before { + content: "\e081"; +} + +.glyphicon-minus-sign:before { + content: "\e082"; +} + +.glyphicon-remove-sign:before { + content: "\e083"; +} + +.glyphicon-ok-sign:before { + content: "\e084"; +} + +.glyphicon-question-sign:before { + content: "\e085"; +} + +.glyphicon-info-sign:before { + content: "\e086"; +} + +.glyphicon-screenshot:before { + content: "\e087"; +} + +.glyphicon-remove-circle:before { + content: "\e088"; +} + +.glyphicon-ok-circle:before { + content: "\e089"; +} + +.glyphicon-ban-circle:before { + content: "\e090"; +} + +.glyphicon-arrow-left:before { + content: "\e091"; +} + +.glyphicon-arrow-right:before { + content: "\e092"; +} + +.glyphicon-arrow-up:before { + content: "\e093"; +} + +.glyphicon-arrow-down:before { + content: "\e094"; +} + +.glyphicon-share-alt:before { + content: "\e095"; +} + +.glyphicon-resize-full:before { + content: "\e096"; +} + +.glyphicon-resize-small:before { + content: "\e097"; +} + +.glyphicon-exclamation-sign:before { + content: "\e101"; +} + +.glyphicon-gift:before { + content: "\e102"; +} + +.glyphicon-leaf:before { + content: "\e103"; +} + +.glyphicon-fire:before { + content: "\e104"; +} + +.glyphicon-eye-open:before { + content: "\e105"; +} + +.glyphicon-eye-close:before { + content: "\e106"; +} + +.glyphicon-warning-sign:before { + content: "\e107"; +} + +.glyphicon-plane:before { + content: "\e108"; +} + +.glyphicon-calendar:before { + content: "\e109"; +} + +.glyphicon-random:before { + content: "\e110"; +} + +.glyphicon-comment:before { + content: "\e111"; +} + +.glyphicon-magnet:before { + content: "\e112"; +} + +.glyphicon-chevron-up:before { + content: "\e113"; +} + +.glyphicon-chevron-down:before { + content: "\e114"; +} + +.glyphicon-retweet:before { + content: "\e115"; +} + +.glyphicon-shopping-cart:before { + content: "\e116"; +} + +.glyphicon-folder-close:before { + content: "\e117"; +} + +.glyphicon-folder-open:before { + content: "\e118"; +} + +.glyphicon-resize-vertical:before { + content: "\e119"; +} + +.glyphicon-resize-horizontal:before { + content: "\e120"; +} + +.glyphicon-hdd:before { + content: "\e121"; +} + +.glyphicon-bullhorn:before { + content: "\e122"; +} + +.glyphicon-bell:before { + content: "\e123"; +} + +.glyphicon-certificate:before { + content: "\e124"; +} + +.glyphicon-thumbs-up:before { + content: "\e125"; +} + +.glyphicon-thumbs-down:before { + content: "\e126"; +} + +.glyphicon-hand-right:before { + content: "\e127"; +} + +.glyphicon-hand-left:before { + content: "\e128"; +} + +.glyphicon-hand-up:before { + content: "\e129"; +} + +.glyphicon-hand-down:before { + content: "\e130"; +} + +.glyphicon-circle-arrow-right:before { + content: "\e131"; +} + +.glyphicon-circle-arrow-left:before { + content: "\e132"; +} + +.glyphicon-circle-arrow-up:before { + content: "\e133"; +} + +.glyphicon-circle-arrow-down:before { + content: "\e134"; +} + +.glyphicon-globe:before { + content: "\e135"; +} + +.glyphicon-wrench:before { + content: "\e136"; +} + +.glyphicon-tasks:before { + content: "\e137"; +} + +.glyphicon-filter:before { + content: "\e138"; +} + +.glyphicon-briefcase:before { + content: "\e139"; +} + +.glyphicon-fullscreen:before { + content: "\e140"; +} + +.glyphicon-dashboard:before { + content: "\e141"; +} + +.glyphicon-paperclip:before { + content: "\e142"; +} + +.glyphicon-heart-empty:before { + content: "\e143"; +} + +.glyphicon-link:before { + content: "\e144"; +} + +.glyphicon-phone:before { + content: "\e145"; +} + +.glyphicon-pushpin:before { + content: "\e146"; +} + +.glyphicon-usd:before { + content: "\e148"; +} + +.glyphicon-gbp:before { + content: "\e149"; +} + +.glyphicon-sort:before { + content: "\e150"; +} + +.glyphicon-sort-by-alphabet:before { + content: "\e151"; +} + +.glyphicon-sort-by-alphabet-alt:before { + content: "\e152"; +} + +.glyphicon-sort-by-order:before { + content: "\e153"; +} + +.glyphicon-sort-by-order-alt:before { + content: "\e154"; +} + +.glyphicon-sort-by-attributes:before { + content: "\e155"; +} + +.glyphicon-sort-by-attributes-alt:before { + content: "\e156"; +} + +.glyphicon-unchecked:before { + content: "\e157"; +} + +.glyphicon-expand:before { + content: "\e158"; +} + +.glyphicon-collapse-down:before { + content: "\e159"; +} + +.glyphicon-collapse-up:before { + content: "\e160"; +} + +.glyphicon-log-in:before { + content: "\e161"; +} + +.glyphicon-flash:before { + content: "\e162"; +} + +.glyphicon-log-out:before { + content: "\e163"; +} + +.glyphicon-new-window:before { + content: "\e164"; +} + +.glyphicon-record:before { + content: "\e165"; +} + +.glyphicon-save:before { + content: "\e166"; +} + +.glyphicon-open:before { + content: "\e167"; +} + +.glyphicon-saved:before { + content: "\e168"; +} + +.glyphicon-import:before { + content: "\e169"; +} + +.glyphicon-export:before { + content: "\e170"; +} + +.glyphicon-send:before { + content: "\e171"; +} + +.glyphicon-floppy-disk:before { + content: "\e172"; +} + +.glyphicon-floppy-saved:before { + content: "\e173"; +} + +.glyphicon-floppy-remove:before { + content: "\e174"; +} + +.glyphicon-floppy-save:before { + content: "\e175"; +} + +.glyphicon-floppy-open:before { + content: "\e176"; +} + +.glyphicon-credit-card:before { + content: "\e177"; +} + +.glyphicon-transfer:before { + content: "\e178"; +} + +.glyphicon-cutlery:before { + content: "\e179"; +} + +.glyphicon-header:before { + content: "\e180"; +} + +.glyphicon-compressed:before { + content: "\e181"; +} + +.glyphicon-earphone:before { + content: "\e182"; +} + +.glyphicon-phone-alt:before { + content: "\e183"; +} + +.glyphicon-tower:before { + content: "\e184"; +} + +.glyphicon-stats:before { + content: "\e185"; +} + +.glyphicon-sd-video:before { + content: "\e186"; +} + +.glyphicon-hd-video:before { + content: "\e187"; +} + +.glyphicon-subtitles:before { + content: "\e188"; +} + +.glyphicon-sound-stereo:before { + content: "\e189"; +} + +.glyphicon-sound-dolby:before { + content: "\e190"; +} + +.glyphicon-sound-5-1:before { + content: "\e191"; +} + +.glyphicon-sound-6-1:before { + content: "\e192"; +} + +.glyphicon-sound-7-1:before { + content: "\e193"; +} + +.glyphicon-copyright-mark:before { + content: "\e194"; +} + +.glyphicon-registration-mark:before { + content: "\e195"; +} + +.glyphicon-cloud-download:before { + content: "\e197"; +} + +.glyphicon-cloud-upload:before { + content: "\e198"; +} + +.glyphicon-tree-conifer:before { + content: "\e199"; +} + +.glyphicon-tree-deciduous:before { + content: "\e200"; +} + +* { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} + +*:before, +*:after { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} + +html { + font-size: 10px; + + -webkit-tap-highlight-color: rgba(0, 0, 0, 0); +} + +body { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; + line-height: 1.42857143; + color: #000; + background-color: #fff; +} + +input, +button, +select, +textarea { + font-family: inherit; + font-size: inherit; + line-height: inherit; +} + +a { + color: #3071a9; + text-decoration: none; +} + +a:hover, +a:focus { + color: #2a6496; + text-decoration: underline; +} + +a:focus { + outline: thin dotted; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +figure { + margin: 0; +} + +img { + vertical-align: middle; +} + +.img-responsive, +.thumbnail>img, +.thumbnail a>img, +.carousel-inner>.item>img, +.carousel-inner>.item>a>img { + display: block; + max-width: 100%; + height: auto; +} + +.img-rounded { + border-radius: 6px; +} + +.img-thumbnail { + display: inline-block; + max-width: 100%; + height: auto; + padding: 4px; + line-height: 1.42857143; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 4px; + -webkit-transition: all .2s ease-in-out; + -o-transition: all .2s ease-in-out; + transition: all .2s ease-in-out; +} + +.img-circle { + border-radius: 50%; +} + +hr { + margin-top: 20px; + margin-bottom: 20px; + border: 0; + border-top: 1px solid #eee; +} + +.sr-only { + position: absolute; + width: 1px; + height: 1px; + padding: 0; + margin: -1px; + overflow: hidden; + clip: rect(0, 0, 0, 0); + border: 0; +} + +.sr-only-focusable:active, +.sr-only-focusable:focus { + position: static; + width: auto; + height: auto; + margin: 0; + overflow: visible; + clip: auto; +} + +h1, +h2, +h3, +h4, +h5, +h6, +.h1, +.h2, +.h3, +.h4, +.h5, +.h6 { + font-family: inherit; + font-weight: 500; + line-height: 1.1; + color: inherit; +} + +h1 small, +h2 small, +h3 small, +h4 small, +h5 small, +h6 small, +.h1 small, +.h2 small, +.h3 small, +.h4 small, +.h5 small, +.h6 small, +h1 .small, +h2 .small, +h3 .small, +h4 .small, +h5 .small, +h6 .small, +.h1 .small, +.h2 .small, +.h3 .small, +.h4 .small, +.h5 .small, +.h6 .small { + font-weight: normal; + line-height: 1; + color: #777; +} + +h1, +.h1, +h2, +.h2, +h3, +.h3 { + margin-top: 10px; + margin-bottom: 10px; +} + +h1 small, +.h1 small, +h2 small, +.h2 small, +h3 small, +.h3 small, +h1 .small, +.h1 .small, +h2 .small, +.h2 .small, +h3 .small, +.h3 .small { + font-size: 65%; +} + +h4, +.h4, +h5, +.h5, +h6, +.h6 { + margin-top: 10px; + margin-bottom: 10px; +} + +h4 small, +.h4 small, +h5 small, +.h5 small, +h6 small, +.h6 small, +h4 .small, +.h4 .small, +h5 .small, +.h5 .small, +h6 .small, +.h6 .small { + font-size: 75%; +} + +h1, +.h1 { + font-size: 30px; +} + +h2, +.h2 { + font-size: 24px; +} + +h3, +.h3 { + font-size: 18px; +} + +h4, +.h4 { + font-size: 14px; +} + +h5, +.h5 { + font-size: 12px; +} + +h6, +.h6 { + font-size: 10px; +} + +p { + margin: 0 0 10px; +} + +.lead { + margin-bottom: 20px; + font-size: 16px; + font-weight: 300; + line-height: 1.4; +} + +@media (min-width: 768px) { + .lead { + font-size: 21px; + } +} + +small, +.small { + font-size: 85%; +} + +mark, +.mark { + padding: .2em; + background-color: #fcf8e3; +} + +.text-left { + text-align: left; +} + +.text-right { + text-align: right; +} + +.text-center { + text-align: center; +} + +.text-justify { + text-align: justify; +} + +.text-nowrap { + white-space: nowrap; +} + +.text-lowercase { + text-transform: lowercase; +} + +.text-uppercase { + text-transform: uppercase; +} + +.text-capitalize { + text-transform: capitalize; +} + +.text-muted { + color: #777; +} + +.text-primary { + color: #428bca; +} + +a.text-primary:hover { + color: #3071a9; +} + +.text-success { + color: #3c763d; +} + +a.text-success:hover { + color: #2b542c; +} + +.text-info { + color: #31708f; +} + +a.text-info:hover { + color: #245269; +} + +.text-warning { + color: #8a6d3b; +} + +a.text-warning:hover { + color: #66512c; +} + +.text-danger { + color: #a94442; +} + +a.text-danger:hover { + color: #843534; +} + +.bg-primary { + color: #fff; + background-color: #428bca; +} + +a.bg-primary:hover { + background-color: #3071a9; +} + +.bg-success { + background-color: #dff0d8; +} + +a.bg-success:hover { + background-color: #c1e2b3; +} + +.bg-info { + background-color: #d9edf7; +} + +a.bg-info:hover { + background-color: #afd9ee; +} + +.bg-warning { + background-color: #fcf8e3; +} + +a.bg-warning:hover { + background-color: #f7ecb5; +} + +.bg-danger { + background-color: #f2dede; +} + +a.bg-danger:hover { + background-color: #e4b9b9; +} + +.page-header { + padding-bottom: 9px; + margin: 10px 0 10px; + border-bottom: 1px solid #eee; +} + +ul, +ol { + margin-top: 0; + margin-bottom: 10px; +} + +ul ul, +ol ul, +ul ol, +ol ol { + margin-bottom: 0; +} + +.list-unstyled { + padding-left: 0; + list-style: none; +} + +.list-inline { + padding-left: 0; + margin-left: -5px; + list-style: none; +} + +.list-inline>li { + display: inline-block; + padding-right: 5px; + padding-left: 5px; +} + +dl { + margin-top: 0; + margin-bottom: 20px; +} + +dt, +dd { + line-height: 1.42857143; +} + +dt { + font-weight: bold; +} + +dd { + margin-left: 0; +} + +@media (min-width: 768px) { + .dl-horizontal dt { + float: left; + width: 160px; + overflow: hidden; + clear: left; + text-align: right; + text-overflow: ellipsis; + white-space: nowrap; + } + + .dl-horizontal dd { + margin-left: 180px; + } +} + +abbr[title], +abbr[data-original-title] { + cursor: help; + border-bottom: 1px dotted #777; +} + +.initialism { + font-size: 90%; + text-transform: uppercase; +} + +blockquote { + padding: 10px 20px; + margin: 0 0 20px; + font-size: 17.5px; + border-left: 5px solid #eee; +} + +blockquote p:last-child, +blockquote ul:last-child, +blockquote ol:last-child { + margin-bottom: 0; +} + +blockquote footer, +blockquote small, +blockquote .small { + display: block; + font-size: 80%; + line-height: 1.42857143; + color: #777; +} + +blockquote footer:before, +blockquote small:before, +blockquote .small:before { + content: '\2014 \00A0'; +} + +.blockquote-reverse, +blockquote.pull-right { + padding-right: 15px; + padding-left: 0; + text-align: right; + border-right: 5px solid #eee; + border-left: 0; +} + +.blockquote-reverse footer:before, +blockquote.pull-right footer:before, +.blockquote-reverse small:before, +blockquote.pull-right small:before, +.blockquote-reverse .small:before, +blockquote.pull-right .small:before { + content: ''; +} + +.blockquote-reverse footer:after, +blockquote.pull-right footer:after, +.blockquote-reverse small:after, +blockquote.pull-right small:after, +.blockquote-reverse .small:after, +blockquote.pull-right .small:after { + content: '\00A0 \2014'; +} + +address { + margin-bottom: 20px; + font-style: normal; + line-height: 1.42857143; +} + +code, +kbd, +pre, +samp { + font-family: Menlo, Monaco, Consolas, "Courier New", monospace; +} + +code { + padding: 2px 4px; + font-size: 90%; + color: #c7254e; + background-color: #f9f2f4; + border-radius: 4px; +} + +kbd { + padding: 2px 4px; + font-size: 90%; + color: #fff; + background-color: #333; + border-radius: 3px; + -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25); + box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25); +} + +kbd kbd { + padding: 0; + font-size: 100%; + font-weight: bold; + -webkit-box-shadow: none; + box-shadow: none; +} + +pre { + display: block; + padding: 9.5px; + margin: 0 0 10px; + font-size: 13px; + line-height: 1.42857143; + color: #333; + word-break: break-all; + word-wrap: break-word; + background-color: #f5f5f5; + border: 1px solid #ccc; + border-radius: 4px; +} + +pre code { + padding: 0; + font-size: inherit; + color: inherit; + white-space: pre-wrap; + background-color: transparent; + border-radius: 0; +} + +.pre-scrollable { + max-height: 340px; + overflow-y: scroll; +} + +.container { + padding-right: 15px; + padding-left: 15px; +} + +/* +@media (min-width: 768px) { + .container { + width: 750px; + } +} +@media (min-width: 992px) { + .container { + width: 970px; + } +} +@media (min-width: 1200px) { + .container { + width: 1170px; + } +}*/ + +.container-fluid { + padding-right: 15px; + padding-left: 15px; + margin-right: auto; + margin-left: auto; +} + +.row { + margin-right: -15px; + margin-left: -15px; +} + +.col-xs-1, +.col-sm-1, +.col-md-1, +.col-lg-1, +.col-xs-2, +.col-sm-2, +.col-md-2, +.col-lg-2, +.col-xs-3, +.col-sm-3, +.col-md-3, +.col-lg-3, +.col-xs-4, +.col-sm-4, +.col-md-4, +.col-lg-4, +.col-xs-5, +.col-sm-5, +.col-md-5, +.col-lg-5, +.col-xs-6, +.col-sm-6, +.col-md-6, +.col-lg-6, +.col-xs-7, +.col-sm-7, +.col-md-7, +.col-lg-7, +.col-xs-8, +.col-sm-8, +.col-md-8, +.col-lg-8, +.col-xs-9, +.col-sm-9, +.col-md-9, +.col-lg-9, +.col-xs-10, +.col-sm-10, +.col-md-10, +.col-lg-10, +.col-xs-11, +.col-sm-11, +.col-md-11, +.col-lg-11, +.col-xs-12, +.col-sm-12, +.col-md-12, +.col-lg-12 { + position: relative; + min-height: 1px; + padding-right: 15px; + padding-left: 15px; +} + +.col-xs-1, +.col-xs-2, +.col-xs-3, +.col-xs-4, +.col-xs-5, +.col-xs-6, +.col-xs-7, +.col-xs-8, +.col-xs-9, +.col-xs-10, +.col-xs-11, +.col-xs-12 { + float: left; +} + +.col-xs-12 { + width: 100%; +} + +.col-xs-11 { + width: 91.66666667%; +} + +.col-xs-10 { + width: 83.33333333%; +} + +.col-xs-9 { + width: 75%; +} + +.col-xs-8 { + width: 66.66666667%; +} + +.col-xs-7 { + width: 58.33333333%; +} + +.col-xs-6 { + width: 50%; +} + +.col-xs-5 { + width: 41.66666667%; +} + +.col-xs-4 { + width: 33.33333333%; +} + +.col-xs-3 { + width: 25%; +} + +.col-xs-2 { + width: 16.66666667%; +} + +.col-xs-1 { + width: 8.33333333%; +} + +.col-xs-pull-12 { + right: 100%; +} + +.col-xs-pull-11 { + right: 91.66666667%; +} + +.col-xs-pull-10 { + right: 83.33333333%; +} + +.col-xs-pull-9 { + right: 75%; +} + +.col-xs-pull-8 { + right: 66.66666667%; +} + +.col-xs-pull-7 { + right: 58.33333333%; +} + +.col-xs-pull-6 { + right: 50%; +} + +.col-xs-pull-5 { + right: 41.66666667%; +} + +.col-xs-pull-4 { + right: 33.33333333%; +} + +.col-xs-pull-3 { + right: 25%; +} + +.col-xs-pull-2 { + right: 16.66666667%; +} + +.col-xs-pull-1 { + right: 8.33333333%; +} + +.col-xs-pull-0 { + right: auto; +} + +.col-xs-push-12 { + left: 100%; +} + +.col-xs-push-11 { + left: 91.66666667%; +} + +.col-xs-push-10 { + left: 83.33333333%; +} + +.col-xs-push-9 { + left: 75%; +} + +.col-xs-push-8 { + left: 66.66666667%; +} + +.col-xs-push-7 { + left: 58.33333333%; +} + +.col-xs-push-6 { + left: 50%; +} + +.col-xs-push-5 { + left: 41.66666667%; +} + +.col-xs-push-4 { + left: 33.33333333%; +} + +.col-xs-push-3 { + left: 25%; +} + +.col-xs-push-2 { + left: 16.66666667%; +} + +.col-xs-push-1 { + left: 8.33333333%; +} + +.col-xs-push-0 { + left: auto; +} + +.col-xs-offset-12 { + margin-left: 100%; +} + +.col-xs-offset-11 { + margin-left: 91.66666667%; +} + +.col-xs-offset-10 { + margin-left: 83.33333333%; +} + +.col-xs-offset-9 { + margin-left: 75%; +} + +.col-xs-offset-8 { + margin-left: 66.66666667%; +} + +.col-xs-offset-7 { + margin-left: 58.33333333%; +} + +.col-xs-offset-6 { + margin-left: 50%; +} + +.col-xs-offset-5 { + margin-left: 41.66666667%; +} + +.col-xs-offset-4 { + margin-left: 33.33333333%; +} + +.col-xs-offset-3 { + margin-left: 25%; +} + +.col-xs-offset-2 { + margin-left: 16.66666667%; +} + +.col-xs-offset-1 { + margin-left: 8.33333333%; +} + +.col-xs-offset-0 { + margin-left: 0; +} + +/* +@media (min-width: 768px) { + .col-sm-1, .col-sm-2, .col-sm-3, .col-sm-4, .col-sm-5, .col-sm-6, .col-sm-7, .col-sm-8, .col-sm-9, .col-sm-10, .col-sm-11, .col-sm-12 { + float: left; + } + .col-sm-12 { + width: 100%; + } + .col-sm-11 { + width: 91.66666667%; + } + .col-sm-10 { + width: 83.33333333%; + } + .col-sm-9 { + width: 75%; + } + .col-sm-8 { + width: 66.66666667%; + } + .col-sm-7 { + width: 58.33333333%; + } + .col-sm-6 { + width: 50%; + } + .col-sm-5 { + width: 41.66666667%; + } + .col-sm-4 { + width: 33.33333333%; + } + .col-sm-3 { + width: 25%; + } + .col-sm-2 { + width: 16.66666667%; + } + .col-sm-1 { + width: 8.33333333%; + } + .col-sm-pull-12 { + right: 100%; + } + .col-sm-pull-11 { + right: 91.66666667%; + } + .col-sm-pull-10 { + right: 83.33333333%; + } + .col-sm-pull-9 { + right: 75%; + } + .col-sm-pull-8 { + right: 66.66666667%; + } + .col-sm-pull-7 { + right: 58.33333333%; + } + .col-sm-pull-6 { + right: 50%; + } + .col-sm-pull-5 { + right: 41.66666667%; + } + .col-sm-pull-4 { + right: 33.33333333%; + } + .col-sm-pull-3 { + right: 25%; + } + .col-sm-pull-2 { + right: 16.66666667%; + } + .col-sm-pull-1 { + right: 8.33333333%; + } + .col-sm-pull-0 { + right: auto; + } + .col-sm-push-12 { + left: 100%; + } + .col-sm-push-11 { + left: 91.66666667%; + } + .col-sm-push-10 { + left: 83.33333333%; + } + .col-sm-push-9 { + left: 75%; + } + .col-sm-push-8 { + left: 66.66666667%; + } + .col-sm-push-7 { + left: 58.33333333%; + } + .col-sm-push-6 { + left: 50%; + } + .col-sm-push-5 { + left: 41.66666667%; + } + .col-sm-push-4 { + left: 33.33333333%; + } + .col-sm-push-3 { + left: 25%; + } + .col-sm-push-2 { + left: 16.66666667%; + } + .col-sm-push-1 { + left: 8.33333333%; + } + .col-sm-push-0 { + left: auto; + } + .col-sm-offset-12 { + margin-left: 100%; + } + .col-sm-offset-11 { + margin-left: 91.66666667%; + } + .col-sm-offset-10 { + margin-left: 83.33333333%; + } + .col-sm-offset-9 { + margin-left: 75%; + } + .col-sm-offset-8 { + margin-left: 66.66666667%; + } + .col-sm-offset-7 { + margin-left: 58.33333333%; + } + .col-sm-offset-6 { + margin-left: 50%; + } + .col-sm-offset-5 { + margin-left: 41.66666667%; + } + .col-sm-offset-4 { + margin-left: 33.33333333%; + } + .col-sm-offset-3 { + margin-left: 25%; + } + .col-sm-offset-2 { + margin-left: 16.66666667%; + } + .col-sm-offset-1 { + margin-left: 8.33333333%; + } + .col-sm-offset-0 { + margin-left: 0; + } +} +@media (min-width: 992px) { + .col-md-1, .col-md-2, .col-md-3, .col-md-4, .col-md-5, .col-md-6, .col-md-7, .col-md-8, .col-md-9, .col-md-10, .col-md-11, .col-md-12 { + float: left; + } + .col-md-12 { + width: 100%; + } + .col-md-11 { + width: 91.66666667%; + } + .col-md-10 { + width: 83.33333333%; + } + .col-md-9 { + width: 75%; + } + .col-md-8 { + width: 66.66666667%; + } + .col-md-7 { + width: 58.33333333%; + } + .col-md-6 { + width: 50%; + } + .col-md-5 { + width: 41.66666667%; + } + .col-md-4 { + width: 33.33333333%; + } + .col-md-3 { + width: 25%; + } + .col-md-2 { + width: 16.66666667%; + } + .col-md-1 { + width: 8.33333333%; + } + .col-md-pull-12 { + right: 100%; + } + .col-md-pull-11 { + right: 91.66666667%; + } + .col-md-pull-10 { + right: 83.33333333%; + } + .col-md-pull-9 { + right: 75%; + } + .col-md-pull-8 { + right: 66.66666667%; + } + .col-md-pull-7 { + right: 58.33333333%; + } + .col-md-pull-6 { + right: 50%; + } + .col-md-pull-5 { + right: 41.66666667%; + } + .col-md-pull-4 { + right: 33.33333333%; + } + .col-md-pull-3 { + right: 25%; + } + .col-md-pull-2 { + right: 16.66666667%; + } + .col-md-pull-1 { + right: 8.33333333%; + } + .col-md-pull-0 { + right: auto; + } + .col-md-push-12 { + left: 100%; + } + .col-md-push-11 { + left: 91.66666667%; + } + .col-md-push-10 { + left: 83.33333333%; + } + .col-md-push-9 { + left: 75%; + } + .col-md-push-8 { + left: 66.66666667%; + } + .col-md-push-7 { + left: 58.33333333%; + } + .col-md-push-6 { + left: 50%; + } + .col-md-push-5 { + left: 41.66666667%; + } + .col-md-push-4 { + left: 33.33333333%; + } + .col-md-push-3 { + left: 25%; + } + .col-md-push-2 { + left: 16.66666667%; + } + .col-md-push-1 { + left: 8.33333333%; + } + .col-md-push-0 { + left: auto; + } + .col-md-offset-12 { + margin-left: 100%; + } + .col-md-offset-11 { + margin-left: 91.66666667%; + } + .col-md-offset-10 { + margin-left: 83.33333333%; + } + .col-md-offset-9 { + margin-left: 75%; + } + .col-md-offset-8 { + margin-left: 66.66666667%; + } + .col-md-offset-7 { + margin-left: 58.33333333%; + } + .col-md-offset-6 { + margin-left: 50%; + } + .col-md-offset-5 { + margin-left: 41.66666667%; + } + .col-md-offset-4 { + margin-left: 33.33333333%; + } + .col-md-offset-3 { + margin-left: 25%; + } + .col-md-offset-2 { + margin-left: 16.66666667%; + } + .col-md-offset-1 { + margin-left: 8.33333333%; + } + .col-md-offset-0 { + margin-left: 0; + } +} +@media (min-width: 1200px) { + .col-lg-1, .col-lg-2, .col-lg-3, .col-lg-4, .col-lg-5, .col-lg-6, .col-lg-7, .col-lg-8, .col-lg-9, .col-lg-10, .col-lg-11, .col-lg-12 { + float: left; + } + .col-lg-12 { + width: 100%; + } + .col-lg-11 { + width: 91.66666667%; + } + .col-lg-10 { + width: 83.33333333%; + } + .col-lg-9 { + width: 75%; + } + .col-lg-8 { + width: 66.66666667%; + } + .col-lg-7 { + width: 58.33333333%; + } + .col-lg-6 { + width: 50%; + } + .col-lg-5 { + width: 41.66666667%; + } + .col-lg-4 { + width: 33.33333333%; + } + .col-lg-3 { + width: 25%; + } + .col-lg-2 { + width: 16.66666667%; + } + .col-lg-1 { + width: 8.33333333%; + } + .col-lg-pull-12 { + right: 100%; + } + .col-lg-pull-11 { + right: 91.66666667%; + } + .col-lg-pull-10 { + right: 83.33333333%; + } + .col-lg-pull-9 { + right: 75%; + } + .col-lg-pull-8 { + right: 66.66666667%; + } + .col-lg-pull-7 { + right: 58.33333333%; + } + .col-lg-pull-6 { + right: 50%; + } + .col-lg-pull-5 { + right: 41.66666667%; + } + .col-lg-pull-4 { + right: 33.33333333%; + } + .col-lg-pull-3 { + right: 25%; + } + .col-lg-pull-2 { + right: 16.66666667%; + } + .col-lg-pull-1 { + right: 8.33333333%; + } + .col-lg-pull-0 { + right: auto; + } + .col-lg-push-12 { + left: 100%; + } + .col-lg-push-11 { + left: 91.66666667%; + } + .col-lg-push-10 { + left: 83.33333333%; + } + .col-lg-push-9 { + left: 75%; + } + .col-lg-push-8 { + left: 66.66666667%; + } + .col-lg-push-7 { + left: 58.33333333%; + } + .col-lg-push-6 { + left: 50%; + } + .col-lg-push-5 { + left: 41.66666667%; + } + .col-lg-push-4 { + left: 33.33333333%; + } + .col-lg-push-3 { + left: 25%; + } + .col-lg-push-2 { + left: 16.66666667%; + } + .col-lg-push-1 { + left: 8.33333333%; + } + .col-lg-push-0 { + left: auto; + } + .col-lg-offset-12 { + margin-left: 100%; + } + .col-lg-offset-11 { + margin-left: 91.66666667%; + } + .col-lg-offset-10 { + margin-left: 83.33333333%; + } + .col-lg-offset-9 { + margin-left: 75%; + } + .col-lg-offset-8 { + margin-left: 66.66666667%; + } + .col-lg-offset-7 { + margin-left: 58.33333333%; + } + .col-lg-offset-6 { + margin-left: 50%; + } + .col-lg-offset-5 { + margin-left: 41.66666667%; + } + .col-lg-offset-4 { + margin-left: 33.33333333%; + } + .col-lg-offset-3 { + margin-left: 25%; + } + .col-lg-offset-2 { + margin-left: 16.66666667%; + } + .col-lg-offset-1 { + margin-left: 8.33333333%; + } + .col-lg-offset-0 { + margin-left: 0; + } +} +*/ + +table { + background-color: transparent; +} + +caption { + padding-top: 8px; + padding-bottom: 8px; + color: #777; + text-align: left; +} + +th { + text-align: left; +} + +.table { + //width: 100%; + //max-width: 100%; + margin-bottom: 20px; +} + +.table>thead>tr>th, +.table>tbody>tr>th, +.table>tfoot>tr>th, +.table>thead>tr>td, +.table>tbody>tr>td, +.table>tfoot>tr>td { + padding: 8px; + line-height: 1.42857143; + vertical-align: top; + border-top: 1px solid #ddd; +} + +.table>thead>tr>th { + vertical-align: middle; + border-bottom: 2px solid #ddd; +} + +.table>caption+thead>tr:first-child>th, +.table>colgroup+thead>tr:first-child>th, +.table>thead:first-child>tr:first-child>th, +.table>caption+thead>tr:first-child>td, +.table>colgroup+thead>tr:first-child>td, +.table>thead:first-child>tr:first-child>td { + border-top: 0; +} + +.table>tbody+tbody { + border-top: 2px solid #ddd; +} + +.table .table { + background-color: #fff; +} + +.table-condensed>thead>tr>th, +.table-condensed>tbody>tr>th, +.table-condensed>tfoot>tr>th, +.table-condensed>thead>tr>td, +.table-condensed>tbody>tr>td, +.table-condensed>tfoot>tr>td { + padding: 5px; +} + +.table-bordered { + border: 1px solid #000; +} + +.table-bordered>thead>tr>th, +.table-bordered>tbody>tr>th, +.table-bordered>tfoot>tr>th, +.table-bordered>thead>tr>td, +.table-bordered>tbody>tr>td, +.table-bordered>tfoot>tr>td { + border: 1px solid #000; +} + +.table-bordered>thead>tr>th, +.table-bordered>thead>tr>td { + border-bottom-width: 2px; +} + +.table-striped>tbody>tr:nth-child(odd) { + background-color: #f9f9f9; +} + +.table-hover>tbody>tr:hover { + background-color: #f5f5f5; +} + +table col[class*="col-"] { + position: static; + display: table-column; + float: none; +} + +table td[class*="col-"], +table th[class*="col-"] { + position: static; + display: table-cell; + float: none; +} + +.table>thead>tr>td.active, +.table>tbody>tr>td.active, +.table>tfoot>tr>td.active, +.table>thead>tr>th.active, +.table>tbody>tr>th.active, +.table>tfoot>tr>th.active, +.table>thead>tr.active>td, +.table>tbody>tr.active>td, +.table>tfoot>tr.active>td, +.table>thead>tr.active>th, +.table>tbody>tr.active>th, +.table>tfoot>tr.active>th { + background-color: #f5f5f5; +} + +.table-hover>tbody>tr>td.active:hover, +.table-hover>tbody>tr>th.active:hover, +.table-hover>tbody>tr.active:hover>td, +.table-hover>tbody>tr:hover>.active, +.table-hover>tbody>tr.active:hover>th { + background-color: #e8e8e8; +} + +.table>thead>tr>td.success, +.table>tbody>tr>td.success, +.table>tfoot>tr>td.success, +.table>thead>tr>th.success, +.table>tbody>tr>th.success, +.table>tfoot>tr>th.success, +.table>thead>tr.success>td, +.table>tbody>tr.success>td, +.table>tfoot>tr.success>td, +.table>thead>tr.success>th, +.table>tbody>tr.success>th, +.table>tfoot>tr.success>th { + background-color: #dff0d8; +} + +.table-hover>tbody>tr>td.success:hover, +.table-hover>tbody>tr>th.success:hover, +.table-hover>tbody>tr.success:hover>td, +.table-hover>tbody>tr:hover>.success, +.table-hover>tbody>tr.success:hover>th { + background-color: #d0e9c6; +} + +.table>thead>tr>td.info, +.table>tbody>tr>td.info, +.table>tfoot>tr>td.info, +.table>thead>tr>th.info, +.table>tbody>tr>th.info, +.table>tfoot>tr>th.info, +.table>thead>tr.info>td, +.table>tbody>tr.info>td, +.table>tfoot>tr.info>td, +.table>thead>tr.info>th, +.table>tbody>tr.info>th, +.table>tfoot>tr.info>th { + background-color: #d9edf7; +} + +.table-hover>tbody>tr>td.info:hover, +.table-hover>tbody>tr>th.info:hover, +.table-hover>tbody>tr.info:hover>td, +.table-hover>tbody>tr:hover>.info, +.table-hover>tbody>tr.info:hover>th { + background-color: #c4e3f3; +} + +.table>thead>tr>td.warning, +.table>tbody>tr>td.warning, +.table>tfoot>tr>td.warning, +.table>thead>tr>th.warning, +.table>tbody>tr>th.warning, +.table>tfoot>tr>th.warning, +.table>thead>tr.warning>td, +.table>tbody>tr.warning>td, +.table>tfoot>tr.warning>td, +.table>thead>tr.warning>th, +.table>tbody>tr.warning>th, +.table>tfoot>tr.warning>th { + background-color: #fcf8e3; +} + +.table-hover>tbody>tr>td.warning:hover, +.table-hover>tbody>tr>th.warning:hover, +.table-hover>tbody>tr.warning:hover>td, +.table-hover>tbody>tr:hover>.warning, +.table-hover>tbody>tr.warning:hover>th { + background-color: #faf2cc; +} + +.table>thead>tr>td.danger, +.table>tbody>tr>td.danger, +.table>tfoot>tr>td.danger, +.table>thead>tr>th.danger, +.table>tbody>tr>th.danger, +.table>tfoot>tr>th.danger, +.table>thead>tr.danger>td, +.table>tbody>tr.danger>td, +.table>tfoot>tr.danger>td, +.table>thead>tr.danger>th, +.table>tbody>tr.danger>th, +.table>tfoot>tr.danger>th { + background-color: #f2dede; +} + +.table-hover>tbody>tr>td.danger:hover, +.table-hover>tbody>tr>th.danger:hover, +.table-hover>tbody>tr.danger:hover>td, +.table-hover>tbody>tr:hover>.danger, +.table-hover>tbody>tr.danger:hover>th { + background-color: #ebcccc; +} + +.table-responsive { + min-height: .01%; + overflow-x: auto; +} + +@media screen and (max-width: 767px) { + .table-responsive { + width: 100%; + margin-bottom: 15px; + overflow-y: hidden; + -ms-overflow-style: -ms-autohiding-scrollbar; + border: 1px solid #ddd; + } + + .table-responsive>.table { + margin-bottom: 0; + } + + .table-responsive>.table>thead>tr>th, + .table-responsive>.table>tbody>tr>th, + .table-responsive>.table>tfoot>tr>th, + .table-responsive>.table>thead>tr>td, + .table-responsive>.table>tbody>tr>td, + .table-responsive>.table>tfoot>tr>td { + white-space: nowrap; + } + + .table-responsive>.table-bordered { + border: 0; + } + + .table-responsive>.table-bordered>thead>tr>th:first-child, + .table-responsive>.table-bordered>tbody>tr>th:first-child, + .table-responsive>.table-bordered>tfoot>tr>th:first-child, + .table-responsive>.table-bordered>thead>tr>td:first-child, + .table-responsive>.table-bordered>tbody>tr>td:first-child, + .table-responsive>.table-bordered>tfoot>tr>td:first-child { + border-left: 0; + } + + .table-responsive>.table-bordered>thead>tr>th:last-child, + .table-responsive>.table-bordered>tbody>tr>th:last-child, + .table-responsive>.table-bordered>tfoot>tr>th:last-child, + .table-responsive>.table-bordered>thead>tr>td:last-child, + .table-responsive>.table-bordered>tbody>tr>td:last-child, + .table-responsive>.table-bordered>tfoot>tr>td:last-child { + border-right: 0; + } + + .table-responsive>.table-bordered>tbody>tr:last-child>th, + .table-responsive>.table-bordered>tfoot>tr:last-child>th, + .table-responsive>.table-bordered>tbody>tr:last-child>td, + .table-responsive>.table-bordered>tfoot>tr:last-child>td { + border-bottom: 0; + } +} + +fieldset { + min-width: 0; + padding: 0; + margin: 0; + border: 0; +} + +legend { + display: block; + width: 100%; + padding: 0; + margin-bottom: 20px; + font-size: 21px; + line-height: inherit; + color: #333; + border: 0; + border-bottom: 1px solid #e5e5e5; +} + +label { + display: inline-block; + max-width: 100%; + margin-bottom: 5px; + font-weight: bold; +} + +input[type="search"] { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} + +input[type="radio"], +input[type="checkbox"] { + margin: 4px 0 0; + margin-top: 1px \9; + line-height: normal; +} + +input[type="file"] { + display: block; +} + +input[type="range"] { + display: block; + width: 100%; +} + +select[multiple], +select[size] { + height: auto; +} + +input[type="file"]:focus, +input[type="radio"]:focus, +input[type="checkbox"]:focus { + outline: thin dotted; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +output { + display: block; + padding-top: 7px; + font-size: 14px; + line-height: 1.42857143; + color: #555; +} + +.form-control { + display: block; + width: 100%; + height: 34px; + padding: 6px 12px; + font-size: 14px; + line-height: 1.42857143; + color: #000; + background-color: #fff; + background-image: none; + border: 1px solid #ccc; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + -webkit-transition: border-color ease-in-out .15s, -webkit-box-shadow ease-in-out .15s; + -o-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s; + transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s; +} + +.form-control:focus { + border-color: #66afe9; + outline: 0; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 8px rgba(102, 175, 233, .6); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 8px rgba(102, 175, 233, .6); +} + +.form-control::-moz-placeholder { + color: #999; + opacity: 1; +} + +.form-control:-ms-input-placeholder { + color: #999; +} + +.form-control::-webkit-input-placeholder { + color: #999; +} + +.form-control[disabled], +.form-control[readonly], +fieldset[disabled] .form-control { + cursor: not-allowed; + background-color: #eee; + opacity: 1; +} + +textarea.form-control { + height: auto; +} + +input[type="search"] { + -webkit-appearance: none; +} + +input[type="date"], +input[type="time"], +input[type="datetime-local"], +input[type="month"] { + line-height: 34px; + line-height: 1.42857143 \0; +} + +input[type="date"].input-sm, +input[type="time"].input-sm, +input[type="datetime-local"].input-sm, +input[type="month"].input-sm { + line-height: 30px; + line-height: 1.5 \0; +} + +input[type="date"].input-lg, +input[type="time"].input-lg, +input[type="datetime-local"].input-lg, +input[type="month"].input-lg { + line-height: 46px; + line-height: 1.33 \0; +} + +_:-ms-fullscreen, +:root input[type="date"], +_:-ms-fullscreen, +:root input[type="time"], +_:-ms-fullscreen, +:root input[type="datetime-local"], +_:-ms-fullscreen, +:root input[type="month"] { + line-height: 1.42857143; +} + +_:-ms-fullscreen.input-sm, +:root input[type="date"].input-sm, +_:-ms-fullscreen.input-sm, +:root input[type="time"].input-sm, +_:-ms-fullscreen.input-sm, +:root input[type="datetime-local"].input-sm, +_:-ms-fullscreen.input-sm, +:root input[type="month"].input-sm { + line-height: 1.5; +} + +_:-ms-fullscreen.input-lg, +:root input[type="date"].input-lg, +_:-ms-fullscreen.input-lg, +:root input[type="time"].input-lg, +_:-ms-fullscreen.input-lg, +:root input[type="datetime-local"].input-lg, +_:-ms-fullscreen.input-lg, +:root input[type="month"].input-lg { + line-height: 1.33; +} + +.form-group { + margin-bottom: 15px; +} + +.radio, +.checkbox { + position: relative; + display: block; + margin-top: 10px; + margin-bottom: 10px; +} + +.radio label, +.checkbox label { + min-height: 20px; + padding-left: 20px; + margin-bottom: 0; + font-weight: normal; + cursor: pointer; +} + +.radio input[type="radio"], +.radio-inline input[type="radio"], +.checkbox input[type="checkbox"], +.checkbox-inline input[type="checkbox"] { + position: absolute; + margin-top: 4px \9; + margin-left: -20px; +} + +.radio+.radio, +.checkbox+.checkbox { + margin-top: -5px; +} + +.radio-inline, +.checkbox-inline { + display: inline-block; + padding-left: 20px; + margin-bottom: 0; + font-weight: normal; + vertical-align: middle; + cursor: pointer; +} + +.radio-inline+.radio-inline, +.checkbox-inline+.checkbox-inline { + margin-top: 0; + margin-left: 10px; +} + +input[type="radio"][disabled], +input[type="checkbox"][disabled], +input[type="radio"].disabled, +input[type="checkbox"].disabled, +fieldset[disabled] input[type="radio"], +fieldset[disabled] input[type="checkbox"] { + cursor: not-allowed; +} + +.radio-inline.disabled, +.checkbox-inline.disabled, +fieldset[disabled] .radio-inline, +fieldset[disabled] .checkbox-inline { + cursor: not-allowed; +} + +.radio.disabled label, +.checkbox.disabled label, +fieldset[disabled] .radio label, +fieldset[disabled] .checkbox label { + cursor: not-allowed; +} + +.form-control-static { + padding-top: 7px; + padding-bottom: 7px; + margin-bottom: 0; +} + +.form-control-static.input-lg, +.form-control-static.input-sm { + padding-right: 0; + padding-left: 0; +} + +.input-sm, +.form-group-sm .form-control { + height: 30px; + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} + +select.input-sm, +select.form-group-sm .form-control { + height: 30px; + line-height: 30px; +} + +textarea.input-sm, +textarea.form-group-sm .form-control, +select[multiple].input-sm, +select[multiple].form-group-sm .form-control { + height: auto; +} + +.input-lg, +.form-group-lg .form-control { + height: 46px; + padding: 10px 16px; + font-size: 18px; + line-height: 1.33; + border-radius: 6px; +} + +select.input-lg, +select.form-group-lg .form-control { + height: 46px; + line-height: 46px; +} + +textarea.input-lg, +textarea.form-group-lg .form-control, +select[multiple].input-lg, +select[multiple].form-group-lg .form-control { + height: auto; +} + +.has-feedback { + position: relative; +} + +.has-feedback .form-control { + padding-right: 42.5px; +} + +.form-control-feedback { + position: absolute; + top: 0; + right: 0; + z-index: 2; + display: block; + width: 34px; + height: 34px; + line-height: 34px; + text-align: center; + pointer-events: none; +} + +.input-lg+.form-control-feedback { + width: 46px; + height: 46px; + line-height: 46px; +} + +.input-sm+.form-control-feedback { + width: 30px; + height: 30px; + line-height: 30px; +} + +.has-success .help-block, +.has-success .control-label, +.has-success .radio, +.has-success .checkbox, +.has-success .radio-inline, +.has-success .checkbox-inline, +.has-success.radio label, +.has-success.checkbox label, +.has-success.radio-inline label, +.has-success.checkbox-inline label { + color: #3c763d; +} + +.has-success .form-control { + border-color: #3c763d; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); +} + +.has-success .form-control:focus { + border-color: #2b542c; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168; +} + +.has-success .input-group-addon { + color: #3c763d; + background-color: #dff0d8; + border-color: #3c763d; +} + +.has-success .form-control-feedback { + color: #3c763d; +} + +.has-warning .help-block, +.has-warning .control-label, +.has-warning .radio, +.has-warning .checkbox, +.has-warning .radio-inline, +.has-warning .checkbox-inline, +.has-warning.radio label, +.has-warning.checkbox label, +.has-warning.radio-inline label, +.has-warning.checkbox-inline label { + color: #8a6d3b; +} + +.has-warning .form-control { + border-color: #8a6d3b; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); +} + +.has-warning .form-control:focus { + border-color: #66512c; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b; +} + +.has-warning .input-group-addon { + color: #8a6d3b; + background-color: #fcf8e3; + border-color: #8a6d3b; +} + +.has-warning .form-control-feedback { + color: #8a6d3b; +} + +.has-error .help-block, +.has-error .control-label, +.has-error .radio, +.has-error .checkbox, +.has-error .radio-inline, +.has-error .checkbox-inline, +.has-error.radio label, +.has-error.checkbox label, +.has-error.radio-inline label, +.has-error.checkbox-inline label { + color: #a94442; +} + +.has-error .form-control { + border-color: #a94442; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); +} + +.has-error .form-control:focus { + border-color: #843534; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483; +} + +.has-error .input-group-addon { + color: #a94442; + background-color: #f2dede; + border-color: #a94442; +} + +.has-error .form-control-feedback { + color: #a94442; +} + +.has-feedback label~.form-control-feedback { + top: 25px; +} + +.has-feedback label.sr-only~.form-control-feedback { + top: 0; +} + +.help-block { + display: block; + margin-top: 5px; + margin-bottom: 10px; + color: #737373; +} + +@media (min-width: 768px) { + .form-inline .form-group { + display: inline-block; + margin-bottom: 0; + vertical-align: middle; + } + + .form-inline .form-control { + display: inline-block; + width: auto; + vertical-align: middle; + } + + .form-inline .form-control-static { + display: inline-block; + } + + .form-inline .input-group { + display: inline-table; + vertical-align: middle; + } + + .form-inline .input-group .input-group-addon, + .form-inline .input-group .input-group-btn, + .form-inline .input-group .form-control { + width: auto; + } + + .form-inline .input-group>.form-control { + width: 100%; + } + + .form-inline .control-label { + margin-bottom: 0; + vertical-align: middle; + } + + .form-inline .radio, + .form-inline .checkbox { + display: inline-block; + margin-top: 0; + margin-bottom: 0; + vertical-align: middle; + } + + .form-inline .radio label, + .form-inline .checkbox label { + padding-left: 0; + } + + .form-inline .radio input[type="radio"], + .form-inline .checkbox input[type="checkbox"] { + position: relative; + margin-left: 0; + } + + .form-inline .has-feedback .form-control-feedback { + top: 0; + } +} + +.form-horizontal .radio, +.form-horizontal .checkbox, +.form-horizontal .radio-inline, +.form-horizontal .checkbox-inline { + padding-top: 7px; + margin-top: 0; + margin-bottom: 0; +} + +.form-horizontal .radio, +.form-horizontal .checkbox { + min-height: 27px; +} + +.form-horizontal .form-group { + margin-right: -15px; + margin-left: -15px; +} + +.form-horizontal .control-label { + padding-top: 7px; + margin-bottom: 0; + text-align: right; +} + +.form-horizontal .control-label.text-left{ + text-align: left; +} + +.form-horizontal .has-feedback .form-control-feedback { + right: 15px; +} + +@media (min-width: 768px) { + .form-horizontal .form-group-lg .control-label { + padding-top: 14.3px; + } +} + +@media (min-width: 768px) { + .form-horizontal .form-group-sm .control-label { + padding-top: 6px; + } +} + +.btn { + display: inline-block; + padding: 6px 12px; + margin-bottom: 0; + font-size: 14px; + font-weight: normal; + line-height: 1.42857143; + text-align: center; + white-space: nowrap; + vertical-align: middle; + -ms-touch-action: manipulation; + touch-action: manipulation; + cursor: pointer; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; + background-image: none; + border: 1px solid transparent; + border-radius: 4px; +} + +.btn:focus, +.btn:active:focus, +.btn.active:focus, +.btn.focus, +.btn:active.focus, +.btn.active.focus { + outline: thin dotted; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +.btn:hover, +.btn:focus, +.btn.focus { + color: #333; + text-decoration: none; +} + +.btn:active, +.btn.active { + background-image: none; + outline: 0; + -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); + box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); +} + +.btn.disabled, +.btn[disabled], +fieldset[disabled] .btn { + pointer-events: none; + cursor: not-allowed; + filter: alpha(opacity=65); + -webkit-box-shadow: none; + box-shadow: none; + opacity: .65; +} + +.btn-default { + color: #333; + background-color: #fff; + border-color: #ccc; +} + +.btn-default:hover, +.btn-default:focus, +.btn-default.focus, +.btn-default:active, +.btn-default.active, +.open>.dropdown-toggle.btn-default { + color: #333; + background-color: #e6e6e6; + border-color: #adadad; +} + +.btn-default:active, +.btn-default.active, +.open>.dropdown-toggle.btn-default { + background-image: none; +} + +.btn-default.disabled, +.btn-default[disabled], +fieldset[disabled] .btn-default, +.btn-default.disabled:hover, +.btn-default[disabled]:hover, +fieldset[disabled] .btn-default:hover, +.btn-default.disabled:focus, +.btn-default[disabled]:focus, +fieldset[disabled] .btn-default:focus, +.btn-default.disabled.focus, +.btn-default[disabled].focus, +fieldset[disabled] .btn-default.focus, +.btn-default.disabled:active, +.btn-default[disabled]:active, +fieldset[disabled] .btn-default:active, +.btn-default.disabled.active, +.btn-default[disabled].active, +fieldset[disabled] .btn-default.active { + background-color: #fff; + border-color: #ccc; +} + +.btn-default .badge { + color: #fff; + background-color: #333; +} + +.btn-primary { + color: #fff; + background-color: #369; + border-color: #357ebd; +} + +.btn-primary:hover, +.btn-primary:focus, +.btn-primary.focus, +.btn-primary:active, +.btn-primary.active, +.open>.dropdown-toggle.btn-primary { + color: #fff; + background-color: #3071a9; + border-color: #285e8e; +} + +.btn-primary:active, +.btn-primary.active, +.open>.dropdown-toggle.btn-primary { + background-image: none; +} + +.btn-primary.disabled, +.btn-primary[disabled], +fieldset[disabled] .btn-primary, +.btn-primary.disabled:hover, +.btn-primary[disabled]:hover, +fieldset[disabled] .btn-primary:hover, +.btn-primary.disabled:focus, +.btn-primary[disabled]:focus, +fieldset[disabled] .btn-primary:focus, +.btn-primary.disabled.focus, +.btn-primary[disabled].focus, +fieldset[disabled] .btn-primary.focus, +.btn-primary.disabled:active, +.btn-primary[disabled]:active, +fieldset[disabled] .btn-primary:active, +.btn-primary.disabled.active, +.btn-primary[disabled].active, +fieldset[disabled] .btn-primary.active { + background-color: #428bca; + border-color: #357ebd; +} + +.btn-primary .badge { + color: #428bca; + background-color: #fff; +} + +.btn-success { + color: #fff; + background-color: #5cb85c; + border-color: #4cae4c; +} + +.btn-success:hover, +.btn-success:focus, +.btn-success.focus, +.btn-success:active, +.btn-success.active, +.open>.dropdown-toggle.btn-success { + color: #fff; + background-color: #449d44; + border-color: #398439; +} + +.btn-success:active, +.btn-success.active, +.open>.dropdown-toggle.btn-success { + background-image: none; +} + +.btn-success.disabled, +.btn-success[disabled], +fieldset[disabled] .btn-success, +.btn-success.disabled:hover, +.btn-success[disabled]:hover, +fieldset[disabled] .btn-success:hover, +.btn-success.disabled:focus, +.btn-success[disabled]:focus, +fieldset[disabled] .btn-success:focus, +.btn-success.disabled.focus, +.btn-success[disabled].focus, +fieldset[disabled] .btn-success.focus, +.btn-success.disabled:active, +.btn-success[disabled]:active, +fieldset[disabled] .btn-success:active, +.btn-success.disabled.active, +.btn-success[disabled].active, +fieldset[disabled] .btn-success.active { + background-color: #5cb85c; + border-color: #4cae4c; +} + +.btn-success .badge { + color: #5cb85c; + background-color: #fff; +} + +.btn-info { + color: #fff; + background-color: #5bc0de; + border-color: #46b8da; +} + +.btn-info:hover, +.btn-info:focus, +.btn-info.focus, +.btn-info:active, +.btn-info.active, +.open>.dropdown-toggle.btn-info { + color: #fff; + background-color: #31b0d5; + border-color: #269abc; +} + +.btn-info:active, +.btn-info.active, +.open>.dropdown-toggle.btn-info { + background-image: none; +} + +.btn-info.disabled, +.btn-info[disabled], +fieldset[disabled] .btn-info, +.btn-info.disabled:hover, +.btn-info[disabled]:hover, +fieldset[disabled] .btn-info:hover, +.btn-info.disabled:focus, +.btn-info[disabled]:focus, +fieldset[disabled] .btn-info:focus, +.btn-info.disabled.focus, +.btn-info[disabled].focus, +fieldset[disabled] .btn-info.focus, +.btn-info.disabled:active, +.btn-info[disabled]:active, +fieldset[disabled] .btn-info:active, +.btn-info.disabled.active, +.btn-info[disabled].active, +fieldset[disabled] .btn-info.active { + background-color: #5bc0de; + border-color: #46b8da; +} + +.btn-info .badge { + color: #5bc0de; + background-color: #fff; +} + +.btn-warning { + color: #fff; + background-color: #f0ad4e; + border-color: #eea236; +} + +.btn-warning:hover, +.btn-warning:focus, +.btn-warning.focus, +.btn-warning:active, +.btn-warning.active, +.open>.dropdown-toggle.btn-warning { + color: #fff; + background-color: #ec971f; + border-color: #d58512; +} + +.btn-warning:active, +.btn-warning.active, +.open>.dropdown-toggle.btn-warning { + background-image: none; +} + +.btn-warning.disabled, +.btn-warning[disabled], +fieldset[disabled] .btn-warning, +.btn-warning.disabled:hover, +.btn-warning[disabled]:hover, +fieldset[disabled] .btn-warning:hover, +.btn-warning.disabled:focus, +.btn-warning[disabled]:focus, +fieldset[disabled] .btn-warning:focus, +.btn-warning.disabled.focus, +.btn-warning[disabled].focus, +fieldset[disabled] .btn-warning.focus, +.btn-warning.disabled:active, +.btn-warning[disabled]:active, +fieldset[disabled] .btn-warning:active, +.btn-warning.disabled.active, +.btn-warning[disabled].active, +fieldset[disabled] .btn-warning.active { + background-color: #f0ad4e; + border-color: #eea236; +} + +.btn-warning .badge { + color: #f0ad4e; + background-color: #fff; +} + +.btn-danger { + color: #fff; + background-color: #d9534f; + border-color: #d43f3a; +} + +.btn-danger:hover, +.btn-danger:focus, +.btn-danger.focus, +.btn-danger:active, +.btn-danger.active, +.open>.dropdown-toggle.btn-danger { + color: #fff; + background-color: #c9302c; + border-color: #ac2925; +} + +.btn-danger:active, +.btn-danger.active, +.open>.dropdown-toggle.btn-danger { + background-image: none; +} + +.btn-danger.disabled, +.btn-danger[disabled], +fieldset[disabled] .btn-danger, +.btn-danger.disabled:hover, +.btn-danger[disabled]:hover, +fieldset[disabled] .btn-danger:hover, +.btn-danger.disabled:focus, +.btn-danger[disabled]:focus, +fieldset[disabled] .btn-danger:focus, +.btn-danger.disabled.focus, +.btn-danger[disabled].focus, +fieldset[disabled] .btn-danger.focus, +.btn-danger.disabled:active, +.btn-danger[disabled]:active, +fieldset[disabled] .btn-danger:active, +.btn-danger.disabled.active, +.btn-danger[disabled].active, +fieldset[disabled] .btn-danger.active { + background-color: #d9534f; + border-color: #d43f3a; +} + +.btn-danger .badge { + color: #d9534f; + background-color: #fff; +} + +.btn-link { + font-weight: normal; + color: #428bca; + border-radius: 0; +} + +.btn-link, +.btn-link:active, +.btn-link.active, +.btn-link[disabled], +fieldset[disabled] .btn-link { + background-color: transparent; + -webkit-box-shadow: none; + box-shadow: none; +} + +.btn-link, +.btn-link:hover, +.btn-link:focus, +.btn-link:active { + border-color: transparent; +} + +.btn-link:hover, +.btn-link:focus { + color: #2a6496; + text-decoration: underline; + background-color: transparent; +} + +.btn-link[disabled]:hover, +fieldset[disabled] .btn-link:hover, +.btn-link[disabled]:focus, +fieldset[disabled] .btn-link:focus { + color: #777; + text-decoration: none; +} + +.btn-lg, +.btn-group-lg>.btn { + padding: 10px 16px; + font-size: 18px; + line-height: 1.33; + border-radius: 6px; +} + +.btn-sm, +.btn-group-sm>.btn { + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} + +.btn-xs, +.btn-group-xs>.btn { + padding: 1px 5px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} + +.btn-block { + display: block; + width: 100%; +} + +.btn-block+.btn-block { + margin-top: 5px; +} + +input[type="submit"].btn-block, +input[type="reset"].btn-block, +input[type="button"].btn-block { + width: 100%; +} + +.fade { + opacity: 0; + -webkit-transition: opacity .15s linear; + -o-transition: opacity .15s linear; + transition: opacity .15s linear; +} + +.fade.in { + opacity: 1; +} + +.collapse { + display: none; + visibility: hidden; +} + +.collapse.in { + display: block; + visibility: visible; +} + +tr.collapse.in { + display: table-row; +} + +tbody.collapse.in { + display: table-row-group; +} + +.collapsing { + position: relative; + height: 0; + overflow: hidden; + -webkit-transition-timing-function: ease; + -o-transition-timing-function: ease; + transition-timing-function: ease; + -webkit-transition-duration: .35s; + -o-transition-duration: .35s; + transition-duration: .35s; + -webkit-transition-property: height, visibility; + -o-transition-property: height, visibility; + transition-property: height, visibility; +} + +.caret { + display: inline-block; + width: 0; + height: 0; + margin-left: 2px; + vertical-align: middle; + border-top: 4px solid; + border-right: 4px solid transparent; + border-left: 4px solid transparent; +} + +.dropdown { + position: relative; +} + +.dropdown-toggle:focus { + outline: 0; +} + +.dropdown-menu { + position: absolute; + top: 100%; + left: 0; + z-index: 1000; + display: none; + float: left; + min-width: 160px; + padding: 5px 0; + margin: 2px 0 0; + font-size: 14px; + text-align: left; + list-style: none; + background-color: #fff; + -webkit-background-clip: padding-box; + background-clip: padding-box; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, .15); + border-radius: 4px; + -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, .175); + box-shadow: 0 6px 12px rgba(0, 0, 0, .175); +} + +.dropdown-menu.pull-right { + right: 0; + left: auto; +} + +.dropdown-menu .divider { + height: 1px; + margin: 9px 0; + overflow: hidden; + background-color: #e5e5e5; +} + +.dropdown-menu>li>a { + display: block; + padding: 3px 20px; + clear: both; + font-weight: normal; + line-height: 1.42857143; + color: #333; + white-space: nowrap; +} + +.dropdown-menu>li>a:hover, +.dropdown-menu>li>a:focus { + color: #262626; + text-decoration: none; + background-color: #f5f5f5; +} + +.dropdown-menu>.active>a, +.dropdown-menu>.active>a:hover, +.dropdown-menu>.active>a:focus { + color: #fff; + text-decoration: none; + background-color: #428bca; + outline: 0; +} + +.dropdown-menu>.disabled>a, +.dropdown-menu>.disabled>a:hover, +.dropdown-menu>.disabled>a:focus { + color: #777; +} + +.dropdown-menu>.disabled>a:hover, +.dropdown-menu>.disabled>a:focus { + text-decoration: none; + cursor: not-allowed; + background-color: transparent; + background-image: none; + filter: progid:DXImageTransform.Microsoft.gradient(enabled=false); +} + +.open>.dropdown-menu { + display: block; +} + +.open>a { + outline: 0; +} + +.dropdown-menu-right { + right: 0; + left: auto; +} + +.dropdown-menu-left { + right: auto; + left: 0; +} + +.dropdown-header { + display: block; + padding: 3px 20px; + font-size: 12px; + line-height: 1.42857143; + color: #777; + white-space: nowrap; +} + +.dropdown-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 990; +} + +.pull-right>.dropdown-menu { + right: 0; + left: auto; +} + +.dropup .caret, +.navbar-fixed-bottom .dropdown .caret { + content: ""; + border-top: 0; + border-bottom: 4px solid; +} + +.dropup .dropdown-menu, +.navbar-fixed-bottom .dropdown .dropdown-menu { + top: auto; + bottom: 100%; + margin-bottom: 1px; +} + +@media (min-width: 768px) { + .navbar-right .dropdown-menu { + right: 0; + left: auto; + } + + .navbar-right .dropdown-menu-left { + right: auto; + left: 0; + } +} + +.btn-group, +.btn-group-vertical { + position: relative; + display: inline-block; + vertical-align: middle; +} + +.btn-group>.btn, +.btn-group-vertical>.btn { + position: relative; + float: left; +} + +.btn-group>.btn:hover, +.btn-group-vertical>.btn:hover, +.btn-group>.btn:focus, +.btn-group-vertical>.btn:focus, +.btn-group>.btn:active, +.btn-group-vertical>.btn:active, +.btn-group>.btn.active, +.btn-group-vertical>.btn.active { + z-index: 2; +} + +.btn-group>.btn:focus, +.btn-group-vertical>.btn:focus { + outline: 0; +} + +.btn-group .btn+.btn, +.btn-group .btn+.btn-group, +.btn-group .btn-group+.btn, +.btn-group .btn-group+.btn-group { + margin-left: -1px; +} + +.btn-toolbar { + margin-left: -5px; +} + +.btn-toolbar .btn-group, +.btn-toolbar .input-group { + float: left; +} + +.btn-toolbar>.btn, +.btn-toolbar>.btn-group, +.btn-toolbar>.input-group { + margin-left: 5px; +} + +.btn-group>.btn:not(:first-child):not(:last-child):not(.dropdown-toggle) { + border-radius: 0; +} + +.btn-group>.btn:first-child { + margin-left: 0; +} + +.btn-group>.btn:first-child:not(:last-child):not(.dropdown-toggle) { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} + +.btn-group>.btn:last-child:not(:first-child), +.btn-group>.dropdown-toggle:not(:first-child) { + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} + +.btn-group>.btn-group { + float: left; +} + +.btn-group>.btn-group:not(:first-child):not(:last-child)>.btn { + border-radius: 0; +} + +.btn-group>.btn-group:first-child>.btn:last-child, +.btn-group>.btn-group:first-child>.dropdown-toggle { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} + +.btn-group>.btn-group:last-child>.btn:first-child { + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} + +.btn-group .dropdown-toggle:active, +.btn-group.open .dropdown-toggle { + outline: 0; +} + +.btn-group>.btn+.dropdown-toggle { + padding-right: 8px; + padding-left: 8px; +} + +.btn-group>.btn-lg+.dropdown-toggle { + padding-right: 12px; + padding-left: 12px; +} + +.btn-group.open .dropdown-toggle { + -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); + box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); +} + +.btn-group.open .dropdown-toggle.btn-link { + -webkit-box-shadow: none; + box-shadow: none; +} + +.btn .caret { + margin-left: 0; +} + +.btn-lg .caret { + border-width: 5px 5px 0; + border-bottom-width: 0; +} + +.dropup .btn-lg .caret { + border-width: 0 5px 5px; +} + +.btn-group-vertical>.btn, +.btn-group-vertical>.btn-group, +.btn-group-vertical>.btn-group>.btn { + display: block; + float: none; + width: 100%; + max-width: 100%; +} + +.btn-group-vertical>.btn-group>.btn { + float: none; +} + +.btn-group-vertical>.btn+.btn, +.btn-group-vertical>.btn+.btn-group, +.btn-group-vertical>.btn-group+.btn, +.btn-group-vertical>.btn-group+.btn-group { + margin-top: -1px; + margin-left: 0; +} + +.btn-group-vertical>.btn:not(:first-child):not(:last-child) { + border-radius: 0; +} + +.btn-group-vertical>.btn:first-child:not(:last-child) { + border-top-right-radius: 4px; + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; +} + +.btn-group-vertical>.btn:last-child:not(:first-child) { + border-top-left-radius: 0; + border-top-right-radius: 0; + border-bottom-left-radius: 4px; +} + +.btn-group-vertical>.btn-group:not(:first-child):not(:last-child)>.btn { + border-radius: 0; +} + +.btn-group-vertical>.btn-group:first-child:not(:last-child)>.btn:last-child, +.btn-group-vertical>.btn-group:first-child:not(:last-child)>.dropdown-toggle { + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; +} + +.btn-group-vertical>.btn-group:last-child:not(:first-child)>.btn:first-child { + border-top-left-radius: 0; + border-top-right-radius: 0; +} + +.btn-group-justified { + display: table; + width: 100%; + table-layout: fixed; + border-collapse: separate; +} + +.btn-group-justified>.btn, +.btn-group-justified>.btn-group { + display: table-cell; + float: none; + width: 1%; +} + +.btn-group-justified>.btn-group .btn { + width: 100%; +} + +.btn-group-justified>.btn-group .dropdown-menu { + left: auto; +} + +[data-toggle="buttons"]>.btn input[type="radio"], +[data-toggle="buttons"]>.btn-group>.btn input[type="radio"], +[data-toggle="buttons"]>.btn input[type="checkbox"], +[data-toggle="buttons"]>.btn-group>.btn input[type="checkbox"] { + position: absolute; + clip: rect(0, 0, 0, 0); + pointer-events: none; +} + +.input-group { + position: relative; + display: table; + border-collapse: separate; +} + +.input-group[class*="col-"] { + float: none; + padding-right: 0; + padding-left: 0; +} + +.input-group .form-control { + position: relative; + z-index: 2; + float: left; + width: 100%; + margin-bottom: 0; +} + +.input-group-lg>.form-control, +.input-group-lg>.input-group-addon, +.input-group-lg>.input-group-btn>.btn { + height: 46px; + padding: 10px 16px; + font-size: 18px; + line-height: 1.33; + border-radius: 6px; +} + +select.input-group-lg>.form-control, +select.input-group-lg>.input-group-addon, +select.input-group-lg>.input-group-btn>.btn { + height: 46px; + line-height: 46px; +} + +textarea.input-group-lg>.form-control, +textarea.input-group-lg>.input-group-addon, +textarea.input-group-lg>.input-group-btn>.btn, +select[multiple].input-group-lg>.form-control, +select[multiple].input-group-lg>.input-group-addon, +select[multiple].input-group-lg>.input-group-btn>.btn { + height: auto; +} + +.input-group-sm>.form-control, +.input-group-sm>.input-group-addon, +.input-group-sm>.input-group-btn>.btn { + height: 30px; + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} + +select.input-group-sm>.form-control, +select.input-group-sm>.input-group-addon, +select.input-group-sm>.input-group-btn>.btn { + height: 30px; + line-height: 30px; +} + +textarea.input-group-sm>.form-control, +textarea.input-group-sm>.input-group-addon, +textarea.input-group-sm>.input-group-btn>.btn, +select[multiple].input-group-sm>.form-control, +select[multiple].input-group-sm>.input-group-addon, +select[multiple].input-group-sm>.input-group-btn>.btn { + height: auto; +} + +.input-group-addon, +.input-group-btn, +.input-group .form-control { + display: table-cell; +} + +.input-group-addon:not(:first-child):not(:last-child), +.input-group-btn:not(:first-child):not(:last-child), +.input-group .form-control:not(:first-child):not(:last-child) { + border-radius: 0; +} + +.input-group-addon, +.input-group-btn { + width: 1%; + white-space: nowrap; + vertical-align: middle; +} + +.input-group-addon { + padding: 6px 12px; + font-size: 14px; + font-weight: normal; + line-height: 1; + color: #555; + text-align: center; + background-color: #eee; + border: 1px solid #ccc; + border-radius: 4px; +} + +.input-group-addon.input-sm { + padding: 5px 10px; + font-size: 12px; + border-radius: 3px; +} + +.input-group-addon.input-lg { + padding: 10px 16px; + font-size: 18px; + border-radius: 6px; +} + +.input-group-addon input[type="radio"], +.input-group-addon input[type="checkbox"] { + margin-top: 0; +} + +.input-group .form-control:first-child, +.input-group-addon:first-child, +.input-group-btn:first-child>.btn, +.input-group-btn:first-child>.btn-group>.btn, +.input-group-btn:first-child>.dropdown-toggle, +.input-group-btn:last-child>.btn:not(:last-child):not(.dropdown-toggle), +.input-group-btn:last-child>.btn-group:not(:last-child)>.btn { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} + +.input-group-addon:first-child { + border-right: 0; +} + +.input-group .form-control:last-child, +.input-group-addon:last-child, +.input-group-btn:last-child>.btn, +.input-group-btn:last-child>.btn-group>.btn, +.input-group-btn:last-child>.dropdown-toggle, +.input-group-btn:first-child>.btn:not(:first-child), +.input-group-btn:first-child>.btn-group:not(:first-child)>.btn { + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} + +.input-group-addon:last-child { + border-left: 0; +} + +.input-group-btn { + position: relative; + font-size: 0; + white-space: nowrap; +} + +.input-group-btn>.btn { + position: relative; +} + +.input-group-btn>.btn+.btn { + margin-left: -1px; +} + +.input-group-btn>.btn:hover, +.input-group-btn>.btn:focus, +.input-group-btn>.btn:active { + z-index: 2; +} + +.input-group-btn:first-child>.btn, +.input-group-btn:first-child>.btn-group { + margin-right: -1px; +} + +.input-group-btn:last-child>.btn, +.input-group-btn:last-child>.btn-group { + margin-left: -1px; +} + +.nav { + padding-left: 0; + margin-bottom: 0; + list-style: none; +} + +.nav>li { + margin-right: 10px; + position: relative; + display: block; +} + +.nav>li>a { + position: relative; + display: block; + padding: 10px 15px; +} + +.nav>li>a:hover, +.nav>li>a:focus { + text-decoration: none; + background-color: #eee; +} + +.nav>li.disabled>a { + color: #777; +} + +.nav>li.disabled>a:hover, +.nav>li.disabled>a:focus { + color: #777; + text-decoration: none; + cursor: not-allowed; + background-color: transparent; +} + +.nav .open>a, +.nav .open>a:hover, +.nav .open>a:focus { + background-color: #eee; + border-color: #428bca; +} + +.nav .nav-divider { + height: 1px; + margin: 9px 0; + overflow: hidden; + background-color: #e5e5e5; +} + +.nav>li>a>img { + max-width: none; +} + +.nav-tabs { + border-bottom: 1px solid #ddd; +} + +.nav-tabs>li { + float: left; + margin-bottom: -1px; +} + +.nav-tabs>li>a { + margin-right: 2px; + line-height: 1.42857143; + border: 1px solid transparent; + border-radius: 4px 4px 0 0; +} + +.nav-tabs>li>a:hover { + border-color: #eee #eee #ddd; +} + +.nav-tabs>li.active>a, +.nav-tabs>li.active>a:hover, +.nav-tabs>li.active>a:focus { + color: #555; + cursor: default; + background-color: #fff; + border: 1px solid #ddd; + border-bottom-color: transparent; +} + +.nav-tabs.nav-justified { + width: 100%; + border-bottom: 0; +} + +.nav-tabs.nav-justified>li { + float: none; +} + +.nav-tabs.nav-justified>li>a { + margin-bottom: 5px; + text-align: center; +} + +.nav-tabs.nav-justified>.dropdown .dropdown-menu { + top: auto; + left: auto; +} + +.nav-tabs.nav-justified>li { + display: table-cell; + width: 1%; +} + +.nav-tabs.nav-justified>li>a { + margin-bottom: 0; +} + +.nav-tabs.nav-justified>li>a { + margin-right: 0; + border-radius: 4px; +} + +.nav-tabs.nav-justified>.active>a, +.nav-tabs.nav-justified>.active>a:hover, +.nav-tabs.nav-justified>.active>a:focus { + border: 1px solid #ddd; +} + +.nav-tabs.nav-justified>li>a { + border-bottom: 1px solid #ddd; + border-radius: 4px 4px 0 0; +} + +.nav-tabs.nav-justified>.active>a, +.nav-tabs.nav-justified>.active>a:hover, +.nav-tabs.nav-justified>.active>a:focus { + border-bottom-color: #fff; +} + +.nav-pills>li { + float: left; +} + +.nav-pills>li>a { + border-radius: 4px; +} + +.nav-pills>li+li { + margin-left: 2px; +} + +.nav-pills>li.active>a, +.nav-pills>li.active>a:hover, +.nav-pills>li.active>a:focus { + color: #fff; + background-color: #3071a9; + /* Tab cell background color */ +} + +.nav-stacked>li { + float: none; +} + +.nav-stacked>li+li { + margin-top: 2px; + margin-left: 0; +} + +.nav-justified { + width: 100%; +} + +.nav-justified>li { + float: none; +} + +.nav-justified>li>a { + margin-bottom: 5px; + text-align: center; +} + +.nav-justified>.dropdown .dropdown-menu { + top: auto; + left: auto; +} + +.nav-justified>li { + display: table-cell; + width: 1%; +} + +.nav-justified>li>a { + margin-bottom: 0; +} + +.nav-tabs-justified { + border-bottom: 0; +} + +.nav-tabs-justified>li>a { + margin-right: 0; + border-radius: 4px; +} + +.nav-tabs-justified>.active>a, +.nav-tabs-justified>.active>a:hover, +.nav-tabs-justified>.active>a:focus { + border: 1px solid #ddd; +} + +.nav-tabs-justified>li>a { + border-bottom: 1px solid #ddd; + border-radius: 4px 4px 0 0; +} + +.nav-tabs-justified>.active>a, +.nav-tabs-justified>.active>a:hover, +.nav-tabs-justified>.active>a:focus { + border-bottom-color: #fff; +} + +.tab-content>.tab-pane { + display: none; + visibility: hidden; +} + +.tab-content>.active { + display: block; + visibility: visible; +} + +.nav-tabs .dropdown-menu { + margin-top: -1px; + border-top-left-radius: 0; + border-top-right-radius: 0; +} + +.navbar { + position: relative; + min-height: 30px; + border: 1px solid transparent; +} + +/* +@media (min-width: 768px) { + .navbar { + border-radius: 4px; + } +} +@media (min-width: 768px) { + .navbar-header { + float: left; + } +} +*/ + +.navbar-collapse { + padding-right: 15px; + padding-left: 15px; + overflow-x: visible; + -webkit-overflow-scrolling: touch; + border-top: 1px solid transparent; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1); +} + +.navbar-collapse.in { + overflow-y: auto; +} + +/* +@media (min-width: 768px) { + .navbar-collapse { + width: auto; + border-top: 0; + -webkit-box-shadow: none; + box-shadow: none; + } + .navbar-collapse.collapse { + display: block !important; + height: auto !important; + padding-bottom: 0; + overflow: visible !important; + visibility: visible !important; + } + .navbar-collapse.in { + overflow-y: visible; + } + .navbar-fixed-top .navbar-collapse, + .navbar-static-top .navbar-collapse, + .navbar-fixed-bottom .navbar-collapse { + padding-right: 0; + padding-left: 0; + } +} +*/ + +.navbar-fixed-top .navbar-collapse, +.navbar-fixed-bottom .navbar-collapse { + max-height: 340px; +} + +@media (max-device-width: 480px) and (orientation: landscape) { + + .navbar-fixed-top .navbar-collapse, + .navbar-fixed-bottom .navbar-collapse { + max-height: 200px; + } +} + +.container>.navbar-header, +.container-fluid>.navbar-header, +.container>.navbar-collapse, +.container-fluid>.navbar-collapse { + margin-right: -15px; + margin-left: -15px; +} + +@media (min-width: 768px) { + + .container>.navbar-header, + .container-fluid>.navbar-header, + .container>.navbar-collapse, + .container-fluid>.navbar-collapse { + margin-right: 0; + margin-left: 0; + } +} + +.navbar-static-top { + z-index: 1000; + border-width: 0 0 1px; +} + +@media (min-width: 768px) { + .navbar-static-top { + border-radius: 0; + } +} + +.navbar-fixed-top, +.navbar-fixed-bottom { + position: fixed; + right: 0; + left: 0; + z-index: 1030; +} + +@media (min-width: 768px) { + + .navbar-fixed-top, + .navbar-fixed-bottom { + border-radius: 0; + } +} + +.navbar-fixed-top { + top: 0; + border-width: 0 0 1px; +} + +.navbar-fixed-bottom { + bottom: 0; + margin-bottom: 0; + border-width: 1px 0 0; +} + +.navbar-brand { + float: left; + height: 30px; + padding: 6px 15px; + font-size: 15px; + line-height: 18px; +} + +.navbar-brand:hover, +.navbar-brand:focus { + text-decoration: none; +} + +.navbar-brand>img { + display: block; +} + +@media (min-width: 768px) { + + .navbar>.container .navbar-brand, + .navbar>.container-fluid .navbar-brand { + margin-left: -15px; + } +} + +.navbar-toggle { + position: relative; + float: right; + padding: 9px 10px; + margin-top: 8px; + margin-right: 15px; + margin-bottom: 8px; + background-color: transparent; + background-image: none; + border: 1px solid transparent; + border-radius: 4px; +} + +.navbar-toggle:focus { + outline: 0; +} + +.navbar-toggle .icon-bar { + display: block; + width: 22px; + height: 2px; + border-radius: 1px; +} + +.navbar-toggle .icon-bar+.icon-bar { + margin-top: 4px; +} + +@media (min-width: 768px) { + .navbar-toggle { + display: none; + } +} + +.navbar-nav { + margin: 7.5px -15px; +} + +.navbar-nav>li>a { + padding-top: 10px; + padding-bottom: 10px; + line-height: 20px; +} + +.navbar-nav>li, +.navbar-nav { + float: left !important; +} + +.navbar-nav.navbar-right:last-child { + margin-right: -15px !important; +} + +.navbar-right { + float: right !important; +} + +/* +@media (max-width: 767px) { + .navbar-nav .open .dropdown-menu { + position: static; + float: none; + width: auto; + margin-top: 0; + background-color: transparent; + border: 0; + -webkit-box-shadow: none; + box-shadow: none; + } + .navbar-nav .open .dropdown-menu > li > a, + .navbar-nav .open .dropdown-menu .dropdown-header { + padding: 5px 15px 5px 25px; + } + .navbar-nav .open .dropdown-menu > li > a { + line-height: 20px; + } + .navbar-nav .open .dropdown-menu > li > a:hover, + .navbar-nav .open .dropdown-menu > li > a:focus { + background-image: none; + } +} + + .navbar-nav { + float: left; + margin: 0; + } + .navbar-nav > li { + float: left; + } + .navbar-nav > li > a { + padding-top: 15px; + padding-bottom: 15px; + } + +.navbar-form { + padding: 10px 15px; + margin-top: 8px; + margin-right: -15px; + margin-bottom: 8px; + margin-left: -15px; + border-top: 1px solid transparent; + border-bottom: 1px solid transparent; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1); +} +@media (min-width: 768px) { + .navbar-form .form-group { + display: inline-block; + margin-bottom: 0; + vertical-align: middle; + } + .navbar-form .form-control { + display: inline-block; + width: auto; + vertical-align: middle; + } + .navbar-form .form-control-static { + display: inline-block; + } + .navbar-form .input-group { + display: inline-table; + vertical-align: middle; + } + .navbar-form .input-group .input-group-addon, + .navbar-form .input-group .input-group-btn, + .navbar-form .input-group .form-control { + width: auto; + } + .navbar-form .input-group > .form-control { + width: 100%; + } + .navbar-form .control-label { + margin-bottom: 0; + vertical-align: middle; + } + .navbar-form .radio, + .navbar-form .checkbox { + display: inline-block; + margin-top: 0; + margin-bottom: 0; + vertical-align: middle; + } + .navbar-form .radio label, + .navbar-form .checkbox label { + padding-left: 0; + } + .navbar-form .radio input[type="radio"], + .navbar-form .checkbox input[type="checkbox"] { + position: relative; + margin-left: 0; + } + .navbar-form .has-feedback .form-control-feedback { + top: 0; + } +} +@media (max-width: 767px) { + .navbar-form .form-group { + margin-bottom: 5px; + } + .navbar-form .form-group:last-child { + margin-bottom: 0; + } +} +@media (min-width: 768px) { + .navbar-form { + width: auto; + padding-top: 0; + padding-bottom: 0; + margin-right: 0; + margin-left: 0; + border: 0; + -webkit-box-shadow: none; + box-shadow: none; + } +} +*/ + +.navbar-nav>li>.dropdown-menu { + margin-top: 0; + border-top-left-radius: 0; + border-top-right-radius: 0; +} + +.navbar-fixed-bottom .navbar-nav>li>.dropdown-menu { + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; +} + +.navbar-btn { + margin-top: 8px; + margin-bottom: 8px; +} + +.navbar-btn.btn-sm { + margin-top: 10px; + margin-bottom: 10px; +} + +.navbar-btn.btn-xs { + margin-top: 14px; + margin-bottom: 14px; +} + +.navbar-text { + margin-top: 15px; + margin-bottom: 15px; +} + +.navbar-text { + float: left; + margin-right: 15px; + margin-left: 15px; +} + + +.navbar-left { + float: left !important; +} + +.navbar-right { + float: right !important; + margin-right: -15px; +} + +.navbar-right~.navbar-right { + margin-right: 0; +} + +.navbar-default { + background-color: #f8f8f8; + border-color: #e7e7e7; +} + +.navbar-default .navbar-brand { + color: #777; +} + +.navbar-default .navbar-brand:hover, +.navbar-default .navbar-brand:focus { + color: #5e5e5e; + background-color: transparent; +} + +.navbar-default .navbar-text { + color: #777; +} + +.navbar-default .navbar-nav>li>a { + color: #777; +} + +.navbar-default .navbar-nav>li>a:hover, +.navbar-default .navbar-nav>li>a:focus { + color: #333; + background-color: transparent; +} + +.navbar-default .navbar-nav>.active>a, +.navbar-default .navbar-nav>.active>a:hover, +.navbar-default .navbar-nav>.active>a:focus { + color: #555; + background-color: #e7e7e7; +} + +.navbar-default .navbar-nav>.disabled>a, +.navbar-default .navbar-nav>.disabled>a:hover, +.navbar-default .navbar-nav>.disabled>a:focus { + color: #ccc; + background-color: transparent; +} + +.navbar-default .navbar-toggle { + border-color: #ddd; +} + +.navbar-default .navbar-toggle:hover, +.navbar-default .navbar-toggle:focus { + background-color: #ddd; +} + +.navbar-default .navbar-toggle .icon-bar { + background-color: #888; +} + +.navbar-default .navbar-collapse, +.navbar-default .navbar-form { + border-color: #e7e7e7; +} + +.navbar-default .navbar-nav>.open>a, +.navbar-default .navbar-nav>.open>a:hover, +.navbar-default .navbar-nav>.open>a:focus { + color: #555; + background-color: #e7e7e7; +} + +@media (max-width: 767px) { + .navbar-default .navbar-nav .open .dropdown-menu>li>a { + color: #777; + } + + .navbar-default .navbar-nav .open .dropdown-menu>li>a:hover, + .navbar-default .navbar-nav .open .dropdown-menu>li>a:focus { + color: #333; + background-color: transparent; + } + + .navbar-default .navbar-nav .open .dropdown-menu>.active>a, + .navbar-default .navbar-nav .open .dropdown-menu>.active>a:hover, + .navbar-default .navbar-nav .open .dropdown-menu>.active>a:focus { + color: #555; + background-color: #e7e7e7; + } + + .navbar-default .navbar-nav .open .dropdown-menu>.disabled>a, + .navbar-default .navbar-nav .open .dropdown-menu>.disabled>a:hover, + .navbar-default .navbar-nav .open .dropdown-menu>.disabled>a:focus { + color: #ccc; + background-color: transparent; + } +} + +.navbar-default .navbar-link { + color: #777; +} + +.navbar-default .navbar-link:hover { + color: #333; +} + +.navbar-default .btn-link { + color: #777; +} + +.navbar-default .btn-link:hover, +.navbar-default .btn-link:focus { + color: #333; +} + +.navbar-default .btn-link[disabled]:hover, +fieldset[disabled] .navbar-default .btn-link:hover, +.navbar-default .btn-link[disabled]:focus, +fieldset[disabled] .navbar-default .btn-link:focus { + color: #ccc; +} + +.navbar-inverse { + background-color: #336699; + border-color: #080808; +} + +.navbar-inverse .navbar-brand { + color: #ffffff; +} + +.navbar-inverse .navbar-brand:hover, +.navbar-inverse .navbar-brand:focus { + color: #ffffff; + background-color: transparent; +} + +.navbar-inverse .navbar-text { + color: #ffffff; +} + +.navbar-inverse .navbar-nav>li>a { + color: #ffffff; +} + +.navbar-inverse .navbar-nav>li>a:hover, +.navbar-inverse .navbar-nav>li>a:focus { + color: #ffffff; + background-color: transparent; +} + +.navbar-inverse .navbar-nav>.active>a, +.navbar-inverse .navbar-nav>.active>a:hover, +.navbar-inverse .navbar-nav>.active>a:focus { + color: #fff; + background-color: #080808; +} + +.navbar-inverse .navbar-nav>.disabled>a, +.navbar-inverse .navbar-nav>.disabled>a:hover, +.navbar-inverse .navbar-nav>.disabled>a:focus { + color: #444; + background-color: transparent; +} + +.navbar-inverse .navbar-toggle { + border-color: #333; +} + +.navbar-inverse .navbar-toggle:hover, +.navbar-inverse .navbar-toggle:focus { + background-color: #333; +} + +.navbar-inverse .navbar-toggle .icon-bar { + background-color: #fff; +} + +.navbar-inverse .navbar-collapse, +.navbar-inverse .navbar-form { + border-color: #101010; +} + +.navbar-inverse .navbar-nav>.open>a, +.navbar-inverse .navbar-nav>.open>a:hover, +.navbar-inverse .navbar-nav>.open>a:focus { + color: #fff; + background-color: #080808; +} + +@media (max-width: 767px) { + .navbar-inverse .navbar-nav .open .dropdown-menu>.dropdown-header { + border-color: #080808; + } + + .navbar-inverse .navbar-nav .open .dropdown-menu .divider { + background-color: #080808; + } + + .navbar-inverse .navbar-nav .open .dropdown-menu>li>a { + color: #9d9d9d; + } + + .navbar-inverse .navbar-nav .open .dropdown-menu>li>a:hover, + .navbar-inverse .navbar-nav .open .dropdown-menu>li>a:focus { + color: #fff; + background-color: transparent; + } + + .navbar-inverse .navbar-nav .open .dropdown-menu>.active>a, + .navbar-inverse .navbar-nav .open .dropdown-menu>.active>a:hover, + .navbar-inverse .navbar-nav .open .dropdown-menu>.active>a:focus { + color: #fff; + background-color: #080808; + } + + .navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a, + .navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a:hover, + .navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a:focus { + color: #444; + background-color: transparent; + } +} + +.navbar-inverse .navbar-link { + color: #9d9d9d; +} + +.navbar-inverse .navbar-link:hover { + color: #fff; +} + +.navbar-inverse .btn-link { + color: #9d9d9d; +} + +.navbar-inverse .btn-link:hover, +.navbar-inverse .btn-link:focus { + color: #fff; +} + +.navbar-inverse .btn-link[disabled]:hover, +fieldset[disabled] .navbar-inverse .btn-link:hover, +.navbar-inverse .btn-link[disabled]:focus, +fieldset[disabled] .navbar-inverse .btn-link:focus { + color: #444; +} + +.breadcrumb { + padding: 8px 15px; + margin-bottom: 20px; + list-style: none; + background-color: #f5f5f5; + border-radius: 4px; +} + +.breadcrumb>li { + display: inline-block; +} + +.breadcrumb>li+li:before { + padding: 0 5px; + color: #ccc; + content: "/\00a0"; +} + +.breadcrumb>.active { + color: #777; +} + +.pagination { + display: inline-block; + padding-left: 0; + margin: 20px 0; + border-radius: 4px; +} + +.pagination>li { + display: inline; +} + +.pagination>li>a, +.pagination>li>span { + position: relative; + float: left; + padding: 6px 12px; + margin-left: -1px; + line-height: 1.42857143; + color: #428bca; + text-decoration: none; + background-color: #fff; + border: 1px solid #ddd; +} + +.pagination>li:first-child>a, +.pagination>li:first-child>span { + margin-left: 0; + border-top-left-radius: 4px; + border-bottom-left-radius: 4px; +} + +.pagination>li:last-child>a, +.pagination>li:last-child>span { + border-top-right-radius: 4px; + border-bottom-right-radius: 4px; +} + +.pagination>li>a:hover, +.pagination>li>span:hover, +.pagination>li>a:focus, +.pagination>li>span:focus { + color: #2a6496; + background-color: #eee; + border-color: #ddd; +} + +.pagination>.active>a, +.pagination>.active>span, +.pagination>.active>a:hover, +.pagination>.active>span:hover, +.pagination>.active>a:focus, +.pagination>.active>span:focus { + z-index: 2; + color: #fff; + cursor: default; + background-color: #3071a9; + border-color: #428bca; +} + +.pagination>.disabled>span, +.pagination>.disabled>span:hover, +.pagination>.disabled>span:focus, +.pagination>.disabled>a, +.pagination>.disabled>a:hover, +.pagination>.disabled>a:focus { + color: #777; + cursor: not-allowed; + background-color: #fff; + border-color: #ddd; +} + +.pagination-lg>li>a, +.pagination-lg>li>span { + padding: 10px 16px; + font-size: 18px; +} + +.pagination-lg>li:first-child>a, +.pagination-lg>li:first-child>span { + border-top-left-radius: 6px; + border-bottom-left-radius: 6px; +} + +.pagination-lg>li:last-child>a, +.pagination-lg>li:last-child>span { + border-top-right-radius: 6px; + border-bottom-right-radius: 6px; +} + +.pagination-sm>li>a, +.pagination-sm>li>span { + padding: 5px 10px; + font-size: 12px; +} + +.pagination-sm>li:first-child>a, +.pagination-sm>li:first-child>span { + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; +} + +.pagination-sm>li:last-child>a, +.pagination-sm>li:last-child>span { + border-top-right-radius: 3px; + border-bottom-right-radius: 3px; +} + +.pager { + padding-left: 0; + margin: 20px 0; + text-align: center; + list-style: none; +} + +.pager li { + display: inline; +} + +.pager li>a, +.pager li>span { + display: inline-block; + padding: 5px 14px; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 15px; +} + +.pager li>a:hover, +.pager li>a:focus { + text-decoration: none; + background-color: #eee; +} + +.pager .next>a, +.pager .next>span { + float: right; +} + +.pager .previous>a, +.pager .previous>span { + float: left; +} + +.pager .disabled>a, +.pager .disabled>a:hover, +.pager .disabled>a:focus, +.pager .disabled>span { + color: #777; + cursor: not-allowed; + background-color: #fff; +} + +.label { + display: inline; + padding: .2em .6em .3em; + font-size: 75%; + font-weight: bold; + line-height: 1; + color: #fff; + text-align: center; + white-space: nowrap; + vertical-align: baseline; + border-radius: .25em; +} + +a.label:hover, +a.label:focus { + color: #fff; + text-decoration: none; + cursor: pointer; +} + +.label:empty { + display: none; +} + +.btn .label { + position: relative; + top: -1px; +} + +.label-default { + background-color: #777; +} + +.label-default[href]:hover, +.label-default[href]:focus { + background-color: #5e5e5e; +} + +.label-primary { + background-color: #428bca; +} + +.label-primary[href]:hover, +.label-primary[href]:focus { + background-color: #3071a9; +} + +.label-success { + background-color: #5cb85c; +} + +.label-success[href]:hover, +.label-success[href]:focus { + background-color: #449d44; +} + +.label-info { + background-color: #5bc0de; +} + +.label-info[href]:hover, +.label-info[href]:focus { + background-color: #31b0d5; +} + +.label-warning { + background-color: #f0ad4e; +} + +.label-warning[href]:hover, +.label-warning[href]:focus { + background-color: #ec971f; +} + +.label-danger { + background-color: #d9534f; +} + +.label-danger[href]:hover, +.label-danger[href]:focus { + background-color: #c9302c; +} + +.badge { + display: inline-block; + min-width: 10px; + padding: 3px 7px; + font-size: 12px; + font-weight: bold; + line-height: 1; + color: #fff; + text-align: center; + white-space: nowrap; + vertical-align: baseline; + background-color: #777; + border-radius: 10px; +} + +.badge:empty { + display: none; +} + +.btn .badge { + position: relative; + top: -1px; +} + +.btn-xs .badge { + top: 0; + padding: 1px 5px; +} + +a.badge:hover, +a.badge:focus { + color: #fff; + text-decoration: none; + cursor: pointer; +} + +a.list-group-item.active>.badge, +.nav-pills>.active>a>.badge { + color: #3071a9; + background-color: #fff; +} + +.nav-pills>li>a>.badge { + margin-left: 3px; +} + +.jumbotron { + margin-bottom: 10px; + color: inherit; + background-color: #eee; +} + +.jumbotron h1, +.jumbotron .h1 { + color: inherit; +} + +.jumbotron p { + margin-bottom: 15px; + font-size: 21px; + font-weight: 200; +} + +.jumbotron>hr { + border-top-color: #d5d5d5; +} + +.container .jumbotron, +.container-fluid .jumbotron { + border-radius: 6px; +} + +.jumbotron .container { + max-width: 100%; +} + +/*@media screen and (min-width: 768px) { + .jumbotron { + padding: 48px 0; + } + .container .jumbotron { + padding-right: 60px; + padding-left: 60px; + } + .jumbotron h1, + .jumbotron .h1 { + font-size: 63px; + } +}*/ + +.thumbnail { + display: block; + padding: 4px; + margin-bottom: 20px; + line-height: 1.42857143; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 4px; + -webkit-transition: border .2s ease-in-out; + -o-transition: border .2s ease-in-out; + transition: border .2s ease-in-out; +} + +.thumbnail>img, +.thumbnail a>img { + margin-right: auto; + margin-left: auto; +} + +a.thumbnail:hover, +a.thumbnail:focus, +a.thumbnail.active { + border-color: #428bca; +} + +.thumbnail .caption { + padding: 9px; + color: #333; +} + +.alert { + padding: 10px; + margin-bottom: 5px; + border: 1px solid transparent; + border-radius: 4px; +} + +.alert h4 { + margin-top: 0; + color: inherit; +} + +.alert .alert-link { + font-weight: bold; +} + +.alert>p, +.alert>ul { + margin-bottom: 0; +} + +.alert>p+p { + margin-top: 5px; +} + +.alert-dismissable, +.alert-dismissible { + padding-right: 35px; +} + +.alert-dismissable .close, +.alert-dismissible .close { + position: relative; + top: -2px; + right: -21px; + color: inherit; +} + +.alert-success { + color: #3c763d; + background-color: #dff0d8; + border-color: #d6e9c6; +} + +.alert-success hr { + border-top-color: #c9e2b3; +} + +.alert-success .alert-link { + color: #2b542c; +} + +.alert-info { + color: #31708f; + background-color: #d9edf7; + border-color: #bce8f1; +} + +.alert-info hr { + border-top-color: #a6e1ec; +} + +.alert-info .alert-link { + color: #245269; +} + +.alert-warning { + color: #8a6d3b; + background-color: #fcf8e3; + border-color: #faebcc; +} + +.alert-warning hr { + border-top-color: #f7e1b5; +} + +.alert-warning .alert-link { + color: #66512c; +} + +.alert-danger { + color: #a94442; + background-color: #f2dede; + border-color: #ebccd1; +} + +.alert-danger hr { + border-top-color: #e4b9c0; +} + +.alert-danger .alert-link { + color: #843534; +} + +@-webkit-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + + to { + background-position: 0 0; + } +} + +@-o-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + + to { + background-position: 0 0; + } +} + +@keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + + to { + background-position: 0 0; + } +} + +.progress { + height: 20px; + margin-bottom: 20px; + overflow: hidden; + background-color: #f5f5f5; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1); +} + +.progress-bar { + float: left; + width: 0; + height: 100%; + font-size: 12px; + line-height: 20px; + color: #fff; + text-align: center; + background-color: #428bca; + -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15); + box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15); + -webkit-transition: width .6s ease; + -o-transition: width .6s ease; + transition: width .6s ease; +} + +.progress-striped .progress-bar, +.progress-bar-striped { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + -webkit-background-size: 40px 40px; + background-size: 40px 40px; +} + +.progress.active .progress-bar, +.progress-bar.active { + -webkit-animation: progress-bar-stripes 2s linear infinite; + -o-animation: progress-bar-stripes 2s linear infinite; + animation: progress-bar-stripes 2s linear infinite; +} + +.progress-bar-success { + background-color: #5cb85c; +} + +.progress-striped .progress-bar-success { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} + +.progress-bar-info { + background-color: #5bc0de; +} + +.progress-striped .progress-bar-info { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} + +.progress-bar-warning { + background-color: #f0ad4e; +} + +.progress-striped .progress-bar-warning { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} + +.progress-bar-danger { + background-color: #d9534f; +} + +.progress-striped .progress-bar-danger { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} + +.media { + margin-top: 15px; +} + +.media:first-child { + margin-top: 0; +} + +.media-right, +.media>.pull-right { + padding-left: 10px; +} + +.media-left, +.media>.pull-left { + padding-right: 10px; +} + +.media-left, +.media-right, +.media-body { + display: table-cell; + vertical-align: top; +} + +.media-middle { + vertical-align: middle; +} + +.media-bottom { + vertical-align: bottom; +} + +.media-heading { + margin-top: 0; + margin-bottom: 5px; +} + +.media-list { + padding-left: 0; + list-style: none; +} + +.list-group { + padding-left: 0; + margin-bottom: 20px; +} + +.list-group-item { + position: relative; + display: block; + padding: 10px 15px; + margin-bottom: -1px; + background-color: #fff; + border: 1px solid #ddd; +} + +.list-group-item:first-child { + border-top-left-radius: 4px; + border-top-right-radius: 4px; +} + +.list-group-item:last-child { + margin-bottom: 0; + border-bottom-right-radius: 4px; + border-bottom-left-radius: 4px; +} + +.list-group-item>.badge { + float: right; +} + +.list-group-item>.badge+.badge { + margin-right: 5px; +} + +a.list-group-item { + color: #555; +} + +a.list-group-item .list-group-item-heading { + color: #333; +} + +a.list-group-item:hover, +a.list-group-item:focus { + color: #555; + text-decoration: none; + background-color: #f5f5f5; +} + +.list-group-item.disabled, +.list-group-item.disabled:hover, +.list-group-item.disabled:focus { + color: #777; + cursor: not-allowed; + background-color: #eee; +} + +.list-group-item.disabled .list-group-item-heading, +.list-group-item.disabled:hover .list-group-item-heading, +.list-group-item.disabled:focus .list-group-item-heading { + color: inherit; +} + +.list-group-item.disabled .list-group-item-text, +.list-group-item.disabled:hover .list-group-item-text, +.list-group-item.disabled:focus .list-group-item-text { + color: #777; +} + +.list-group-item.active, +.list-group-item.active:hover, +.list-group-item.active:focus { + z-index: 2; + color: #fff; + background-color: #428bca; + border-color: #428bca; +} + +.list-group-item.active .list-group-item-heading, +.list-group-item.active:hover .list-group-item-heading, +.list-group-item.active:focus .list-group-item-heading, +.list-group-item.active .list-group-item-heading>small, +.list-group-item.active:hover .list-group-item-heading>small, +.list-group-item.active:focus .list-group-item-heading>small, +.list-group-item.active .list-group-item-heading>.small, +.list-group-item.active:hover .list-group-item-heading>.small, +.list-group-item.active:focus .list-group-item-heading>.small { + color: inherit; +} + +.list-group-item.active .list-group-item-text, +.list-group-item.active:hover .list-group-item-text, +.list-group-item.active:focus .list-group-item-text { + color: #e1edf7; +} + +.list-group-item-success { + color: #3c763d; + background-color: #dff0d8; +} + +a.list-group-item-success { + color: #3c763d; +} + +a.list-group-item-success .list-group-item-heading { + color: inherit; +} + +a.list-group-item-success:hover, +a.list-group-item-success:focus { + color: #3c763d; + background-color: #d0e9c6; +} + +a.list-group-item-success.active, +a.list-group-item-success.active:hover, +a.list-group-item-success.active:focus { + color: #fff; + background-color: #3c763d; + border-color: #3c763d; +} + +.list-group-item-info { + color: #31708f; + background-color: #d9edf7; +} + +a.list-group-item-info { + color: #31708f; +} + +a.list-group-item-info .list-group-item-heading { + color: inherit; +} + +a.list-group-item-info:hover, +a.list-group-item-info:focus { + color: #31708f; + background-color: #c4e3f3; +} + +a.list-group-item-info.active, +a.list-group-item-info.active:hover, +a.list-group-item-info.active:focus { + color: #fff; + background-color: #31708f; + border-color: #31708f; +} + +.list-group-item-warning { + color: #8a6d3b; + background-color: #fcf8e3; +} + +a.list-group-item-warning { + color: #8a6d3b; +} + +a.list-group-item-warning .list-group-item-heading { + color: inherit; +} + +a.list-group-item-warning:hover, +a.list-group-item-warning:focus { + color: #8a6d3b; + background-color: #faf2cc; +} + +a.list-group-item-warning.active, +a.list-group-item-warning.active:hover, +a.list-group-item-warning.active:focus { + color: #fff; + background-color: #8a6d3b; + border-color: #8a6d3b; +} + +.list-group-item-danger { + color: #a94442; + background-color: #f2dede; +} + +a.list-group-item-danger { + color: #a94442; +} + +a.list-group-item-danger .list-group-item-heading { + color: inherit; +} + +a.list-group-item-danger:hover, +a.list-group-item-danger:focus { + color: #a94442; + background-color: #ebcccc; +} + +a.list-group-item-danger.active, +a.list-group-item-danger.active:hover, +a.list-group-item-danger.active:focus { + color: #fff; + background-color: #a94442; + border-color: #a94442; +} + +.list-group-item-heading { + margin-top: 0; + margin-bottom: 5px; +} + +.list-group-item-text { + margin-bottom: 0; + line-height: 1.3; +} + +.panel { + margin-bottom: 20px; + background-color: #fff; + border: 1px solid transparent; + border-radius: 4px; + -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, .05); + box-shadow: 0 1px 1px rgba(0, 0, 0, .05); +} + +.panel-body { + padding: 15px; +} + +.panel-heading { + padding: 10px 15px; + border-bottom: 1px solid transparent; + border-top-left-radius: 3px; + border-top-right-radius: 3px; + cursor: pointer; +} + +.panel-heading>.dropdown .dropdown-toggle { + color: inherit; +} + +.panel-title { + margin-top: 0; + margin-bottom: 0; + font-size: 16px; + color: inherit; +} + +.panel-title>a { + color: inherit; +} + +.panel-footer { + padding: 10px 15px; + background-color: #f5f5f5; + border-top: 1px solid #ddd; + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} + +.panel>.list-group, +.panel>.panel-collapse>.list-group { + margin-bottom: 0; +} + +.panel>.list-group .list-group-item, +.panel>.panel-collapse>.list-group .list-group-item { + border-width: 1px 0; + border-radius: 0; +} + +.panel>.list-group:first-child .list-group-item:first-child, +.panel>.panel-collapse>.list-group:first-child .list-group-item:first-child { + border-top: 0; + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} + +.panel>.list-group:last-child .list-group-item:last-child, +.panel>.panel-collapse>.list-group:last-child .list-group-item:last-child { + border-bottom: 0; + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} + +.panel-heading+.list-group .list-group-item:first-child { + border-top-width: 0; +} + +.list-group+.panel-footer { + border-top-width: 0; +} + +.panel>.table, +.panel>.table-responsive>.table, +.panel>.panel-collapse>.table { + margin-bottom: 0; +} + +.panel>.table caption, +.panel>.table-responsive>.table caption, +.panel>.panel-collapse>.table caption { + padding-right: 15px; + padding-left: 15px; +} + +.panel>.table:first-child, +.panel>.table-responsive:first-child>.table:first-child { + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} + +.panel>.table:first-child>thead:first-child>tr:first-child, +.panel>.table-responsive:first-child>.table:first-child>thead:first-child>tr:first-child, +.panel>.table:first-child>tbody:first-child>tr:first-child, +.panel>.table-responsive:first-child>.table:first-child>tbody:first-child>tr:first-child { + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} + +.panel>.table:first-child>thead:first-child>tr:first-child td:first-child, +.panel>.table-responsive:first-child>.table:first-child>thead:first-child>tr:first-child td:first-child, +.panel>.table:first-child>tbody:first-child>tr:first-child td:first-child, +.panel>.table-responsive:first-child>.table:first-child>tbody:first-child>tr:first-child td:first-child, +.panel>.table:first-child>thead:first-child>tr:first-child th:first-child, +.panel>.table-responsive:first-child>.table:first-child>thead:first-child>tr:first-child th:first-child, +.panel>.table:first-child>tbody:first-child>tr:first-child th:first-child, +.panel>.table-responsive:first-child>.table:first-child>tbody:first-child>tr:first-child th:first-child { + border-top-left-radius: 3px; +} + +.panel>.table:first-child>thead:first-child>tr:first-child td:last-child, +.panel>.table-responsive:first-child>.table:first-child>thead:first-child>tr:first-child td:last-child, +.panel>.table:first-child>tbody:first-child>tr:first-child td:last-child, +.panel>.table-responsive:first-child>.table:first-child>tbody:first-child>tr:first-child td:last-child, +.panel>.table:first-child>thead:first-child>tr:first-child th:last-child, +.panel>.table-responsive:first-child>.table:first-child>thead:first-child>tr:first-child th:last-child, +.panel>.table:first-child>tbody:first-child>tr:first-child th:last-child, +.panel>.table-responsive:first-child>.table:first-child>tbody:first-child>tr:first-child th:last-child { + border-top-right-radius: 3px; +} + +.panel>.table:last-child, +.panel>.table-responsive:last-child>.table:last-child { + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} + +.panel>.table:last-child>tbody:last-child>tr:last-child, +.panel>.table-responsive:last-child>.table:last-child>tbody:last-child>tr:last-child, +.panel>.table:last-child>tfoot:last-child>tr:last-child, +.panel>.table-responsive:last-child>.table:last-child>tfoot:last-child>tr:last-child { + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} + +.panel>.table:last-child>tbody:last-child>tr:last-child td:first-child, +.panel>.table-responsive:last-child>.table:last-child>tbody:last-child>tr:last-child td:first-child, +.panel>.table:last-child>tfoot:last-child>tr:last-child td:first-child, +.panel>.table-responsive:last-child>.table:last-child>tfoot:last-child>tr:last-child td:first-child, +.panel>.table:last-child>tbody:last-child>tr:last-child th:first-child, +.panel>.table-responsive:last-child>.table:last-child>tbody:last-child>tr:last-child th:first-child, +.panel>.table:last-child>tfoot:last-child>tr:last-child th:first-child, +.panel>.table-responsive:last-child>.table:last-child>tfoot:last-child>tr:last-child th:first-child { + border-bottom-left-radius: 3px; +} + +.panel>.table:last-child>tbody:last-child>tr:last-child td:last-child, +.panel>.table-responsive:last-child>.table:last-child>tbody:last-child>tr:last-child td:last-child, +.panel>.table:last-child>tfoot:last-child>tr:last-child td:last-child, +.panel>.table-responsive:last-child>.table:last-child>tfoot:last-child>tr:last-child td:last-child, +.panel>.table:last-child>tbody:last-child>tr:last-child th:last-child, +.panel>.table-responsive:last-child>.table:last-child>tbody:last-child>tr:last-child th:last-child, +.panel>.table:last-child>tfoot:last-child>tr:last-child th:last-child, +.panel>.table-responsive:last-child>.table:last-child>tfoot:last-child>tr:last-child th:last-child { + border-bottom-right-radius: 3px; +} + +.panel>.panel-body+.table, +.panel>.panel-body+.table-responsive, +.panel>.table+.panel-body, +.panel>.table-responsive+.panel-body { + border-top: 1px solid #ddd; +} + +.panel>.table>tbody:first-child>tr:first-child th, +.panel>.table>tbody:first-child>tr:first-child td { + border-top: 0; +} + +.panel>.table-bordered, +.panel>.table-responsive>.table-bordered { + border: 0; +} + +.panel>.table-bordered>thead>tr>th:first-child, +.panel>.table-responsive>.table-bordered>thead>tr>th:first-child, +.panel>.table-bordered>tbody>tr>th:first-child, +.panel>.table-responsive>.table-bordered>tbody>tr>th:first-child, +.panel>.table-bordered>tfoot>tr>th:first-child, +.panel>.table-responsive>.table-bordered>tfoot>tr>th:first-child, +.panel>.table-bordered>thead>tr>td:first-child, +.panel>.table-responsive>.table-bordered>thead>tr>td:first-child, +.panel>.table-bordered>tbody>tr>td:first-child, +.panel>.table-responsive>.table-bordered>tbody>tr>td:first-child, +.panel>.table-bordered>tfoot>tr>td:first-child, +.panel>.table-responsive>.table-bordered>tfoot>tr>td:first-child { + border-left: 0; +} + +.panel>.table-bordered>thead>tr>th:last-child, +.panel>.table-responsive>.table-bordered>thead>tr>th:last-child, +.panel>.table-bordered>tbody>tr>th:last-child, +.panel>.table-responsive>.table-bordered>tbody>tr>th:last-child, +.panel>.table-bordered>tfoot>tr>th:last-child, +.panel>.table-responsive>.table-bordered>tfoot>tr>th:last-child, +.panel>.table-bordered>thead>tr>td:last-child, +.panel>.table-responsive>.table-bordered>thead>tr>td:last-child, +.panel>.table-bordered>tbody>tr>td:last-child, +.panel>.table-responsive>.table-bordered>tbody>tr>td:last-child, +.panel>.table-bordered>tfoot>tr>td:last-child, +.panel>.table-responsive>.table-bordered>tfoot>tr>td:last-child { + border-right: 0; +} + +.panel>.table-bordered>thead>tr:first-child>td, +.panel>.table-responsive>.table-bordered>thead>tr:first-child>td, +.panel>.table-bordered>tbody>tr:first-child>td, +.panel>.table-responsive>.table-bordered>tbody>tr:first-child>td, +.panel>.table-bordered>thead>tr:first-child>th, +.panel>.table-responsive>.table-bordered>thead>tr:first-child>th, +.panel>.table-bordered>tbody>tr:first-child>th, +.panel>.table-responsive>.table-bordered>tbody>tr:first-child>th { + border-bottom: 0; +} + +.panel>.table-bordered>tbody>tr:last-child>td, +.panel>.table-responsive>.table-bordered>tbody>tr:last-child>td, +.panel>.table-bordered>tfoot>tr:last-child>td, +.panel>.table-responsive>.table-bordered>tfoot>tr:last-child>td, +.panel>.table-bordered>tbody>tr:last-child>th, +.panel>.table-responsive>.table-bordered>tbody>tr:last-child>th, +.panel>.table-bordered>tfoot>tr:last-child>th, +.panel>.table-responsive>.table-bordered>tfoot>tr:last-child>th { + border-bottom: 0; +} + +.panel>.table-responsive { + margin-bottom: 0; + border: 0; +} + +.panel-group { + margin-bottom: 20px; +} + +.panel-group .panel { + margin-bottom: 0; + border-radius: 4px; +} + +.panel-group .panel+.panel { + margin-top: 5px; +} + +.panel-group .panel-heading { + border-bottom: 0; +} + +.panel-group .panel-heading+.panel-collapse>.panel-body, +.panel-group .panel-heading+.panel-collapse>.list-group { + border-top: 1px solid #ddd; +} + +.panel-group .panel-footer { + border-top: 0; +} + +.panel-group .panel-footer+.panel-collapse .panel-body { + border-bottom: 1px solid #ddd; +} + +.panel-default { + border-color: #ddd; +} + +.panel-default>.panel-heading { + color: #333; + background-color: #f5f5f5; + border-color: #ddd; +} + +.panel-default>.panel-heading+.panel-collapse>.panel-body { + border-top-color: #ddd; +} + +.panel-default>.panel-heading .badge { + color: #f5f5f5; + background-color: #333; +} + +.panel-default>.panel-footer+.panel-collapse>.panel-body { + border-bottom-color: #ddd; +} + +.panel-primary { + border-color: #428bca; +} + +.panel-primary>.panel-heading { + color: #fff; + background-color: #428bca; + border-color: #428bca; +} + +.panel-primary>.panel-heading+.panel-collapse>.panel-body { + border-top-color: #428bca; +} + +.panel-primary>.panel-heading .badge { + color: #428bca; + background-color: #fff; +} + +.panel-primary>.panel-footer+.panel-collapse>.panel-body { + border-bottom-color: #428bca; +} + +.panel-success { + border-color: #d6e9c6; +} + +.panel-success>.panel-heading { + color: #3c763d; + background-color: #dff0d8; + border-color: #d6e9c6; +} + +.panel-success>.panel-heading+.panel-collapse>.panel-body { + border-top-color: #d6e9c6; +} + +.panel-success>.panel-heading .badge { + color: #dff0d8; + background-color: #3c763d; +} + +.panel-success>.panel-footer+.panel-collapse>.panel-body { + border-bottom-color: #d6e9c6; +} + +.panel-info { + border-color: #bce8f1; +} + +.panel-info>.panel-heading { + color: #31708f; + background-color: #d9edf7; + border-color: #bce8f1; +} + +.panel-info>.panel-heading+.panel-collapse>.panel-body { + border-top-color: #bce8f1; +} + +.panel-info>.panel-heading .badge { + color: #d9edf7; + background-color: #31708f; +} + +.panel-info>.panel-footer+.panel-collapse>.panel-body { + border-bottom-color: #bce8f1; +} + +.panel-warning { + border-color: #faebcc; +} + +.panel-warning>.panel-heading { + color: #8a6d3b; + background-color: #fcf8e3; + border-color: #faebcc; +} + +.panel-warning>.panel-heading+.panel-collapse>.panel-body { + border-top-color: #faebcc; +} + +.panel-warning>.panel-heading .badge { + color: #fcf8e3; + background-color: #8a6d3b; +} + +.panel-warning>.panel-footer+.panel-collapse>.panel-body { + border-bottom-color: #faebcc; +} + +.panel-danger { + border-color: #ebccd1; +} + +.panel-danger>.panel-heading { + color: #a94442; + background-color: #f2dede; + border-color: #ebccd1; +} + +.panel-danger>.panel-heading+.panel-collapse>.panel-body { + border-top-color: #ebccd1; +} + +.panel-danger>.panel-heading .badge { + color: #f2dede; + background-color: #a94442; +} + +.panel-danger>.panel-footer+.panel-collapse>.panel-body { + border-bottom-color: #ebccd1; +} + +.embed-responsive { + position: relative; + display: block; + height: 0; + padding: 0; + overflow: hidden; +} + +.embed-responsive .embed-responsive-item, +.embed-responsive iframe, +.embed-responsive embed, +.embed-responsive object, +.embed-responsive video { + position: absolute; + top: 0; + bottom: 0; + left: 0; + width: 100%; + height: 100%; + border: 0; +} + +.embed-responsive.embed-responsive-16by9 { + padding-bottom: 56.25%; +} + +.embed-responsive.embed-responsive-4by3 { + padding-bottom: 75%; +} + +.well { + min-height: 20px; + padding: 19px; + margin-bottom: 20px; + background-color: #f5f5f5; + border: 1px solid #e3e3e3; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05); +} + +.well blockquote { + border-color: #ddd; + border-color: rgba(0, 0, 0, .15); +} + +.well-lg { + padding: 24px; + border-radius: 6px; +} + +.well-sm { + padding: 9px; + border-radius: 3px; +} + +.close { + float: right; + font-size: 21px; + font-weight: bold; + line-height: 1; + color: #000; + text-shadow: 0 1px 0 #fff; + filter: alpha(opacity=20); + opacity: .2; +} + +.close:hover, +.close:focus { + color: #000; + text-decoration: none; + cursor: pointer; + filter: alpha(opacity=50); + opacity: .5; +} + +button.close { + -webkit-appearance: none; + padding: 0; + cursor: pointer; + background: transparent; + border: 0; +} + +.modal-open { + overflow: hidden; +} + +.modal { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 1040; + display: none; + overflow: hidden; + -webkit-overflow-scrolling: touch; + outline: 0; +} + +.modal.fade .modal-dialog { + -webkit-transition: -webkit-transform .3s ease-out; + -o-transition: -o-transform .3s ease-out; + transition: transform .3s ease-out; + -webkit-transform: translate(0, -25%); + -ms-transform: translate(0, -25%); + -o-transform: translate(0, -25%); + transform: translate(0, -25%); +} + +.modal.in .modal-dialog { + -webkit-transform: translate(0, 0); + -ms-transform: translate(0, 0); + -o-transform: translate(0, 0); + transform: translate(0, 0); +} + +.modal-open .modal { + overflow-x: hidden; + overflow-y: auto; +} + +.modal-dialog { + position: relative; + width: auto; + margin: 10px; +} + +.modal-content { + position: relative; + background-color: #fff; + -webkit-background-clip: padding-box; + background-clip: padding-box; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, .2); + border-radius: 6px; + outline: 0; + -webkit-box-shadow: 0 3px 9px rgba(0, 0, 0, .5); + box-shadow: 0 3px 9px rgba(0, 0, 0, .5); +} + +.modal-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + background-color: #000; +} + +.modal-backdrop.fade { + filter: alpha(opacity=0); + opacity: 0; +} + +.modal-backdrop.in { + filter: alpha(opacity=50); + opacity: .5; +} + +.modal-header { + min-height: 16.42857143px; + padding: 15px; + border-bottom: 1px solid #e5e5e5; +} + +.modal-header .close { + margin-top: -2px; +} + +.modal-title { + margin: 0; + line-height: 1.42857143; +} + +.modal-body { + position: relative; + padding: 15px; +} + +.modal-footer { + padding: 15px; + text-align: right; + border-top: 1px solid #e5e5e5; +} + +.modal-footer .btn+.btn { + margin-bottom: 0; + margin-left: 5px; +} + +.modal-footer .btn-group .btn+.btn { + margin-left: -1px; +} + +.modal-footer .btn-block+.btn-block { + margin-left: 0; +} + +.modal-scrollbar-measure { + position: absolute; + top: -9999px; + width: 50px; + height: 50px; + overflow: scroll; +} + +@media (min-width: 768px) { + .modal-dialog { + width: 600px; + margin: 30px auto; + } + + .modal-content { + -webkit-box-shadow: 0 5px 15px rgba(0, 0, 0, .5); + box-shadow: 0 5px 15px rgba(0, 0, 0, .5); + } + + .modal-sm { + width: 300px; + } +} + +@media (min-width: 992px) { + .modal-lg { + width: 900px; + } +} + +.tooltip { + position: absolute; + z-index: 1070; + display: block; + font-size: 12px; + line-height: 1.4; + visibility: visible; + filter: alpha(opacity=0); + opacity: 0; +} + +.tooltip.in { + filter: alpha(opacity=90); + opacity: .9; +} + +.tooltip.top { + padding: 5px 0; + margin-top: -3px; +} + +.tooltip.right { + padding: 0 5px; + margin-left: 3px; +} + +.tooltip.bottom { + padding: 5px 0; + margin-top: 3px; +} + +.tooltip.left { + padding: 0 5px; + margin-left: -3px; +} + +.tooltip-inner { + max-width: 200px; + padding: 3px 8px; + color: #fff; + text-align: center; + text-decoration: none; + background-color: #000; + border-radius: 4px; +} + +.tooltip-arrow { + position: absolute; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; +} + +.tooltip.top .tooltip-arrow { + bottom: 0; + left: 50%; + margin-left: -5px; + border-width: 5px 5px 0; + border-top-color: #000; +} + +.tooltip.top-left .tooltip-arrow { + bottom: 0; + left: 5px; + border-width: 5px 5px 0; + border-top-color: #000; +} + +.tooltip.top-right .tooltip-arrow { + right: 5px; + bottom: 0; + border-width: 5px 5px 0; + border-top-color: #000; +} + +.tooltip.right .tooltip-arrow { + top: 50%; + left: 0; + margin-top: -5px; + border-width: 5px 5px 5px 0; + border-right-color: #000; +} + +.tooltip.left .tooltip-arrow { + top: 50%; + right: 0; + margin-top: -5px; + border-width: 5px 0 5px 5px; + border-left-color: #000; +} + +.tooltip.bottom .tooltip-arrow { + top: 0; + left: 50%; + margin-left: -5px; + border-width: 0 5px 5px; + border-bottom-color: #000; +} + +.tooltip.bottom-left .tooltip-arrow { + top: 0; + left: 5px; + border-width: 0 5px 5px; + border-bottom-color: #000; +} + +.tooltip.bottom-right .tooltip-arrow { + top: 0; + right: 5px; + border-width: 0 5px 5px; + border-bottom-color: #000; +} + +.popover { + position: absolute; + top: 0; + left: 0; + z-index: 1060; + display: none; + max-width: 276px; + padding: 1px; + font-size: 14px; + font-weight: normal; + line-height: 1.42857143; + text-align: left; + white-space: normal; + background-color: #fff; + -webkit-background-clip: padding-box; + background-clip: padding-box; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, .2); + border-radius: 6px; + -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, .2); + box-shadow: 0 5px 10px rgba(0, 0, 0, .2); +} + +.popover.top { + margin-top: -10px; +} + +.popover.right { + margin-left: 10px; +} + +.popover.bottom { + margin-top: 10px; +} + +.popover.left { + margin-left: -10px; +} + +.popover-title { + padding: 8px 14px; + margin: 0; + font-size: 14px; + background-color: #f7f7f7; + border-bottom: 1px solid #ebebeb; + border-radius: 5px 5px 0 0; +} + +.popover-content { + padding: 9px 14px; +} + +.popover>.arrow, +.popover>.arrow:after { + position: absolute; + display: block; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; +} + +.popover>.arrow { + border-width: 11px; +} + +.popover>.arrow:after { + content: ""; + border-width: 10px; +} + +.popover.top>.arrow { + bottom: -11px; + left: 50%; + margin-left: -11px; + border-top-color: #999; + border-top-color: rgba(0, 0, 0, .25); + border-bottom-width: 0; +} + +.popover.top>.arrow:after { + bottom: 1px; + margin-left: -10px; + content: " "; + border-top-color: #fff; + border-bottom-width: 0; +} + +.popover.right>.arrow { + top: 50%; + left: -11px; + margin-top: -11px; + border-right-color: #999; + border-right-color: rgba(0, 0, 0, .25); + border-left-width: 0; +} + +.popover.right>.arrow:after { + bottom: -10px; + left: 1px; + content: " "; + border-right-color: #fff; + border-left-width: 0; +} + +.popover.bottom>.arrow { + top: -11px; + left: 50%; + margin-left: -11px; + border-top-width: 0; + border-bottom-color: #999; + border-bottom-color: rgba(0, 0, 0, .25); +} + +.popover.bottom>.arrow:after { + top: 1px; + margin-left: -10px; + content: " "; + border-top-width: 0; + border-bottom-color: #fff; +} + +.popover.left>.arrow { + top: 50%; + right: -11px; + margin-top: -11px; + border-right-width: 0; + border-left-color: #999; + border-left-color: rgba(0, 0, 0, .25); +} + +.popover.left>.arrow:after { + right: 1px; + bottom: -10px; + content: " "; + border-right-width: 0; + border-left-color: #fff; +} + +.carousel { + position: relative; +} + +.carousel-inner { + position: relative; + width: 100%; + overflow: hidden; +} + +.carousel-inner>.item { + position: relative; + display: none; + -webkit-transition: .6s ease-in-out left; + -o-transition: .6s ease-in-out left; + transition: .6s ease-in-out left; +} + +.carousel-inner>.item>img, +.carousel-inner>.item>a>img { + line-height: 1; +} + +@media all and (transform-3d), +(-webkit-transform-3d) { + .carousel-inner>.item { + -webkit-transition: -webkit-transform .6s ease-in-out; + -o-transition: -o-transform .6s ease-in-out; + transition: transform .6s ease-in-out; + + -webkit-backface-visibility: hidden; + backface-visibility: hidden; + -webkit-perspective: 1000; + perspective: 1000; + } + + .carousel-inner>.item.next, + .carousel-inner>.item.active.right { + left: 0; + -webkit-transform: translate3d(100%, 0, 0); + transform: translate3d(100%, 0, 0); + } + + .carousel-inner>.item.prev, + .carousel-inner>.item.active.left { + left: 0; + -webkit-transform: translate3d(-100%, 0, 0); + transform: translate3d(-100%, 0, 0); + } + + .carousel-inner>.item.next.left, + .carousel-inner>.item.prev.right, + .carousel-inner>.item.active { + left: 0; + -webkit-transform: translate3d(0, 0, 0); + transform: translate3d(0, 0, 0); + } +} + +.carousel-inner>.active, +.carousel-inner>.next, +.carousel-inner>.prev { + display: block; +} + +.carousel-inner>.active { + left: 0; +} + +.carousel-inner>.next, +.carousel-inner>.prev { + position: absolute; + top: 0; + width: 100%; +} + +.carousel-inner>.next { + left: 100%; +} + +.carousel-inner>.prev { + left: -100%; +} + +.carousel-inner>.next.left, +.carousel-inner>.prev.right { + left: 0; +} + +.carousel-inner>.active.left { + left: -100%; +} + +.carousel-inner>.active.right { + left: 100%; +} + +.carousel-control { + position: absolute; + top: 0; + bottom: 0; + left: 0; + width: 15%; + font-size: 20px; + color: #fff; + text-align: center; + text-shadow: 0 1px 2px rgba(0, 0, 0, .6); + filter: alpha(opacity=50); + opacity: .5; +} + +.carousel-control.left { + background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%); + background-image: -o-linear-gradient(left, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%); + background-image: -webkit-gradient(linear, left top, right top, from(rgba(0, 0, 0, .5)), to(rgba(0, 0, 0, .0001))); + background-image: linear-gradient(to right, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%); + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#80000000', endColorstr='#00000000', GradientType=1); + background-repeat: repeat-x; +} + +.carousel-control.right { + right: 0; + left: auto; + background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%); + background-image: -o-linear-gradient(left, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%); + background-image: -webkit-gradient(linear, left top, right top, from(rgba(0, 0, 0, .0001)), to(rgba(0, 0, 0, .5))); + background-image: linear-gradient(to right, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%); + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#00000000', endColorstr='#80000000', GradientType=1); + background-repeat: repeat-x; +} + +.carousel-control:hover, +.carousel-control:focus { + color: #fff; + text-decoration: none; + filter: alpha(opacity=90); + outline: 0; + opacity: .9; +} + +.carousel-control .icon-prev, +.carousel-control .icon-next, +.carousel-control .glyphicon-chevron-left, +.carousel-control .glyphicon-chevron-right { + position: absolute; + top: 50%; + z-index: 5; + display: inline-block; +} + +.carousel-control .icon-prev, +.carousel-control .glyphicon-chevron-left { + left: 50%; + margin-left: -10px; +} + +.carousel-control .icon-next, +.carousel-control .glyphicon-chevron-right { + right: 50%; + margin-right: -10px; +} + +.carousel-control .icon-prev, +.carousel-control .icon-next { + width: 20px; + height: 20px; + margin-top: -10px; + font-family: serif; +} + +.carousel-control .icon-prev:before { + content: '\2039'; +} + +.carousel-control .icon-next:before { + content: '\203a'; +} + +.carousel-indicators { + position: absolute; + bottom: 10px; + left: 50%; + z-index: 15; + width: 60%; + padding-left: 0; + margin-left: -30%; + text-align: center; + list-style: none; +} + +.carousel-indicators li { + display: inline-block; + width: 10px; + height: 10px; + margin: 1px; + text-indent: -999px; + cursor: pointer; + background-color: #000 \9; + background-color: rgba(0, 0, 0, 0); + border: 1px solid #fff; + border-radius: 10px; +} + +.carousel-indicators .active { + width: 12px; + height: 12px; + margin: 0; + background-color: #fff; +} + +.carousel-caption { + position: absolute; + right: 15%; + bottom: 20px; + left: 15%; + z-index: 10; + padding-top: 20px; + padding-bottom: 20px; + color: #fff; + text-align: center; + text-shadow: 0 1px 2px rgba(0, 0, 0, .6); +} + +.carousel-caption .btn { + text-shadow: none; +} + +/* +@media screen and (min-width: 768px) { + .carousel-control .glyphicon-chevron-left, + .carousel-control .glyphicon-chevron-right, + .carousel-control .icon-prev, + .carousel-control .icon-next { + width: 30px; + height: 30px; + margin-top: -15px; + font-size: 30px; + } + .carousel-control .glyphicon-chevron-left, + .carousel-control .icon-prev { + margin-left: -15px; + } + .carousel-control .glyphicon-chevron-right, + .carousel-control .icon-next { + margin-right: -15px; + } + .carousel-caption { + right: 20%; + left: 20%; + padding-bottom: 30px; + } + .carousel-indicators { + bottom: 20px; + } +} +*/ +.clearfix:before, +.clearfix:after, +.dl-horizontal dd:before, +.dl-horizontal dd:after, +.container:before, +.container:after, +.container-fluid:before, +.container-fluid:after, +.row:before, +.row:after, +.form-horizontal .form-group:before, +.form-horizontal .form-group:after, +.btn-toolbar:before, +.btn-toolbar:after, +.btn-group-vertical>.btn-group:before, +.btn-group-vertical>.btn-group:after, +.nav:before, +.nav:after, +.navbar:before, +.navbar:after, +.navbar-header:before, +.navbar-header:after, +.navbar-collapse:before, +.navbar-collapse:after, +.pager:before, +.pager:after, +.panel-body:before, +.panel-body:after, +.modal-footer:before, +.modal-footer:after { + display: table; + content: " "; +} + +.clearfix:after, +.dl-horizontal dd:after, +.container:after, +.container-fluid:after, +.row:after, +.form-horizontal .form-group:after, +.btn-toolbar:after, +.btn-group-vertical>.btn-group:after, +.nav:after, +.navbar:after, +.navbar-header:after, +.navbar-collapse:after, +.pager:after, +.panel-body:after, +.modal-footer:after { + clear: both; +} + +.center-block { + display: block; + margin-right: auto; + margin-left: auto; +} + +.pull-right { + float: right !important; +} + +.pull-left { + float: left !important; +} + +.hide { + display: none !important; +} + +.show { + display: block !important; +} + +.invisible { + visibility: hidden; +} + +.text-hide { + font: 0/0 a; + color: transparent; + text-shadow: none; + background-color: transparent; + border: 0; +} + +.hidden { + display: none !important; + visibility: hidden !important; +} + +.affix { + position: fixed; +} + +@-ms-viewport { + width: device-width; +} + +.visible-xs, +.visible-sm, +.visible-md, +.visible-lg { + display: none !important; +} + +.visible-xs-block, +.visible-xs-inline, +.visible-xs-inline-block, +.visible-sm-block, +.visible-sm-inline, +.visible-sm-inline-block, +.visible-md-block, +.visible-md-inline, +.visible-md-inline-block, +.visible-lg-block, +.visible-lg-inline, +.visible-lg-inline-block { + display: none !important; +} + +/* +@media (max-width: 767px) { + .visible-xs { + display: block !important; + } + table.visible-xs { + display: table; + } + tr.visible-xs { + display: table-row !important; + } + th.visible-xs, + td.visible-xs { + display: table-cell !important; + } +} +@media (max-width: 767px) { + .visible-xs-block { + display: block !important; + } +} +@media (max-width: 767px) { + .visible-xs-inline { + display: inline !important; + } +} +@media (max-width: 767px) { + .visible-xs-inline-block { + display: inline-block !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm { + display: block !important; + } + table.visible-sm { + display: table; + } + tr.visible-sm { + display: table-row !important; + } + th.visible-sm, + td.visible-sm { + display: table-cell !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm-block { + display: block !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm-inline { + display: inline !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm-inline-block { + display: inline-block !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md { + display: block !important; + } + table.visible-md { + display: table; + } + tr.visible-md { + display: table-row !important; + } + th.visible-md, + td.visible-md { + display: table-cell !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md-block { + display: block !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md-inline { + display: inline !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md-inline-block { + display: inline-block !important; + } +} +@media (min-width: 1200px) { + .visible-lg { + display: block !important; + } + table.visible-lg { + display: table; + } + tr.visible-lg { + display: table-row !important; + } + th.visible-lg, + td.visible-lg { + display: table-cell !important; + } +} +@media (min-width: 1200px) { + .visible-lg-block { + display: block !important; + } +} +@media (min-width: 1200px) { + .visible-lg-inline { + display: inline !important; + } +} +@media (min-width: 1200px) { + .visible-lg-inline-block { + display: inline-block !important; + } +} +@media (max-width: 767px) { + .hidden-xs { + display: none !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .hidden-sm { + display: none !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .hidden-md { + display: none !important; + } +} +@media (min-width: 1200px) { + .hidden-lg { + display: none !important; + } +} +.visible-print { + display: none !important; +} +@media print { + .visible-print { + display: block !important; + } + table.visible-print { + display: table; + } + tr.visible-print { + display: table-row !important; + } + th.visible-print, + td.visible-print { + display: table-cell !important; + } +} +*/ +.visible-print-block { + display: none !important; +} + +@media print { + .visible-print-block { + display: block !important; + } +} + +.visible-print-inline { + display: none !important; +} + +@media print { + .visible-print-inline { + display: inline !important; + } +} + +.visible-print-inline-block { + display: none !important; +} + +@media print { + .visible-print-inline-block { + display: inline-block !important; + } +} + +@media print { + .hidden-print { + display: none !important; + } +} diff --git a/gn2/wqflask/static/new/css/box_plot.css b/gn2/wqflask/static/new/css/box_plot.css new file mode 100644 index 00000000..4c743b33 --- /dev/null +++ b/gn2/wqflask/static/new/css/box_plot.css @@ -0,0 +1,20 @@ +.box {
+ font: 10px sans-serif;
+}
+
+.box line,
+.box rect,
+.box circle {
+ fill: #fff;
+ stroke: #000;
+ stroke-width: 1.5px;
+}
+
+.box .center {
+ stroke-dasharray: 3,3;
+}
+
+.box .outlier {
+ fill: none;
+ stroke: #ccc;
+}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/broken_links.css b/gn2/wqflask/static/new/css/broken_links.css new file mode 100644 index 00000000..676f32d9 --- /dev/null +++ b/gn2/wqflask/static/new/css/broken_links.css @@ -0,0 +1,5 @@ + +.broken_link{ + color:red; + text-decoration: underline; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/colorbox.css b/gn2/wqflask/static/new/css/colorbox.css new file mode 100644 index 00000000..8b9fb388 --- /dev/null +++ b/gn2/wqflask/static/new/css/colorbox.css @@ -0,0 +1,238 @@ +/* + Colorbox Core Style: + The following CSS is consistent between example themes and should not be altered. +*/ +#colorbox, +#cboxOverlay, +#cboxWrapper { + position: absolute; + top: 0; + left: 0; + z-index: 9999; + overflow: hidden; +} + +#cboxOverlay { + position: fixed; + width: 100%; + height: 100%; +} + +#cboxMiddleLeft, +#cboxBottomLeft { + clear: left; +} + +#cboxContent { + position: relative; +} + +#cboxLoadedContent { + overflow: auto; + -webkit-overflow-scrolling: touch; +} + +#cboxTitle { + margin: 0; +} + +#cboxLoadingOverlay, +#cboxLoadingGraphic { + position: absolute; + top: 0; + left: 0; + width: 100%; + height: 100%; +} + +#cboxPrevious, +#cboxNext, +#cboxClose, +#cboxSlideshow { + cursor: pointer; +} + +.cboxPhoto { + float: left; + margin: auto; + border: 0; + display: block; + max-width: none; + -ms-interpolation-mode: bicubic; +} + +.cboxIframe { + width: 100%; + height: 100%; + display: block; + border: 0; +} + +#colorbox, +#cboxContent, +#cboxLoadedContent { + box-sizing: content-box; + -moz-box-sizing: content-box; + -webkit-box-sizing: content-box; +} + +/* + User Style: + Change the following styles to modify the appearance of Colorbox. They are + ordered & tabbed in a way that represents the nesting of the generated HTML. +*/ +#cboxOverlay { + background: #fff; +} + +#colorbox { + outline: 0; +} + +#cboxTopLeft { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat 0 0; +} + +#cboxTopCenter { + height: 25px; + background: url(images/border1.png) repeat-x 0 -50px; +} + +#cboxTopRight { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat -25px 0; +} + +#cboxBottomLeft { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat 0 -25px; +} + +#cboxBottomCenter { + height: 25px; + background: url(images/border1.png) repeat-x 0 -75px; +} + +#cboxBottomRight { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat -25px -25px; +} + +#cboxMiddleLeft { + width: 25px; + background: url(images/border2.png) repeat-y 0 0; +} + +#cboxMiddleRight { + width: 25px; + background: url(images/border2.png) repeat-y -25px 0; +} + +#cboxContent { + background: #fff; + overflow: hidden; +} + +.cboxIframe { + background: #fff; +} + +#cboxError { + padding: 50px; + border: 1px solid #ccc; +} + +#cboxLoadedContent { + margin-bottom: 20px; +} + +#cboxTitle { + position: absolute; + bottom: 0px; + left: 0; + text-align: center; + width: 100%; + color: #999; +} + +#cboxCurrent { + position: absolute; + bottom: 0px; + left: 100px; + color: #999; +} + +#cboxLoadingOverlay { + background: #fff url(images/loading.gif) no-repeat 5px 5px; +} + +/* these elements are buttons, and may need to have additional styles reset to avoid unwanted base styles */ +#cboxPrevious, +#cboxNext, +#cboxSlideshow, +#cboxClose { + border: 0; + padding: 0; + margin: 0; + overflow: visible; + width: auto; + background: none; +} + +/* avoid outlines on :active (mouseclick), but preserve outlines on :focus (tabbed navigating) */ +#cboxPrevious:active, +#cboxNext:active, +#cboxSlideshow:active, +#cboxClose:active { + outline: 0; +} + +#cboxSlideshow { + position: absolute; + bottom: 0px; + right: 42px; + color: #444; +} + +#cboxPrevious { + position: absolute; + bottom: 0px; + left: 0; + color: #444; +} + +#cboxNext { + position: absolute; + bottom: 0px; + left: 63px; + color: #444; +} + +#cboxClose { + position: absolute; + bottom: 0; + right: 0; + display: block; + color: #444; +} + +/* + The following fixes a problem where IE7 and IE8 replace a PNG's alpha transparency with a black fill + when an alpha filter (opacity change) is set on the element or ancestor element. This style is not applied to or needed in IE9. + See: http://jacklmoore.com/notes/ie-transparency-problems/ +*/ +.cboxIE #cboxTopLeft, +.cboxIE #cboxTopCenter, +.cboxIE #cboxTopRight, +.cboxIE #cboxBottomLeft, +.cboxIE #cboxBottomCenter, +.cboxIE #cboxBottomRight, +.cboxIE #cboxMiddleLeft, +.cboxIE #cboxMiddleRight { + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr=#00FFFFFF, endColorstr=#00FFFFFF); +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/corr_matrix.css b/gn2/wqflask/static/new/css/corr_matrix.css new file mode 100644 index 00000000..cd2b0a80 --- /dev/null +++ b/gn2/wqflask/static/new/css/corr_matrix.css @@ -0,0 +1,30 @@ +.vertical_label { + -webkit-transform: rotate(-90deg); + -moz-transform: rotate(-90deg); + -ms-transform: rotate(-90deg); + -o-transform: rotate(-90deg); + transform: rotate(-90deg); + color: #000 + font-size: 22px; + height: 50px; + width: 100px; + float: left; +} + +.chart { + +} + +.main text { + font: 10px sans-serif; +} + +.axis line, .axis path { + shape-rendering: crispEdges; + stroke: black; + fill: none; +} + +circle { + fill: steelblue; +} diff --git a/gn2/wqflask/static/new/css/corr_scatter_plot.css b/gn2/wqflask/static/new/css/corr_scatter_plot.css new file mode 100644 index 00000000..a2ebb252 --- /dev/null +++ b/gn2/wqflask/static/new/css/corr_scatter_plot.css @@ -0,0 +1,41 @@ +.nvd3 .nv-axis.nv-x text { + font-size: 16px; + font-weight: normal; + fill: black; +} + +.nvd3 .nv-axis.nv-y text { + font-size: 16px; + font-weight: normal; + fill: black; +} + +.nv-x .nv-axis g path.domain { + stroke: black; + stroke-width: 2; +} + +.nv-y .nv-axis g path.domain { + stroke: black; + stroke-width: 2; +} + +.nvd3 .nv-axis.nv-x path.domain { + stroke-opacity: 1; +} + +.nvd3 .nv-axis.nv-y path.domain { + stroke-opacity: 1; +} + +line.nv-regLine { + stroke: red; + stroke-width: 1; +} + +.nv-axisMin-x, +.nv-axisMax-x, +.nv-axisMin-y, +.nv-axisMax-y { + display: none; +} diff --git a/gn2/wqflask/static/new/css/corr_scatter_plot2.css b/gn2/wqflask/static/new/css/corr_scatter_plot2.css new file mode 100644 index 00000000..a2ebb252 --- /dev/null +++ b/gn2/wqflask/static/new/css/corr_scatter_plot2.css @@ -0,0 +1,41 @@ +.nvd3 .nv-axis.nv-x text { + font-size: 16px; + font-weight: normal; + fill: black; +} + +.nvd3 .nv-axis.nv-y text { + font-size: 16px; + font-weight: normal; + fill: black; +} + +.nv-x .nv-axis g path.domain { + stroke: black; + stroke-width: 2; +} + +.nv-y .nv-axis g path.domain { + stroke: black; + stroke-width: 2; +} + +.nvd3 .nv-axis.nv-x path.domain { + stroke-opacity: 1; +} + +.nvd3 .nv-axis.nv-y path.domain { + stroke-opacity: 1; +} + +line.nv-regLine { + stroke: red; + stroke-width: 1; +} + +.nv-axisMin-x, +.nv-axisMax-x, +.nv-axisMin-y, +.nv-axisMax-y { + display: none; +} diff --git a/gn2/wqflask/static/new/css/d3-tip.min.css b/gn2/wqflask/static/new/css/d3-tip.min.css new file mode 100644 index 00000000..3d253caf --- /dev/null +++ b/gn2/wqflask/static/new/css/d3-tip.min.css @@ -0,0 +1 @@ +.d3-tip{line-height:1;font-weight:bold;padding:12px;background:rgba(0,0,0,0.8);color:#fff;border-radius:2px;pointer-events:none}.d3-tip:after{box-sizing:border-box;display:inline;font-size:10px;width:100%;line-height:1;color:rgba(0,0,0,0.8);position:absolute;pointer-events:none}.d3-tip.n:after{content:"\25BC";margin:-1px 0 0 0;top:100%;left:0;text-align:center}.d3-tip.e:after{content:"\25C0";margin:-4px 0 0 0;top:50%;left:-8px}.d3-tip.s:after{content:"\25B2";margin:0 0 1px 0;top:-8px;left:0;text-align:center}.d3-tip.w:after{content:"\25B6";margin:-4px 0 0 -1px;top:50%;left:100%}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/d3panels.min.css b/gn2/wqflask/static/new/css/d3panels.min.css new file mode 100644 index 00000000..7db7b91f --- /dev/null +++ b/gn2/wqflask/static/new/css/d3panels.min.css @@ -0,0 +1 @@ +svg.qtlcharts,svg.d3panels{font-family:sans-serif;font-size:11pt}svg.qtlcharts .title text,svg.d3panels .title text{dominant-baseline:middle;fill:#0074d9;text-anchor:middle}svg.qtlcharts .y.axis text,svg.d3panels .y.axis text{dominant-baseline:middle;text-anchor:end}svg.qtlcharts .y.axis text.title,svg.d3panels .y.axis text.title{text-anchor:middle;fill:slateblue}svg.qtlcharts .x.axis text,svg.d3panels .x.axis text{dominant-baseline:hanging;text-anchor:middle}svg.qtlcharts .x.axis text.title,svg.d3panels .x.axis text.title{fill:slateblue}svg.qtlcharts line.axis.grid,svg.d3panels line.axis.grid{fill:none;stroke-width:1;pointer-events:none}svg.qtlcharts line.x.axis.grid,svg.d3panels line.x.axis.grid{stroke:#c8c8c8;stroke-width:3}svg.qtlcharts line.y.axis.grid,svg.d3panels line.y.axis.grid{stroke:white}svg.qtlcharts .extent,svg.d3panels .extent{fill:#cac;opacity:.3}svg.qtlcharts circle.selected,svg.d3panels circle.selected{fill:hotpink;opacity:1}svg.qtlcharts a,svg.d3panels a{color:#08c;text-decoration:none}svg.qtlcharts a:hover,svg.d3panels a:hover{color:#333;text-decoration:underline}svg.qtlcharts text.crosstab,svg.d3panels text.crosstab{dominant-baseline:middle;text-anchor:end}svg.qtlcharts text.crosstabtitle,svg.d3panels text.crosstabtitle{dominant-baseline:middle;text-anchor:center}.caption{font-family:Sans-serif;font-size:11pt;margin-left:60px;width:600px}div.d3panels-tooltip{position:absolute;text-align:center;width:max-content;height:min-content;padding:5px;font-size:16px;font-family:sans-serif;font-weight:bold;background:darkslateblue;color:white;text-align:center;border:0;border-radius:3px;pointer-events:none;z-index:999}div.d3panels-tooltip-tri{position:absolute;text-align:center;width:32px;height:32px;padding:0;font-size:16px;font-family:sans-serif;font-weight:bold;background:#ffffff00;color:darkslateblue;text-align:center;border:0;pointer-events:none;z-index:998}div.error p{font-family:sans-serif;font-size:16pt;font-weight:bold;padding:5px}div.qtlcharts{font-family:sans-serif;font-size:12pt}div.searchbox{font-family:Sans-serif;font-size:12pt;margin-left:60px}div.searchbox.inactive input{color:#888} diff --git a/gn2/wqflask/static/new/css/docs.css b/gn2/wqflask/static/new/css/docs.css new file mode 100644 index 00000000..665559e6 --- /dev/null +++ b/gn2/wqflask/static/new/css/docs.css @@ -0,0 +1,1080 @@ +/* Add additional stylesheets below +-------------------------------------------------- */ +/* + Bootstrap's documentation styles + Special styles for presenting Bootstrap's documentation and examples +*/ + + + +/* Body and structure +-------------------------------------------------- */ + +body { + position: relative; + padding-top: 0px; +} + +/* Code in headings */ +h3 code { + font-size: 14px; + font-weight: normal; +} + + + +/* Tweak navbar brand link to be super sleek +-------------------------------------------------- */ +/* +body > .navbar { + font-size: 12px; + font-weight: bold; +} +*/ + +/* Change the docs' brand */ + +body>.navbar .navbar-brand { + padding-right: 20px; + padding-left: 20px; + margin-left: 20px; + float: left; + font-weight: bold; + color: #ffffff; + text-shadow: 0 1px 0 rgba(255, 255, 255, .1), 0 0 30px rgba(255, 255, 255, .125); + -webkit-transition: all .2s linear; + -moz-transition: all .2s linear; + transition: all .2s linear; +} + +body>.navbar .brand:hover { + text-decoration: none; + text-shadow: 0 1px 0 rgba(255, 255, 255, .1), 0 0 30px rgba(255, 255, 255, .4); +} + + +/* Sections +-------------------------------------------------- */ + +/* padding for in-page bookmarks and fixed navbar */ +section { + padding-top: 0px; +} + +section>.page-header, +section>.lead { + color: #5a5a5a; +} + +section>ul li { + margin-bottom: 5px; +} + +/* Separators (hr) */ +.bs-docs-separator { + margin: 40px 0 39px; +} + +/* Faded out hr */ +hr.soften { + height: 1px; + margin: 70px 0; + background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, 0), rgba(0, 0, 0, .1), rgba(0, 0, 0, 0)); + background-image: -moz-linear-gradient(left, rgba(0, 0, 0, 0), rgba(0, 0, 0, .1), rgba(0, 0, 0, 0)); + background-image: -ms-linear-gradient(left, rgba(0, 0, 0, 0), rgba(0, 0, 0, .1), rgba(0, 0, 0, 0)); + background-image: -o-linear-gradient(left, rgba(0, 0, 0, 0), rgba(0, 0, 0, .1), rgba(0, 0, 0, 0)); + border: 0; +} + + + +/* Jumbotrons +-------------------------------------------------- */ + +/* Base class +------------------------- */ +.jumbotron { + position: relative; + padding: 0px 0; + color: black; + text-align: left; + text-shadow: 0 1px 3px rgba(0, 0, 0, .4), 0 0 30px rgba(0, 0, 0, .075); + background: #d5d5d5; + /* Old browsers */ + +} + +.jumbotron h1 { + font-size: 60px; + font-weight: bold; + letter-spacing: -1px; + line-height: 1; +} + +.jumbotron p { + font-size: 20px; + font-weight: 300; + line-height: 20px; + margin-bottom: 10px; +} + +/* Link styles (used on .masthead-links as well) */ +.jumbotron a { + color: #336699; + color: rgba(255, 255, 255, .5); + -webkit-transition: all .2s ease-in-out; + -moz-transition: all .2s ease-in-out; + transition: all .2s ease-in-out; +} + +.jumbotron a:hover { + color: #336699; + text-shadow: 0 0 10px rgba(255, 255, 255, .25); +} + +/* Download button */ +.masthead .btn { + padding: 14px 24px; + font-size: 24px; + font-weight: 200; + color: #fff; + /* redeclare to override the `.jumbotron a` */ + border: 0; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 5px rgba(0, 0, 0, .25); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 5px rgba(0, 0, 0, .25); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 5px rgba(0, 0, 0, .25); + -webkit-transition: none; + -moz-transition: none; + transition: none; +} + +.masthead .btn:hover { + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 5px rgba(0, 0, 0, .25); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 5px rgba(0, 0, 0, .25); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 5px rgba(0, 0, 0, .25); +} + +.masthead .btn:active { + -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, .1), 0 1px 0 rgba(255, 255, 255, .1); + -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, .1), 0 1px 0 rgba(255, 255, 255, .1); + box-shadow: inset 0 2px 4px rgba(0, 0, 0, .1), 0 1px 0 rgba(255, 255, 255, .1); +} + + +/* Pattern overlay +------------------------- */ +.jumbotron .container { + position: relative; + z-index: 2; +} + +.jumbotron:after { + content: ''; + display: block; + position: absolute; + top: 0; + right: 0; + bottom: 0; + left: 0; + /*background: url(../img/bs-docs-masthead-pattern.png) repeat center center;*/ + opacity: .4; +} + +/* Masthead (docs home) +------------------------- */ +.masthead { + padding: 70px 0 80px; + margin-bottom: 0; + color: #fff; +} + +.masthead h1 { + font-size: 120px; + line-height: 1; + letter-spacing: -2px; +} + +.masthead p { + font-size: 40px; + font-weight: 200; + line-height: 1.25; +} + +/* Textual links in masthead */ +.masthead-links { + margin: 0; + list-style: none; +} + +.masthead-links li { + display: inline; + padding: 0 10px; + color: rgba(255, 255, 255, .25); +} + +/* Social proof buttons from GitHub & Twitter */ +.bs-docs-social { + padding: 15px 0; + text-align: center; + background-color: #f5f5f5; + border-top: 1px solid #fff; + border-bottom: 1px solid #ddd; +} + +/* Quick links on Home */ +.bs-docs-social-buttons { + margin-left: 0; + margin-bottom: 0; + padding-left: 0; + list-style: none; +} + +.bs-docs-social-buttons li { + display: inline-block; + padding: 5px 8px; + line-height: 1; + *display: inline; + *zoom: 1; +} + +/* Subhead (other pages) +------------------------- */ +.subhead { + text-align: left; + border-bottom: 1px solid #ddd; +} + +.subhead h1 { + font-size: 30px; +} + +.subhead p { + margin-bottom: 10px; +} + +.subhead .navbar { + display: none; +} + + + +/* Marketing section of Overview +-------------------------------------------------- */ + +.marketing { + text-align: center; + color: #5a5a5a; +} + +.marketing h1 { + margin: 60px 0 10px; + font-size: 60px; + font-weight: 200; + line-height: 1; + letter-spacing: -1px; +} + +.marketing h2 { + font-weight: 200; + margin-bottom: 5px; +} + +.marketing p { + font-size: 16px; + line-height: 1.5; +} + +.marketing .marketing-byline { + margin-bottom: 40px; + font-size: 20px; + font-weight: 300; + line-height: 25px; + color: #999; +} + +.marketing img { + display: block; + margin: 0 auto 30px; +} + + + +/* Footer +-------------------------------------------------- */ + +.footer { + padding: 70px 0; + margin-top: 70px; + border-top: 1px solid #e5e5e5; + background-color: #f5f5f5; +} + +.footer p { + margin-bottom: 0; + color: #777; +} + +.footer-links { + margin: 10px 0; +} + +.footer-links li { + display: inline; + margin-right: 10px; +} + + + +/* Special grid styles +-------------------------------------------------- */ + +.show-grid { + margin-top: 10px; + margin-bottom: 20px; +} + +.show-grid [class*="span"] { + background-color: #eee; + text-align: center; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + min-height: 40px; + line-height: 40px; +} + +.show-grid:hover [class*="span"] { + background: #ddd; +} + +.show-grid .show-grid { + margin-top: 0; + margin-bottom: 0; +} + +.show-grid .show-grid [class*="span"] { + background-color: #ccc; +} + + + +/* Mini layout previews +-------------------------------------------------- */ +.mini-layout { + border: 1px solid #ddd; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); + -moz-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); + box-shadow: 0 1px 2px rgba(0, 0, 0, .075); +} + +.mini-layout, +.mini-layout .mini-layout-body, +.mini-layout.fluid .mini-layout-sidebar { + height: 300px; +} + +.mini-layout { + margin-bottom: 20px; + padding: 9px; +} + +.mini-layout div { + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; +} + +.mini-layout .mini-layout-body { + background-color: #dceaf4; + margin: 0 auto; + width: 70%; +} + +.mini-layout.fluid .mini-layout-sidebar, +.mini-layout.fluid .mini-layout-header, +.mini-layout.fluid .mini-layout-body { + float: left; +} + +.mini-layout.fluid .mini-layout-sidebar { + background-color: #bbd8e9; + width: 20%; +} + +.mini-layout.fluid .mini-layout-body { + width: 77.5%; + margin-left: 2.5%; +} + + + +/* Download page +-------------------------------------------------- */ + +.download .page-header { + margin-top: 36px; +} + +.page-header .toggle-all { + margin-top: 5px; +} + +/* Space out h3s when following a section */ +.download h3 { + margin-bottom: 5px; +} + +.download-builder input+h3, +.download-builder .checkbox+h3 { + margin-top: 9px; +} + +/* Fields for variables */ +.download-builder input[type=text] { + margin-bottom: 9px; + font-family: Menlo, Monaco, "Courier New", monospace; + font-size: 12px; + color: #d14; +} + +.download-builder input[type=text]:focus { + background-color: #fff; +} + +/* Custom, larger checkbox labels */ +.download .checkbox { + padding: 6px 10px 6px 25px; + font-size: 13px; + line-height: 18px; + color: #555; + background-color: #f9f9f9; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + cursor: pointer; +} + +.download .checkbox:hover { + color: #333; + background-color: #f5f5f5; +} + +.download .checkbox small { + font-size: 12px; + color: #777; +} + +/* Variables section */ +#variables label { + margin-bottom: 0; +} + +/* Giant download button */ +.download-btn { + margin: 36px 0 108px; +} + +#download p, +#download h4 { + max-width: 50%; + margin: 0 auto; + color: #999; + text-align: center; +} + +#download h4 { + margin-bottom: 0; +} + +#download p { + margin-bottom: 18px; +} + +.download-btn .btn { + display: block; + width: auto; + padding: 19px 24px; + margin-bottom: 27px; + font-size: 30px; + line-height: 1; + text-align: center; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; +} + + + +/* Misc +-------------------------------------------------- */ + +/* Make tables spaced out a bit more */ +h2+table, +h3+table, +h4+table, +h2+.row { + margin-top: 5px; +} + +/* Example sites showcase */ +.example-sites { + xmargin-left: 20px; +} + +.example-sites img { + max-width: 100%; + margin: 0 auto; +} + +.scrollspy-example { + height: 200px; + overflow: auto; + position: relative; +} + + +/* Fake the :focus state to demo it */ +.focused { + border-color: rgba(82, 168, 236, .8); + -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, .1), 0 0 8px rgba(82, 168, 236, .6); + -moz-box-shadow: inset 0 1px 3px rgba(0, 0, 0, .1), 0 0 8px rgba(82, 168, 236, .6); + box-shadow: inset 0 1px 3px rgba(0, 0, 0, .1), 0 0 8px rgba(82, 168, 236, .6); + outline: 0; +} + +/* For input sizes, make them display block */ +.docs-input-sizes select, +.docs-input-sizes input[type=text] { + display: block; + margin-bottom: 9px; +} + +/* Icons +------------------------- */ +.the-icons { + margin-left: 0; + list-style: none; +} + +.the-icons li { + float: left; + width: 25%; + line-height: 25px; +} + +.the-icons i:hover { + background-color: rgba(255, 0, 0, .25); +} + +/* Example page +------------------------- */ +.bootstrap-examples p { + font-size: 13px; + line-height: 18px; +} + +.bootstrap-examples .thumbnail { + margin-bottom: 9px; + background-color: #fff; +} + + + +/* Bootstrap code examples +-------------------------------------------------- */ + +/* Base class */ +.bs-docs-example { + position: relative; + margin: 15px 0; + padding: 39px 19px 14px; + *padding-top: 19px; + background-color: #fff; + border: 1px solid #ddd; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + + +/* Remove spacing between an example and it's code */ +.bs-docs-example+.prettyprint { + margin-top: -20px; + padding-top: 15px; +} + +/* Tweak examples +------------------------- */ +.bs-docs-example>p:last-child { + margin-bottom: 0; +} + +.bs-docs-example .table, +.bs-docs-example .progress, +.bs-docs-example .well, +.bs-docs-example .alert, +.bs-docs-example .hero-unit, +.bs-docs-example .pagination, +.bs-docs-example .navbar, +.bs-docs-example>.nav, +.bs-docs-example blockquote { + margin-bottom: 5px; +} + +.bs-docs-example .pagination { + margin-top: 0; +} + +.bs-navbar-top-example, +.bs-navbar-bottom-example { + z-index: 1; + padding: 0; + height: 90px; + overflow: hidden; + /* cut the drop shadows off */ +} + +.bs-navbar-top-example .navbar-fixed-top, +.bs-navbar-bottom-example .navbar-fixed-bottom { + margin-left: 0; + margin-right: 0; +} + +.bs-navbar-top-example { + -webkit-border-radius: 0 0 4px 4px; + -moz-border-radius: 0 0 4px 4px; + border-radius: 0 0 4px 4px; +} + +.bs-navbar-top-example:after { + top: auto; + bottom: -1px; + -webkit-border-radius: 0 4px 0 4px; + -moz-border-radius: 0 4px 0 4px; + border-radius: 0 4px 0 4px; +} + +.bs-navbar-bottom-example { + -webkit-border-radius: 4px 4px 0 0; + -moz-border-radius: 4px 4px 0 0; + border-radius: 4px 4px 0 0; +} + +.bs-navbar-bottom-example .navbar { + margin-bottom: 0; +} + +form.bs-docs-example { + padding-bottom: 19px; +} + +/* Images */ +.bs-docs-example-images img { + margin: 10px; + display: inline-block; +} + +/* Tooltips */ +.bs-docs-tooltip-examples { + text-align: center; + margin: 0 0 10px; + list-style: none; +} + +.bs-docs-tooltip-examples li { + display: inline; + padding: 0 10px; +} + +/* Popovers */ +.bs-docs-example-popover { + padding-bottom: 24px; + background-color: #f9f9f9; +} + +.bs-docs-example-popover .popover { + position: relative; + display: block; + float: left; + width: 260px; + margin: 20px; +} + + + +/* Responsive docs +-------------------------------------------------- */ + +/* Utility classes table +------------------------- */ +.responsive-utilities th small { + display: block; + font-weight: normal; + color: #999; +} + +.responsive-utilities tbody th { + font-weight: normal; +} + +.responsive-utilities td { + text-align: center; +} + +.responsive-utilities td.is-visible { + color: #468847; + background-color: #dff0d8 !important; +} + +.responsive-utilities td.is-hidden { + color: #ccc; + background-color: #f9f9f9 !important; +} + +/* Responsive tests +------------------------- */ +.responsive-utilities-test { + margin-top: 5px; + margin-left: 0; + list-style: none; + overflow: hidden; + /* clear floats */ +} + +.responsive-utilities-test li { + position: relative; + float: left; + width: 25%; + height: 43px; + font-size: 14px; + font-weight: bold; + line-height: 43px; + color: #999; + text-align: center; + border: 1px solid #ddd; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.responsive-utilities-test li+li { + margin-left: 10px; +} + +.responsive-utilities-test span { + position: absolute; + top: -1px; + left: -1px; + right: -1px; + bottom: -1px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.responsive-utilities-test span { + color: #468847; + background-color: #dff0d8; + border: 1px solid #d6e9c6; +} + + + +/* Sidenav for Docs +-------------------------------------------------- */ + +.bs-docs-sidenav { + width: 228px; + margin: 30px 0 0; + padding: 0; + background-color: #fff; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 1px 4px rgba(0, 0, 0, .065); + -moz-box-shadow: 0 1px 4px rgba(0, 0, 0, .065); + box-shadow: 0 1px 4px rgba(0, 0, 0, .065); +} + +.bs-docs-sidenav>li>a { + display: block; + *width: 190px; + margin: 0 0 -1px; + padding: 8px 14px; + border: 1px solid #e5e5e5; +} + +.bs-docs-sidenav>li:first-child>a { + -webkit-border-radius: 6px 6px 0 0; + -moz-border-radius: 6px 6px 0 0; + border-radius: 6px 6px 0 0; +} + +.bs-docs-sidenav>li:last-child>a { + -webkit-border-radius: 0 0 6px 6px; + -moz-border-radius: 0 0 6px 6px; + border-radius: 0 0 6px 6px; +} + +.bs-docs-sidenav>.active>a { + position: relative; + z-index: 2; + padding: 9px 15px; + border: 0; + text-shadow: 0 1px 0 rgba(0, 0, 0, .15); + -webkit-box-shadow: inset 1px 0 0 rgba(0, 0, 0, .1), inset -1px 0 0 rgba(0, 0, 0, .1); + -moz-box-shadow: inset 1px 0 0 rgba(0, 0, 0, .1), inset -1px 0 0 rgba(0, 0, 0, .1); + box-shadow: inset 1px 0 0 rgba(0, 0, 0, .1), inset -1px 0 0 rgba(0, 0, 0, .1); +} + +/* Chevrons */ +.bs-docs-sidenav .icon-chevron-right { + float: right; + margin-top: 2px; + margin-right: -6px; + opacity: .25; +} + +.bs-docs-sidenav>li>a:hover { + background-color: #f5f5f5; +} + +.bs-docs-sidenav a:hover .icon-chevron-right { + opacity: .5; +} + +.bs-docs-sidenav .active .icon-chevron-right, +.bs-docs-sidenav .active a:hover .icon-chevron-right { + background-image: url(../img/glyphicons-halflings-white.png); + opacity: 1; +} + +.bs-docs-sidenav.affix { + top: 40px; +} + +.bs-docs-sidenav.affix-bottom { + position: absolute; + top: auto; + bottom: 270px; +} + + + + +/* Responsive +-------------------------------------------------- */ + +/* Desktop large +------------------------- */ +@media (min-width: 1200px) { + .bs-docs-container { + max-width: 970px; + } + + .bs-docs-sidenav { + width: 258px; + } +} + +/* Desktop +------------------------- */ +@media (max-width: 980px) { + + /* Unfloat brand */ + body>.navbar-fixed-top .brand { + float: left; + margin-left: 0; + padding-left: 10px; + padding-right: 10px; + } + + /* Inline-block quick links for more spacing */ + .quick-links li { + display: inline-block; + margin: 5px; + } + + /* When affixed, space properly */ + .bs-docs-sidenav { + top: 0; + margin-top: 30px; + margin-right: 0; + } +} + +/* Tablet to desktop +------------------------- */ +@media (min-width: 768px) and (max-width: 980px) { + + /* Remove any padding from the body */ + body { + padding-top: 0; + } + + /* Widen masthead and social buttons to fill body padding */ + .jumbotron { + margin-top: -20px; + /* Offset bottom margin on .navbar */ + } + + /* Adjust sidenav width */ + .bs-docs-sidenav { + width: 166px; + margin-top: 20px; + } + + .bs-docs-sidenav.affix { + top: 0; + } +} + +/* Tablet +------------------------- */ +@media (max-width: 767px) { + + /* Remove any padding from the body */ + body { + padding-top: 0; + } + + /* Widen masthead and social buttons to fill body padding */ + .jumbotron { + padding: 40px 20px; + margin-top: -20px; + /* Offset bottom margin on .navbar */ + margin-right: -20px; + margin-left: -20px; + } + + .masthead h1 { + font-size: 90px; + } + + .masthead p, + .masthead .btn { + font-size: 24px; + } + + .marketing .span4 { + margin-bottom: 40px; + } + + .bs-docs-social { + margin: 0 -20px; + } + + /* Space out the show-grid examples */ + .show-grid [class*="span"] { + margin-bottom: 5px; + } + + /* Sidenav */ + .bs-docs-sidenav { + width: auto; + margin-bottom: 20px; + } + + .bs-docs-sidenav.affix { + position: static; + width: auto; + top: 0; + } + + /* Unfloat the back to top link in footer */ + .footer { + margin-left: -20px; + margin-right: -20px; + padding-left: 20px; + padding-right: 20px; + } + + .footer p { + margin-bottom: 9px; + } +} + +/* Landscape phones +------------------------- */ +@media (max-width: 480px) { + + /* Remove padding above jumbotron */ + body { + padding-top: 0; + } + + /* Change up some type stuff */ + h2 small { + display: block; + } + + /* Downsize the jumbotrons */ + .jumbotron h1 { + font-size: 40px; + } + + .jumbotron p, + .jumbotron .btn { + font-size: 20px; + } + + .jumbotron .btn { + display: block; + margin: 0 auto; + } + + /* center align subhead text like the masthead */ + .subhead h1, + .subhead p { + text-align: left; + } + + /* Marketing on home */ + .marketing h1 { + font-size: 40px; + } + + /* center example sites */ + .example-sites { + margin-left: 0; + } + + .example-sites>li { + float: none; + display: block; + max-width: 280px; + margin: 0 auto 18px; + text-align: center; + } + + .example-sites .thumbnail>img { + max-width: 270px; + } + + /* Do our best to make tables work in narrow viewports */ + table code { + white-space: normal; + word-wrap: break-word; + word-break: break-all; + } + + /* Modal example */ + .modal-example .modal { + position: relative; + top: auto; + right: auto; + bottom: auto; + left: auto; + } + + /* Unfloat the back to top in footer to prevent odd text wrapping */ + .footer .pull-right { + float: none; + } +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/index_page.css b/gn2/wqflask/static/new/css/index_page.css new file mode 100644 index 00000000..34b3cebf --- /dev/null +++ b/gn2/wqflask/static/new/css/index_page.css @@ -0,0 +1,4 @@ +.info-button {
+ border: #A9A9A9;
+ background-color: #D3D3D3;
+}
diff --git a/gn2/wqflask/static/new/css/jupyter_notebooks.css b/gn2/wqflask/static/new/css/jupyter_notebooks.css new file mode 100644 index 00000000..db972a17 --- /dev/null +++ b/gn2/wqflask/static/new/css/jupyter_notebooks.css @@ -0,0 +1,16 @@ +.jupyter-links { + padding: 1.5em; +} + +.jupyter-links:nth-of-type(2n) { + background: #EEEEEE; +} + +.jupyter-links .main-link { + font-size: larger; + display: block; +} + +.jupyter-links .src-link { + font-size: smaller; +} diff --git a/gn2/wqflask/static/new/css/main.css b/gn2/wqflask/static/new/css/main.css new file mode 100644 index 00000000..d5fb8a61 --- /dev/null +++ b/gn2/wqflask/static/new/css/main.css @@ -0,0 +1,40 @@ +@media (max-width: 10px) { + .navbar-header { + float: none; + } + .navbar-toggle { + display: block; + } + .navbar-collapse { + border-top: 1px solid transparent; + box-shadow: inset 0 1px 0 rgba(255,255,255,0.1); + } + .navbar-collapse.collapse { + display: none!important; + } + .navbar-nav { + float: none!important; + margin: 7.5px -15px; + } + .navbar-nav>li { + float: none; + } + .navbar-nav>li>a { + padding-top: 10px; + padding-bottom: 10px; + } + .navbar-text { + float: none; + margin: 15px 0; + } + .navbar-collapse.collapse.in { + display: block!important; + } + .collapsing { + overflow: hidden!important; + } +} + +.checkbox { + min-height: 20px; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/markdown.css b/gn2/wqflask/static/new/css/markdown.css new file mode 100644 index 00000000..859fe7fc --- /dev/null +++ b/gn2/wqflask/static/new/css/markdown.css @@ -0,0 +1,108 @@ +#markdown { + padding: 20px; +} + +#markdown h2, +#markdown h3, +#markdown h4, +#markdown h5 { + font-weight: bold; +} + +#markdown img { + display: block; + margin-right: auto; + margin-left: auto; +} + +.github-btn-container { + margin: 20px 10px; + display: flex; + width: 90vw; + justify-content: flex-end; +} + +.github-btn { + display: flex; + justify-content: center; + border: 3px solid #357ebd; + background: lightgrey; + padding: 3px 4px; + width: 200px; + border-radius: 16px; +} + +.github-btn a { + align-self: center; + font-weight: bold; + color: #357ebd; +} + +.github-btn a img { + height: 40px; + width: 40px; + padding-left:5px; +} + + +.container { + width: 80vw; + margin: auto; + max-width: 80vw; + +} + +.container p { + font-size: 17px; + word-spacing: 0.2em; +} + +.graph-legend h1 { + text-align: center; +} + +.graph-legend, +#guix-graph, +#guix-svg-graph{ + width: 90%; + margin: 10px auto; +} + +#guix-graph { + border: solid 2px black; +} + +#guix-svg-graph img { + width: 100%; +} + +#markdown table { + width: 100%; +} + +#markdown td { + padding: 1em; + text-align: left; +} + +#markdown th { + text-align: center; +} + +#markdown table, +#markdown td, +#markdown th { + border: solid 2px black; +} + +#markdown td, +#markdown th { + padding-top: 8px; + padding-bottom: 8px; +} + +@media(max-width:650px) { + .container { + width: 100vw; + } +} diff --git a/gn2/wqflask/static/new/css/marker_regression.css b/gn2/wqflask/static/new/css/marker_regression.css new file mode 100644 index 00000000..9f56b63d --- /dev/null +++ b/gn2/wqflask/static/new/css/marker_regression.css @@ -0,0 +1,76 @@ +.chr_manhattan_plot .y_axis path, +.chr_manhattan_plot .y_axis line { + fill: none; + stroke: black; + shape-rendering: crispEdges; +} +.chr_manhattan_plot .y_axis text { + font-family: sans-serif; + font-size: 14px; +} + +.chr_manhattan_plot .x_axis path, +.chr_manhattan_plot .x_axis line { + fill: none; + stroke: black; + shape-rendering: crispEdges; +} + +.chr_manhattan_plot .x_axis text { + text-anchor: end; + font-family: sans-serif; + font-size: 10px; +} + +rect.pane { + cursor: move; + fill: none; + pointer-events: all; +} + +/*rect { + stroke: WhiteSmoke; + fill: lightgrey; +}*/ +/*rect { + stroke: WhiteSmoke; + fill: Azure; +}*/ + +tr .outlier { + background-color: #ffff99; +} + +table.dataTable thead th{ + border-right: 1px solid white; + color: white; + background-color: #369; +} + +table.dataTable thead .sorting_asc { + background-image: url("/js/DataTables/images/sort_asc_disabled.png"); +} +table.dataTable thead .sorting_desc { + background-image: url("/js/DataTables/images/sort_desc_disabled.png"); +} + +table.dataTable thead th { + padding: 4px 18px 4px 10px; +} + +table.dataTable tbody td { + padding: 4px 20px 2px 10px; +} + +table.dataTable tbody tr.selected { + background-color: #ffee99; +} + +table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { + border-top: 1px solid #ccc; + border-right: 1px solid #ccc; +} +table.dataTable.cell-border tbody tr th:first-child, +table.dataTable.cell-border tbody tr td:first-child { + border-left: 1px solid #ccc; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/mytooltip.css b/gn2/wqflask/static/new/css/mytooltip.css new file mode 100644 index 00000000..bc44c488 --- /dev/null +++ b/gn2/wqflask/static/new/css/mytooltip.css @@ -0,0 +1,16 @@ +.mytooltiptext { + visibility: hidden; + width: inherit; + background-color: #E5E5AF; + color: #595959; + text-align: left; + padding: 5px 0; + border-radius: 6px; + + position: absolute; + z-index: 1; +} + +.mytooltip:hover .mytooltiptext { + visibility: visible; +} diff --git a/gn2/wqflask/static/new/css/network_graph.css b/gn2/wqflask/static/new/css/network_graph.css new file mode 100644 index 00000000..1a0bafeb --- /dev/null +++ b/gn2/wqflask/static/new/css/network_graph.css @@ -0,0 +1,37 @@ +#content h2, h3, h4, h5, h6 { + color: #545454; + margin-bottom: 1em; + border-bottom: dashed 1px #dfdfdf; + padding-bottom: 0.3em; +} + +#content table td { + padding: 0.5em; + /* border-right: solid 1px #fff; */ +} + +#secondaryContent { + position: relative; + float: left; + width: 18.5em; + background: #fff url('/static/new/images/a1.gif') top right repeat-y; +} + + +input[type="button" i], input[type="submit" i], input[type="reset" i], input[type="file" i]::-webkit-file-upload-button, button { + align-items: flex-start; + text-align: center; + cursor: default; + color: buttontext; + border-image-source: initial; + border-image-slice: initial; + border-image-width: initial; + border-image-outset: initial; + border-image-repeat: initial; + background-color: buttonface; + box-sizing: border-box; + padding: 2px 6px 3px; + border-width: 2px; + border-style: outset; + border-color: buttonface; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/non-responsive.css b/gn2/wqflask/static/new/css/non-responsive.css new file mode 100644 index 00000000..a4bcddd2 --- /dev/null +++ b/gn2/wqflask/static/new/css/non-responsive.css @@ -0,0 +1,114 @@ +/* Template-specific stuff + * + * Customizations just for the template; these are not necessary for anything + * with disabling the responsiveness. + */ + +/* Account for fixed navbar */ +body { + //min-width: 1200px; + padding-top: 70px; + padding-bottom: 30px; +} + +/* Finesse the page header spacing */ +.page-header { + margin-bottom: 10px; +} + +.page-header .lead { + margin-bottom: 10px; +} + + +/* Non-responsive overrides + * + * Utilitze the following CSS to disable the responsive-ness of the container, + * grid system, and navbar. + */ + +/* Reset the container */ +.container { + width: 100%; + max-width: none !important; +} + + +.container .navbar-header, +.container .navbar-collapse { + margin-right: 0; + margin-left: 0; +} + +/* Always float the navbar header */ +.navbar-header { + float: left; +} + +/* Undo the collapsing navbar */ +.navbar-collapse { + display: block !important; + height: auto !important; + padding-bottom: 0; + overflow: visible !important; +} + +.navbar-toggle { + display: none; +} + +.navbar-collapse { + border-top: 0; +} + +/* Always apply the floated nav */ +.navbar-nav { + float: left; + margin: 0; +} + +.navbar-nav>li { + float: left; +} + +.navbar-nav>li>a { + padding: 5px; +} + +/* Redeclare since we override the float above */ +.navbar-nav.navbar-right { + float: right; +} + +/* Undo custom dropdowns */ +.navbar .navbar-nav .open .dropdown-menu { + position: absolute; + float: left; + background-color: #fff; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, .15); + border-width: 0 1px 1px; + border-radius: 0 0 4px 4px; + -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, .175); + box-shadow: 0 6px 12px rgba(0, 0, 0, .175); +} + +.navbar-default .navbar-nav .open .dropdown-menu>li>a { + color: #333; +} + +.navbar .navbar-nav .open .dropdown-menu>li>a:hover, +.navbar .navbar-nav .open .dropdown-menu>li>a:focus, +.navbar .navbar-nav .open .dropdown-menu>.active>a, +.navbar .navbar-nav .open .dropdown-menu>.active>a:hover, +.navbar .navbar-nav .open .dropdown-menu>.active>a:focus { + color: #fff !important; + background-color: #3071a9 !important; +} + +.navbar .navbar-nav .open .dropdown-menu>.disabled>a, +.navbar .navbar-nav .open .dropdown-menu>.disabled>a:hover, +.navbar .navbar-nav .open .dropdown-menu>.disabled>a:focus { + color: #999 !important; + background-color: transparent !important; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/pair_scan.css b/gn2/wqflask/static/new/css/pair_scan.css new file mode 100644 index 00000000..90cec529 --- /dev/null +++ b/gn2/wqflask/static/new/css/pair_scan.css @@ -0,0 +1,6 @@ +/* Unset CSS for tooltip since it will inherit from the bootstrap tooltip class CSS otherwise */
+.tooltip{all:unset;}
+
+.pairscan-container {
+ width: 1000px;
+}
diff --git a/gn2/wqflask/static/new/css/panelutil.css b/gn2/wqflask/static/new/css/panelutil.css new file mode 100644 index 00000000..ccd7eb01 --- /dev/null +++ b/gn2/wqflask/static/new/css/panelutil.css @@ -0,0 +1,91 @@ +
+/* figures will always be within a div with class="qtlcharts" */
+div.qtlcharts {
+ font-family: sans-serif;
+ font-size: 11pt;
+}
+
+div.qtlcharts .title text {
+ dominant-baseline: middle;
+ fill: blue;
+ text-anchor: middle;
+}
+
+div.qtlcharts .y.axis text {
+ dominant-baseline: middle;
+ text-anchor: end;
+}
+
+div.qtlcharts .y.axis text.title {
+ text-anchor: middle;
+ fill: slateblue;
+}
+
+div.qtlcharts .x.axis text {
+ dominant-baseline: hanging;
+ text-anchor: middle;
+}
+
+div.qtlcharts .x.axis text.title {
+ fill: slateblue;
+}
+
+/*div.qtlcharts line.axis.grid {
+ fill: none;
+ stroke-width: 1;
+ pointer-events: none;
+}
+
+div.qtlcharts line.x.axis.grid {
+ stroke: rgb(200, 200, 200);
+ stroke-width: 3;
+}
+
+div.qtlcharts line.y.axis.grid {
+ stroke: white;
+}*/
+
+div.qtlcharts .extent {
+ fill: #cac;
+ opacity: 0.3;
+}
+
+div.qtlcharts circle.selected {
+ fill: hotpink;
+ opacity: 1;
+}
+
+div.qtlcharts a {
+ color: #08c;
+ text-decoration: none;
+}
+
+div.qtlcharts a:hover {
+ color: #333;
+ text-decoration: underline;
+}
+
+
+/* figure captions */
+.caption {
+ font-family: Sans-serif;
+ font-size: 11pt;
+ margin-left: 60px;
+ width: 600px;
+}
+
+
+/* d3 tip for tool tips */
+.d3-tip {
+ background: darkslateblue;
+ color: #fff;
+ stroke: none;
+ font-weight: bold;
+ font-size: 16px;
+ font-family: sans-serif;
+ padding: 5px;
+}
+
+.d3-tip.e:after {
+ color: darkslateblue;
+}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/parsley.css b/gn2/wqflask/static/new/css/parsley.css new file mode 100644 index 00000000..7d244579 --- /dev/null +++ b/gn2/wqflask/static/new/css/parsley.css @@ -0,0 +1,20 @@ +/* Adapted from parsleyjs.org/documentation.html#parsleyclasses */ + +input.parsley-success, textarea.parsley-success { + color: #468847 !important; + background-color: #DFF0D8 !important; + border: 1px solid #D6E9C6 !important; +} +input.parsley-error, textarea.parsley-error { + color: #B94A48 !important; + background-color: #F2DEDE !important; + border: 1px solid #EED3D7 !important; +} +ul.parsley-error-list { + font-size: 11px; + margin: 2px; + list-style-type:none; +} +ul.parsley-error-list li { + line-height: 11px; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/partial_correlations.css b/gn2/wqflask/static/new/css/partial_correlations.css new file mode 100644 index 00000000..84a0877f --- /dev/null +++ b/gn2/wqflask/static/new/css/partial_correlations.css @@ -0,0 +1,109 @@ +#partial-correlations-form { + width: 100%; + display: grid; + grid-column-gap: 1em; +} + +#main-form { + grid-column-start: 1; + grid-column-end: 2; + text-align: left; +} + +#form-display-area { + grid-column-start: 2; + grid-column-end: 3; +} + +#part-corr-success { + grid-column-start: 1; + grid-column-end: 3; +} + +td, th { + border: 1px solid; + text-align: left; + padding: 0.2em 0.5em 0.2em 0.7em; +} + +tr:nth-of-type(2n) { + background: #F9F9F9; +} + +.with-trait { + margin-left: 0.7em; + position: relative; + display: grid; + width: 100%; + grid-column-gap: 1em; + grid-template-columns: 1em 1fr; + text-align: left; +} + +.with-trait:nth-of-type(2n) { + background: #E5E5FF; +} + +.with-trait .selector-element { + grid-column: 1 / 2; + grid-row: 1 / 1; +} + +.with-trait:first-of-type { + padding-top: 2.5em; +} + +.with-trait:first-of-type label *:before{ + position: absolute; + top: 0px; + + text-transform: capitalize; + font-weight: bolder; + content: attr(data-title); + background: #336699; /*#FFCCCC;*/ + color: #FFFFFF; + padding: 0.5em; +} + +.with-trait .label-element { + display: grid; + grid-column-gap: 0.5em; + grid-template-columns: 4fr 2fr 2fr 9fr 2fr 1fr 2fr; + grid-column: 2 / 2; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-dataset { + grid-column: 1; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-name { + grid-column: 2; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-symbol { + grid-column: 3; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-description { + grid-column: 4; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-location { + grid-column: 5; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-mean-expr { + grid-column: 6; + grid-row: 1 / 1; +} + +.with-trait .label-element .trait-max-lrs { + grid-column: 7; + grid-row: 1 / 1; +} diff --git a/gn2/wqflask/static/new/css/prob_plot.css b/gn2/wqflask/static/new/css/prob_plot.css new file mode 100644 index 00000000..2a1f8f53 --- /dev/null +++ b/gn2/wqflask/static/new/css/prob_plot.css @@ -0,0 +1,3 @@ +#prob_plot_title { + text-align: center; +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/scatter-matrix.css b/gn2/wqflask/static/new/css/scatter-matrix.css new file mode 100644 index 00000000..58150b26 --- /dev/null +++ b/gn2/wqflask/static/new/css/scatter-matrix.css @@ -0,0 +1,40 @@ +#scatter-matrix { font-size: 14px; } + +#scatter-matrix .axis { shape-rendering: crispEdges; } +#scatter-matrix .axis line { stroke: #ddd; stroke-width: 1px; } +#scatter-matrix .axis path { display: none; } +#scatter-matrix .axis text { font-size: 0.8em; } + +rect.extent { fill: #000; fill-opacity: .125; stroke: #fff; } +rect.frame { fill: #fff; fill-opacity: .7; stroke: #aaa; } + +circle { fill: #ccc; fill-opacity: .5; } + +.legend circle { fill-opacity: 1; } +.legend text { font-size: 18px; font-style: oblique; } + +.cell text { pointer-events: none; } + +.color-0 { fill: #800; } +.color-1 { fill: #080; } +.color-2 { fill: #008; } +.color-3 { fill: #440; } +.color-4 { fill: #044; } +.color-5 { fill: #404; } +.color-6 { fill: #400; } +.color-7 { fill: #040; } +.color-8 { fill: #004; } +.color-9 { fill: #cc0; } +.color-10 { fill: #0cc; } +.color-11 { fill: #c0c; } +.color-12 { fill: #880; } +.color-13 { fill: #088; } +.color-14 { fill: #808; } +.color-15 { fill: #c00; } +.color-16 { fill: #0c0; } +.color-17 { fill: #00c; } + +.scatter-matrix-filter-control ul { list-style: none; padding-left: 10px; } +.scatter-matrix-variable-control ul { list-style: none; padding-left: 10px; } +.scatter-matrix-drill-control ul { list-style: none; padding-left: 10px; } + diff --git a/gn2/wqflask/static/new/css/show_trait.css b/gn2/wqflask/static/new/css/show_trait.css new file mode 100644 index 00000000..577bb5dd --- /dev/null +++ b/gn2/wqflask/static/new/css/show_trait.css @@ -0,0 +1,311 @@ +tr .outlier { + background-color: #ffff99; +} + +table.dataTable tbody tr.selected { + background-color: #ffee99; +} + +table.metadata { + table-layout: fixed; +} + +table.metadata td:nth-child(1) { + width: 10%; +} + +table summary b { + cursor: pointer; + text-decoration: underline; +} + +table details[open] { + width: 80%; +} + +#bar_chart_container { + overflow-x:scroll; +} + +div.sample_group { + overflow: auto; # needed because it contains float dataTable wrapper +} + +.js-plotly-plot .plotly .modebar { + left: 100px; +} + +table.dataTable thead th, table.dataTable tfoot th{ + border-right: 1px solid white; + color: white; + background-color: #369; +} + +table.dataTable thead .sorting_asc { + background-image: url("/js/DataTables/images/sort_asc_disabled.png"); +} +table.dataTable thead .sorting_desc { + background-image: url("/js/DataTables/images/sort_desc_disabled.png"); +} + +table.dataTable thead th, table.dataTable tfoot { + padding: 4px 18px 4px 10px; +} + +/* Header for a column with a numeric value that should be right-aligned */ +table.dataTable thead th div.numeric_header { + text-align: right; +} + +table.dataTable tbody td { + padding: 2px 15px 0px 10px; +} + +table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { + border-top: 1px solid #ccc; + border-right: 1px solid #ccc; +} +table.dataTable.cell-border tbody tr th:first-child, +table.dataTable.cell-border tbody tr td:first-child { + border-left: 1px solid #ccc; +} + +.checkbox { + min-height: 20px; +} + +.trait_value_input { + text-align: right; +} + +.glyphicon { + position: relative; + top: 2px; +} + +table.dataTable tbody td.column_name-Checkbox { + padding: 1px 0px 0px 9px; /* The left padding here is because text-align:center does not seem to be working properly. No idea why this is. */ + text-align: center; + vertical-align: middle; +} + +table.dataTable tbody td.column_name-Index { + padding: 2px 4px 0px 2px; + text-align: right; +} + +/* the column with +/- in it that appears in the table when there's an SE column */ +table.dataTable tbody td.column_name-PlusMinus { + padding-left: 2px; + padding-right: 2px; + text-align: center; +} + +table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name-SE, table.dataTable tbody td.column_name-num_cases { + text-align: right; +} + +div.btn-toolbar { + margin-bottom:15px; +} + +/* div containing the form options for each segment of the trait page - correlations, statistics, mapping, etc */ +div.section-form-div { + padding: 20px; +} + +table.left-float { + float: left; +} + +div.scatterplot-btn-div { + margin-bottom:40px; +} + +.min-expr-field { + width: 70px; +} + +div.p-range-slider { + width: 200px; + margin-left: 15px; +} + +span.p-range-lower { + margin-top: 5px; + font: 400 12px Arial; + color: #888; + display: inline-block; +} + +span.p-range-upper { + font: 400 12px Arial; + color: #888; + display: inline-block; + margin: 5px 0px 0px 170px; +} + +input.corr-location { + width: 50px; + display: inline; +} + +div.block-div { + margin-bottom: 10px; +} + +div.block-div-2 { + margin-top:10px; + margin-bottom:10px; +} + +div.normalize-div { + margin-top:10px; +} + +div.main { + display: block; +} + +div.options { + float: left; + width: 600px; + padding-top: 0px; +} + +div.descriptions { + float: left; + width: 500px; + min-width: 20%; + margin-bottom: 0px; + padding-left: 15px; +} + +div.covar-options { + padding-top: 7px; +} + +.control-label { + text-align: right; +} + +.chr-select, .maf-select, .scale-select, .reaper-ver-select { + width: 80px; +} + +span.covar-text { + font-size: 13px; + font-weight: 400; +} + +div.select-covar-div { + margin-bottom: 10px; +} + +.select-covar-button { + width: 80px; + padding-right: 10px; +} + +.selected-covariates { + overflow-y: scroll; + resize: none; + width: 400px; +} + +.cofactor-input { + width: 160px; + display: inline-block; +} + +.no-control-radio { + margin-left: 10px; +} + +.map-method-text { + margin-top: 20px; +} + +.rqtl-description { + padding-top: 40px; + display: none; +} + +div.sample-table-container { + padding-bottom: 10px; +} + +div.sample-table-search-container { + display: inline; + height: 40px; +} + +input.sample-table-search { + width: 200px; + display: inline; + float: left; + vertical-align: top; +} + +div.sample-table-export-container { + padding-left: 10px; + display: inline; +} + +div.export-code-container { + padding-top: 20px; + width: 600px; + display: none; +} + +.export-code-field { + padding-top: 0px; + padding-bottom: 0px; + height: 150px; +} + +table.sample-table { + float: left; +} + +input.trait-value-input { + text-align: right; +} + +div.inline-div { + display: inline; +} + +/* div.colorbox_border { + border: 1px solid grey; +} */ +div#cboxContent { + /* box-shadow: + 0 2.8px 2.2px rgba(0, 0, 0, 0.034), + 0 6.7px 5.3px rgba(0, 0, 0, 0.048), + 0 12.5px 10px rgba(0, 0, 0, 0.06), + 0 22.3px 17.9px rgba(0, 0, 0, 0.072), + 0 41.8px 33.4px rgba(0, 0, 0, 0.086), + 0 100px 80px rgba(0, 0, 0, 0.12) */ + + padding: 10px 10px 5px 10px; + + -moz-box-shadow: 3px 3px 5px #535353; + -webkit-box-shadow: 3px 3px 5px #535353; + box-shadow: 3px 3px 5px #535353; + + -moz-border-radius: 6px 6px 6px 6px; + -webkit-border-radius: 6px; + border-radius: 6px 6px 6px 6px; + + /* border: 2px solid grey; */ +} + +#cboxClose { + margin-right: 5px; + margin-bottom: 2px; +} + +div.container { + min-width:750px; +} diff --git a/gn2/wqflask/static/new/css/snp_browser.css b/gn2/wqflask/static/new/css/snp_browser.css new file mode 100644 index 00000000..a7942d2a --- /dev/null +++ b/gn2/wqflask/static/new/css/snp_browser.css @@ -0,0 +1,58 @@ +.form_group { + margin-bottom 5px; +} + +table.dataTable thead th { + vertical-align: bottom; +} + +table.dataTable tbody tr.selected { + background-color: #ffee99; +} + +table.dataTable thead .sorting, +table.dataTable thead .sorting_asc, +table.dataTable thead .sorting_desc, +table.dataTable thead .sorting_asc_disabled, +table.dataTable thead .sorting_desc_disabled { + background-repeat: no-repeat; + background-position: bottom right; +} + +table.dataTable thead th{ + border-right: 1px solid white; + color: white; + background-color: #369; +} + +table.dataTable tbody td { + padding: 4px 20px 2px 10px; +} + +td.A_allele_color { + background-color: #C33232 +} +td.C_allele_color { + background-color: #1569C7 +} +td.T_allele_color { + background-color: #CFCF32 +} +td.G_allele_color { + background-color: #32C332 +} +td.t_allele_color { + background-color: #FF6 +} +td.c_allele_color { + background-color: #5CB3FF +} +td.a_allele_color { + background-color: #F66 +} +td.g_allele_color { + background-color: #CF9 +} +td.default_allele_color { + background-color: #FFFFFF +}
\ No newline at end of file diff --git a/gn2/wqflask/static/new/css/trait_list.css b/gn2/wqflask/static/new/css/trait_list.css new file mode 100644 index 00000000..cc5a9eac --- /dev/null +++ b/gn2/wqflask/static/new/css/trait_list.css @@ -0,0 +1,53 @@ +div.tool-button-container { + min-width: 1050px; +} + +div.collection-table-options { + min-width: 1100px; +} + +div.show-hide-container { + margin-bottom: 5px; + margin-top: 10px; +} + +button.active { + background: #BEBEBE; + -webkit-box-shadow: inset 0px 0px 5px #c1c1c1; + -moz-box-shadow: inset 0px 0px 5px #c1c1c1; + box-shadow: inset 0px 0px 5px #c1c1c1; + outline: none; +} + +div.dts { + display:block !important +} + +div.dts div.dts_loading { + z-index:1 +} + +div.dts div.dts_label { + position:absolute; + right:10px; + background:rgba(0,0,0,0.8); + color:white; + box-shadow:3px 3px 10px rgba(0,0,0,0.5); + text-align:right; + border-radius:3px; + padding:0.4em; + z-index:2; + display:none +} + +div.dts div.dataTables_scrollBody { + background:repeating-linear-gradient(45deg, #edeeff, #edeeff 10px, #fff 10px, #fff 20px) +} + +div.dts div.dataTables_scrollBody table { + z-index:2 +} + +div.dts div.dataTables_paginate,div.dts div.dataTables_length{ + display:none +} diff --git a/gn2/wqflask/static/new/css/typeahead-bootstrap.css b/gn2/wqflask/static/new/css/typeahead-bootstrap.css new file mode 100644 index 00000000..87dd4b5d --- /dev/null +++ b/gn2/wqflask/static/new/css/typeahead-bootstrap.css @@ -0,0 +1,94 @@ +span.twitter-typeahead .tt-menu, +span.twitter-typeahead .tt-dropdown-menu { + cursor: pointer; + position: absolute; + top: 100%; + left: 0; + z-index: 1000; + display: none; + float: left; + min-width: 160px; + padding: 5px 0; + margin: 2px 0 0; + list-style: none; + font-size: 14px; + text-align: left; + background-color: #ffffff; + border: 1px solid #cccccc; + border: 1px solid rgba(0, 0, 0, 0.15); + border-radius: 4px; + -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); + box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); + background-clip: padding-box; +} +span.twitter-typeahead .tt-suggestion { + display: block; + padding: 3px 20px; + clear: both; + font-weight: normal; + line-height: 1.42857143; + color: #333333; + white-space: nowrap; +} +span.twitter-typeahead .tt-suggestion.tt-cursor, +span.twitter-typeahead .tt-suggestion:hover, +span.twitter-typeahead .tt-suggestion:focus { + color: #ffffff; + text-decoration: none; + outline: 0; + background-color: #337ab7; +} +.input-group.input-group-lg span.twitter-typeahead .form-control { + height: 46px; + padding: 10px 16px; + font-size: 18px; + line-height: 1.3333333; + border-radius: 6px; +} +.input-group.input-group-sm span.twitter-typeahead .form-control { + height: 30px; + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} +span.twitter-typeahead { + width: 100%; +} +.input-group span.twitter-typeahead { + display: block !important; + height: 34px; +} +.input-group span.twitter-typeahead .tt-menu, +.input-group span.twitter-typeahead .tt-dropdown-menu { + top: 32px !important; +} +.input-group span.twitter-typeahead:not(:first-child):not(:last-child) .form-control { + border-radius: 0; +} +.input-group span.twitter-typeahead:first-child .form-control { + border-top-left-radius: 4px; + border-bottom-left-radius: 4px; + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} +.input-group span.twitter-typeahead:last-child .form-control { + border-top-left-radius: 0; + border-bottom-left-radius: 0; + border-top-right-radius: 4px; + border-bottom-right-radius: 4px; +} +.input-group.input-group-sm span.twitter-typeahead { + height: 30px; +} +.input-group.input-group-sm span.twitter-typeahead .tt-menu, +.input-group.input-group-sm span.twitter-typeahead .tt-dropdown-menu { + top: 30px !important; +} +.input-group.input-group-lg span.twitter-typeahead { + height: 46px; +} +.input-group.input-group-lg span.twitter-typeahead .tt-menu, +.input-group.input-group-lg span.twitter-typeahead .tt-dropdown-menu { + top: 46px !important; +}
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+ this.name = "InvalidCSSIDSelector"; + } +} + +class InvalidDataAttributeName extends Error { + constructor(message) { + super(message); + this.name = "InvalidDataAttributeName"; + } +} + +/** + * CSSIDSelector: A CSS ID Selector + * @param {String} A CSS selector of the form '#...' + */ +class CSSIDSelector { + constructor(selector) { + if(!selector.startsWith("#")) { + throw new InvalidCSSIDSelector( + "Expected the CSS selector to begin with a `#` character."); + } + let id_str = selector.slice(1, selector.length); + if(document.getElementById(id_str) == null) { + throw new InvalidCSSIDSelector( + "Element with ID '" + id_str + "' does not exist."); + } + this.selector = selector; + } +} + +/** + * TableDataSource: A type to represent a table's data source + * @param {String} A CSS selector for an ID + * @param {String} A `data-*` attribute name + */ +class TableDataSource { + constructor(table_id, data_attribute_name, checkbox_creation_function) { + this.table_id = new CSSIDSelector(table_id); + let data = document.querySelector( + table_id).getAttribute(data_attribute_name); + if(data == null) { + throw new InvalidDataAttributeName( + "data-* attribute '" + data_attribute_name + "' does not exist " + + "for table with ID '" + table_id.slice(1, table_id.length) + + "'."); + } else { + this.data_attribute_name = data_attribute_name; + } + this.checkbox_creation_function = checkbox_creation_function; + } +} + +/** + * Render the table + * @param {String} The selector for the table's ID + * @param {String} The name of the data-* attribute holding the table's data + * @param {Function} The function to call to generate the appropriate checkbox + */ +function render_table(table_data_source) { + table_id = table_data_source.table_id.selector; + data_attr_name = table_data_source.data_attribute_name; + $(table_id + " tbody tr").remove(); + table_data = JSON.parse($(table_id).attr(data_attr_name)).sort((d1, d2) => { + return (d1.dataset_name > d2.dataset_name ? 1 : ( + d1.dataset_name < d2.dataset_name ? -1 : 0)) + }); + if(table_data.length < 1) { + row = $("<tr>") + cell = $('<td colspan="100%" align="center">'); + cell.append( + $('<span class="glyphicon glyphicon-info-sign text-info">')); + cell.append(" "); + cell.append("No genotype datasets remaining."); + row.append(cell); + $(table_id + " tbody").append(row); + } + table_data.forEach(function(dataset) { + row = $("<tr>") + row.append(table_data_source.checkbox_creation_function(dataset)); + row.append(table_cell(dataset.InbredSetName)); + row.append(table_cell(dataset.dataset_name)); + row.append(table_cell(dataset.dataset_fullname)); + row.append(table_cell(dataset.dataset_shortname)); + $(table_id + " tbody").append(row); + }); +} + +function in_array(items, filter_fn) { + return items.filter(filter_fn).length > 0; +} + +function remove_from_table_data(dataset, table_data_source, filter_fn) { + let table_id = table_data_source.table_id.selector; + let data_attr_name = table_data_source.data_attribute_name; + without_dataset = JSON.parse($(table_id).attr(data_attr_name)).filter( + filter_fn); + $(table_id).attr(data_attr_name, JSON.stringify(without_dataset)); +} + +function add_to_table_data(dataset, table_data_source, filter_fn) { + let table_id = table_data_source.table_id.selector; + let data_attr_name = table_data_source.data_attribute_name; + table_data = JSON.parse($(table_id).attr(data_attr_name)); + if(!in_array(table_data, filter_fn)) { + table_data.push(dataset); + } + $(table_id).attr(data_attr_name, JSON.stringify(Array.from(table_data))); +} + +/** + * Switch the dataset/trait from search table to selection table and vice versa + * @param {Object} A dataset/trait object + * @param {TableDataSource} The source table for the dataset/trait + * @param {TableDataSource} The destination table for the dataset/trait + */ +function select_deselect(item, source, destination, filter_fn, render_fn=render_table) { + dest_selector = destination.table_id.selector + dest_data = JSON.parse( + $(dest_selector).attr(destination.data_attribute_name)); + add_to_table_data(item, destination, filter_fn); // Add to destination table + remove_from_table_data(item, source, (arg) => {return !filter_fn(arg)}); // Remove from source table + /***** BEGIN: Re-render tables *****/ + render_fn(destination); + render_fn(source); + /***** END: Re-render tables *****/ +} + +function debounce(func, delay=500) { + var timeout; + return function search(event) { + clearTimeout(timeout); + timeout = setTimeout(func, delay); + }; +} + +/** + * Build a checkbox + * @param {Dataset Object} A JSON.stringify-able object + * @param {String} The name to assign the checkbox + */ +function build_checkbox(data_object, checkbox_name, checkbox_aux_classes="", checked=false) { + cell = $("<td>"); + check = $( + '<input type="checkbox" class="checkbox" ' + + 'name="' + checkbox_name + '">'); + check.val(JSON.stringify(data_object)); + check.prop("checked", checked); + auxilliary_classes = checkbox_aux_classes.trim(); + if(Boolean(auxilliary_classes)) { + check.attr("class", + check.attr("class") + " " + auxilliary_classes.trim()); + } + cell.append(check); + return cell; +} + +function link_checkbox(dataset) { + return build_checkbox(dataset, "selected", "checkbox-selected", true); +} + +function search_checkbox(dataset) { + return build_checkbox(dataset, "search_datasets", "checkbox-search"); +} + +function table_cell(value) { + cell = $("<td>"); + cell.html(value); + return cell; +} diff --git a/gn2/wqflask/static/new/javascript/auth/search_genotypes.js b/gn2/wqflask/static/new/javascript/auth/search_genotypes.js new file mode 100644 index 00000000..d1b8ed9e --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search_genotypes.js @@ -0,0 +1,95 @@ +function toggle_link_button() { + num_groups = $("#frm-link-genotypes select option").length - 1; + num_selected = JSON.parse( + $("#tbl-link-genotypes").attr("data-selected-datasets")).length; + if(num_groups > 0 && num_selected > 0) { + $("#frm-link-genotypes input[type='submit']").prop("disabled", false); + } else { + $("#frm-link-genotypes input[type='submit']").prop("disabled", true); + } +} + +function search_genotypes() { + query = document.getElementById("txt-query").value; + selected = JSON.parse(document.getElementById( + "tbl-link-genotypes").getAttribute("data-selected-datasets")); + species_name = document.getElementById("txt-species-name").value + search_endpoint = "/auth/data/genotype/search" + search_table = new TableDataSource( + "#tbl-genotypes", "data-datasets", search_checkbox); + $.ajax( + search_endpoint, + { + "method": "POST", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "data": JSON.stringify({ + "query": query, + "selected": selected, + "dataset_type": "genotype", + "species_name": species_name}), + "error": function(jqXHR, textStatus, errorThrown) { + data = jqXHR.responseJSON + elt = document.getElementById("search-error").setAttribute( + "style", "display: block;"); + document.getElementById("search-error-text").innerHTML = ( + data.error + " (" + data.status_code + "): " + + data.error_description); + document.getElementById("tbl-genotypes").setAttribute( + "data-datasets", JSON.stringify([])); + render_table(search_table); + }, + "success": function(data, textStatus, jqXHR) { + document.getElementById("search-error").setAttribute( + "style", "display: none;"); + document.getElementById("tbl-genotypes").setAttribute( + "data-datasets", JSON.stringify(data)); + render_table(search_table); + } + }); +} + +/** + * Return function to check whether `dataset` is in array of `datasets`. + * @param {GenotypeDataset} A genotype dataset. + * @param {Array} An array of genotype datasets. + */ +function make_filter(trait) { + return (dst) => { + return (dst.SpeciesId == dataset.SpeciesId && + dst.InbredSetId == dataset.InbredSetId && + dst.GenoFreezeId == dataset.GenoFreezeId); + }; +} + +$(document).ready(function() { + let search_table = new TableDataSource( + "#tbl-genotypes", "data-datasets", search_checkbox); + let link_table = new TableDataSource( + "#tbl-link-genotypes", "data-selected-datasets", link_checkbox); + + $("#frm-search-traits").submit(function(event) { + event.preventDefault(); + return false; + }); + + $("#txt-query").keyup(debounce(search_genotypes)); + + $("#tbl-genotypes").on("change", ".checkbox-search", function(event) { + if(this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, search_table, link_table, make_filter(dataset)); + toggle_link_button(); + } + }); + + $("#tbl-link-genotypes").on("change", ".checkbox-selected", function(event) { + if(!this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, link_table, search_table, make_filter(dataset)); + toggle_link_button(); + } + }); +}); diff --git a/gn2/wqflask/static/new/javascript/auth/search_mrna.js b/gn2/wqflask/static/new/javascript/auth/search_mrna.js new file mode 100644 index 00000000..3eca4ed2 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search_mrna.js @@ -0,0 +1,97 @@ +function toggle_link_button() { + num_groups = $("#frm-link select option").length - 1; + num_selected = JSON.parse( + $("#tbl-link").attr("data-datasets")).length; + if(num_groups > 0 && num_selected > 0) { + $("#frm-link input[type='submit']").prop("disabled", false); + } else { + $("#frm-link input[type='submit']").prop("disabled", true); + } +} + +function search_mrna() { + query = document.getElementById("txt-query").value; + selected = JSON.parse(document.getElementById( + "tbl-link").getAttribute("data-datasets")); + species_name = document.getElementById("txt-species-name").value + search_endpoint = "/auth/data/mrna/search" + search_table = new TableDataSource( + "#tbl-search", "data-datasets", search_checkbox); + $.ajax( + search_endpoint, + { + "method": "POST", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "data": JSON.stringify({ + "query": query, + "selected": selected, + "dataset_type": "mrna", + "species_name": species_name}), + "error": function(jqXHR, textStatus, errorThrown) { + error_data = jqXHR.responseJSON + console.debug("ERROR_DATA:", error_data); + elt = document.getElementById("search-error").setAttribute( + "style", "display: block;"); + document.getElementById("search-error-text").innerHTML = ( + error_data.error + " (" + error_data.status_code + "): " + + error_data.error_description); + document.getElementById("tbl-search").setAttribute( + "data-datasets", JSON.stringify([])); + render_table(search_table); + }, + "success": function(data, textStatus, jqXHR) { + document.getElementById("search-error").setAttribute( + "style", "display: none;"); + document.getElementById("tbl-search").setAttribute( + "data-datasets", JSON.stringify(data)); + render_table(search_table); + } + }); +} + +/** + * Make function to check whether `dataset` is in array of `datasets`. + * @param {mRNADataset} A mrna dataset. + * @param {Array} An array of mrna datasets. + */ +function make_filter(dataset) { + return (dst) => { + return (dst.SpeciesId == dataset.SpeciesId && + dst.InbredSetId == dataset.InbredSetId && + dst.ProbeFreezeId == dataset.ProbeFreezeId && + dst.ProbeSetFreezeId == dataset.ProbeSetFreezeId); + }; +} + +$(document).ready(function() { + let search_table = new TableDataSource( + "#tbl-search", "data-datasets", search_checkbox); + let link_table = new TableDataSource( + "#tbl-link", "data-datasets", link_checkbox); + + $("#frm-search").submit(function(event) { + event.preventDefault(); + return false; + }); + + $("#txt-query").keyup(debounce(search_mrna)); + + $("#tbl-search").on("change", ".checkbox-search", function(event) { + if(this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, search_table, link_table, make_filter(dataset)); + toggle_link_button(); + } + }); + + $("#tbl-link").on("change", ".checkbox-selected", function(event) { + if(!this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, link_table, search_table, make_filter(dataset)); + toggle_link_button(); + } + }); +}); diff --git a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js new file mode 100644 index 00000000..99ecb16e --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js @@ -0,0 +1,188 @@ +/** + * Global variables: Bad idea - figure out how to pass them down a call stack. + */ +search_table = new TableDataSource( + "#tbl-phenotypes", "data-traits", (trait) => { + return build_checkbox(trait, "search_traits", "checkbox-search"); + }); +link_table = new TableDataSource( + "#tbl-link-phenotypes", "data-traits", (trait) => { + return build_checkbox( + trait, "selected", "checkbox-selected", checked=true); + }); + +/** + * Toggle the state for the "Link Traits" button + */ +function toggle_link_button() { + num_groups = $("#frm-link-phenotypes select option").length - 1; + num_selected = JSON.parse( + $("#tbl-link-phenotypes").attr("data-traits")).length; + if(num_groups > 0 && num_selected > 0) { + $("#frm-link-phenotypes input[type='submit']").prop("disabled", false); + } else { + $("#frm-link-phenotypes input[type='submit']").prop("disabled", true); + } +} + +/** + * Default error function: print out debug messages + */ +function default_error_fn(jqXHR, textStatus, errorThrown) { + console.debug("XHR:", jqXHR); + console.debug("STATUS:", textStatus); + console.debug("ERROR:", errorThrown); +} + +/** + * Render the table(s) for the phenotype traits + * @param {TableDataSource} The table to render + */ +function render_pheno_table(table_data_source) { + table_id = table_data_source.table_id.selector; + data_attr_name = table_data_source.data_attribute_name; + $(table_id + " tbody tr").remove(); + table_data = JSON.parse($(table_id).attr(data_attr_name)).sort((t1, t2) => { + return (t1.name > t2.name ? 1 : (t1.name < t2.name ? -1 : 0)) + }); + if(table_data.length < 1) { + row = $("<tr>") + cell = $('<td colspan="100%" align="center">'); + cell.append( + $('<span class="glyphicon glyphicon-info-sign text-info">')); + cell.append(" "); + cell.append("No phenotype traits to select from."); + row.append(cell); + $(table_id + " tbody").append(row); + } + table_data.forEach(function(trait) { + row = $("<tr>") + row.append(table_data_source.checkbox_creation_function(trait)); + row.append(table_cell(trait.name)); + row.append(table_cell(trait.group)); + row.append(table_cell(trait.dataset)); + row.append(table_cell(trait.dataset_fullname)); + row.append(table_cell(trait.description)); + row.append(table_cell(trait.authors.join(", "))); + row.append(table_cell( + '<a href="' + trait.pubmed_link + + '" title="Pubmed link for trait ' + trait.name + '.">' + + trait.year + "</a>")); + row.append(table_cell("Chr:" + trait.geno_chr + "@" + trait.geno_mb)); + row.append(table_cell(trait.lrs)); + row.append(table_cell(trait.additive)); + $(table_id + " tbody").append(row); + }); +} + +function display_search_results(data, textStatus, jqXHR) { + if(data.status == "queued" || data.status == "started") { + setTimeout(() => { + fetch_search_results(data.job_id, display_search_results); + }, 250); + return; + } + if(data.status == "completed") { + $("#tbl-phenotypes").attr( + "data-traits", JSON.stringify(data.search_results)); + // Remove this reference to global variable + render_pheno_table(search_table); + } + $("#txt-search").prop("disabled", false); +} + +/** + * Fetch the search results + * @param {UUID}: The job id to fetch data for + */ +function fetch_search_results(job_id, success, error=default_error_fn) { + host = $("#frm-search-traits").attr("data-gn-server-url"); + endpoint = host + "auth/data/search/phenotype/" + job_id + $("#txt-search").prop("disabled", true); + $.ajax( + endpoint, + { + "method": "GET", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "error": error, + "success": success + } + ); +} + +function search_phenotypes() { + query = document.getElementById("txt-query").value; + selected = JSON.parse(document.getElementById( + "tbl-link-phenotypes").getAttribute("data-traits")); + species_name = document.getElementById("txt-species-name").value + per_page = document.getElementById("txt-per-page").value + search_table = new TableDataSource( + "#tbl-phenotypes", "data-traits", search_checkbox); + endpoint = "/auth/data/phenotype/search" + $.ajax( + endpoint, + { + "method": "POST", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "data": JSON.stringify({ + "query": query, + "species_name": species_name, + "dataset_type": "phenotype", + "per_page": per_page, + "selected_traits": selected + }), + "error": default_error_fn, + "success": (data, textStatus, jqXHR) => { + fetch_search_results(data.job_id, display_search_results); + } + }); +} + +/** + * Return a function to check whether `trait` is in array of `traits`. + * @param {PhenotypeTrait} A phenotype trait. + * @param {Array} An array of phenotype traits. + */ +function make_filter(trait) { + return (trt) => { + return (trt.species == trait.species && + trt.group == trait.group && + trt.dataset == trait.dataset && + trt.name == trait.name); + }; +} + +$(document).ready(function() { + $("#frm-search-traits").submit(event => { + event.preventDefault(); + return false; + }); + + $("#txt-query").keyup(debounce(search_phenotypes)); + + $("#tbl-link-phenotypes").on("change", ".checkbox-selected", function(event) { + if(!this.checked) { + trait = JSON.parse(this.value); + select_deselect(trait, link_table, search_table, + make_filter(trait), render_pheno_table); + toggle_link_button(); + } + }); + + $("#tbl-phenotypes").on("change", ".checkbox-search", function(event) { + if(this.checked) { + trait = JSON.parse(this.value) + select_deselect(trait, search_table, link_table, + make_filter(trait), render_pheno_table); + toggle_link_button(); + } + }); + + setTimeout(() => { + fetch_search_results( + $("#tbl-phenotypes").attr("data-initial-job-id"), + display_search_results); + }, 500); +}); diff --git a/gn2/wqflask/static/new/javascript/auto_hide_column.js b/gn2/wqflask/static/new/javascript/auto_hide_column.js new file mode 100644 index 00000000..1a4dc039 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auto_hide_column.js @@ -0,0 +1,21 @@ + function filterDatatable(datatable){ + let invalidColumns=[] + let columnCount=datatable.columns().header().length; + let numberOfRows=datatable.rows().count(); + for (let col=0; col<columnCount; col++){ + colObj = datatable.column(col).nodes().to$(); + allNAs = true; + for (let i=0;i<numberOfRows;i++){ + cellContent = colObj[i].childNodes[0].data + if (cellContent != "N/A" && cellContent != ""){ + allNAs = false; + break; + } + } + if (allNAs){ + invalidColumns.push(col) + } + } + return datatable.columns(invalidColumns).visible(false); + + }
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/bar_chart.js b/gn2/wqflask/static/new/javascript/bar_chart.js new file mode 100644 index 00000000..d8540580 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/bar_chart.js @@ -0,0 +1,498 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var Bar_Chart, root, + bind = function(fn, me){ return function(){ return fn.apply(me, arguments); }; }, + indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }, + hasProp = {}.hasOwnProperty; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + Bar_Chart = (function() { + function Bar_Chart(sample_lists) { + this.add_legend_discrete = bind(this.add_legend_discrete, this); + this.add_legend_continuous = bind(this.add_legend_continuous, this); + this.remove_legend = bind(this.remove_legend, this); + this.add_legend = bind(this.add_legend, this); + var key, l1, l1_names, l2, l3, longest_sample_name_len, s, sample, x; + this.sample_lists = {}; + l1 = this.sample_lists['samples_primary'] = sample_lists[0] || []; + l2 = this.sample_lists['samples_other'] = sample_lists[1] || []; + l1_names = (function() { + var j, len, results; + results = []; + for (j = 0, len = l1.length; j < len; j++) { + x = l1[j]; + results.push(x.name); + } + return results; + })(); + l3 = l1.concat((function() { + var j, len, ref, results; + results = []; + for (j = 0, len = l2.length; j < len; j++) { + x = l2[j]; + if (ref = x.name, indexOf.call(l1_names, ref) < 0) { + results.push(x); + } + } + return results; + })()); + this.sample_lists['samples_all'] = l3; + longest_sample_name_len = d3.max((function() { + var j, len, results; + results = []; + for (j = 0, len = l3.length; j < len; j++) { + sample = l3[j]; + results.push(sample.name.length); + } + return results; + })()); + this.margin = { + top: 20, + right: 20, + bottom: longest_sample_name_len * 6, + left: 40 + }; + this.attributes = (function() { + var results; + results = []; + for (key in sample_lists[0][0]["extra_attributes"]) { + results.push(key); + } + return results; + })(); + this.sample_attr_vals = (function() { + var j, len, ref, results; + ref = this.sample_lists['samples_all']; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + s = ref[j]; + if (s.value !== null) { + results.push(this.extra(s)); + } + } + return results; + }).call(this); + this.get_distinct_attr_vals(); + this.get_attr_color_dict(this.distinct_attr_vals); + this.attribute_name = "None"; + this.sort_by = "name"; + this.chart = null; + this.select_attribute_box = $("#color_attribute"); + d3.select("#color_attribute").on("change", (function(_this) { + return function() { + _this.attribute_name = _this.select_attribute_box.val(); + return _this.rebuild_bar_graph(); + }; + })(this)); + $(".sort_by_value").on("click", (function(_this) { + return function() { + console.log("sorting by value"); + _this.sort_by = "value"; + return _this.rebuild_bar_graph(); + }; + })(this)); + $(".sort_by_name").on("click", (function(_this) { + return function() { + console.log("sorting by name"); + _this.sort_by = "name"; + return _this.rebuild_bar_graph(); + }; + })(this)); + d3.select("#color_by_trait").on("click", (function(_this) { + return function() { + return _this.open_trait_selection(); + }; + })(this)); + } + + Bar_Chart.prototype.value = function(sample) { + return this.value_dict[sample.name].value; + }; + + Bar_Chart.prototype.variance = function(sample) { + return this.value_dict[sample.name].variance; + }; + + Bar_Chart.prototype.extra = function(sample) { + var attr_vals, attribute, j, len, ref; + attr_vals = {}; + ref = this.attributes; + for (j = 0, len = ref.length; j < len; j++) { + attribute = ref[j]; + attr_vals[attribute] = sample["extra_attributes"][attribute]; + } + return attr_vals; + }; + + Bar_Chart.prototype.redraw = function(samples_dict, selected_group) { + var x; + this.value_dict = samples_dict[selected_group]; + this.raw_data = (function() { + var j, len, ref, results; + ref = this.sample_lists[selected_group]; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + if (x.name in this.value_dict && this.value(x) !== null) { + results.push(x); + } + } + return results; + }).call(this); + return this.rebuild_bar_graph(); + }; + + Bar_Chart.prototype.rebuild_bar_graph = function() { + var container, h, raw_data; + raw_data = this.raw_data.slice(); + if (this.sort_by === 'value') { + raw_data = raw_data.sort((function(_this) { + return function(x, y) { + return _this.value(x) - _this.value(y); + }; + })(this)); + } + console.log("raw_data: ", raw_data); + h = 600; + container = $("#bar_chart_container"); + container.height(h + this.margin.top + this.margin.bottom); + if (this.chart === null) { + this.chart = nv.models.multiBarChart().height(h).errorBarColor((function(_this) { + return function() { + return 'red'; + }; + })(this)).reduceXTicks(false).staggerLabels(false).showControls(false).showLegend(false); + this.chart.multibar.dispatch.on('elementMouseover.tooltip', (function(_this) { + return function(evt) { + var k, ref, v; + evt.value = _this.chart.x()(evt.data); + evt['series'] = [ + { + key: 'Value', + value: evt.data.y, + color: evt.color + } + ]; + if (evt.data.yErr) { + evt['series'].push({ + key: 'SE', + value: evt.data.yErr + }); + } + if (evt.data.attr) { + ref = evt.data.attr; + for (k in ref) { + v = ref[k]; + evt['series'].push({ + key: k, + value: v + }); + } + } + return _this.chart.tooltip.data(evt).hidden(false); + }; + })(this)); + this.chart.tooltip.valueFormatter(function(d, i) { + return d; + }); + } + return nv.addGraph((function(_this) { + return function() { + var d, s, values; + _this.remove_legend(); + values = (function() { + var j, len, results; + results = []; + for (j = 0, len = raw_data.length; j < len; j++) { + s = raw_data[j]; + results.push({ + x: s.name, + y: this.value(s), + yErr: this.variance(s) || 0, + attr: s.extra_attributes + }); + } + return results; + }).call(_this); + if (_this.attribute_name !== "None") { + _this.color_dict = _this.attr_color_dict[_this.attribute_name]; + _this.chart.barColor(function(d) { + return _this.color_dict[d.attr[_this.attribute_name]]; + }); + _this.add_legend(); + } else if (typeof _this.trait_color_dict !== 'undefined') { + _this.color_dict = _this.trait_color_dict; + _this.chart.barColor(function(d) { + return _this.color_dict[d['x']]; + }); + } else { + _this.chart.barColor(function() { + return 'steelblue'; + }); + } + _this.chart.width(raw_data.length * 20); + //User should be able to change Y domain, but should still have good default + _this.chart.yDomain([ + 0.95 * _.min((function() { // ZS: Decreasing this constant decreases the min Y axis value + var j, len, results; + results = []; + for (j = 0, len = values.length; j < len; j++) { + d = values[j]; + results.push(d.y - 0.5 * d.yErr); //ZS: the 0.5 was originally 1.5 + } + return results; + })()), 1.05 * _.max((function() { // ZS: Decreasing this constant decreases the max Y axis value + var j, len, results; + results = []; + for (j = 0, len = values.length; j < len; j++) { + d = values[j]; + results.push(d.y + 0.5 * d.yErr); // //ZS: the 0.5 was originally 1.5 + } + return results; + })()) + ]); + console.log("values: ", values); + + decimal_exists = "False"; + for(i=0; i < values.length; i++){ + if (values[i]['y'] % 1 != 0){ + decimal_exists = "True"; + break; + } + } + if (decimal_exists == "False"){ + _this.chart.yAxis.tickFormat(d3.format('d')) + } + d3.select("#bar_chart_container svg").datum([ + { + values: values + } + ]).style('width', raw_data.length * 20 + 'px').transition().duration(1000).call(_this.chart); + d3.select("#bar_chart_container .nv-x").selectAll('.tick text').style("font-size", "12px").style("text-anchor", "end").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", function(d) { + return "rotate(-90)"; + }); + return _this.chart; + }; + })(this)); + }; + + Bar_Chart.prototype.get_attr_color_dict = function(vals) { + var color, color_range, discrete, distinct_vals, i, j, key, l, len, len1, results, this_color_dict, value; + this.attr_color_dict = {}; + this.is_discrete = {}; + this.minimum_values = {}; + this.maximum_values = {}; + console.log("vals:", vals); + results = []; + for (key in vals) { + if (!hasProp.call(vals, key)) continue; + distinct_vals = vals[key]; + this.min_val = d3.min(distinct_vals); + this.max_val = d3.max(distinct_vals); + this_color_dict = {}; + discrete = distinct_vals.length < 10; + if (discrete) { + color = d3.scale.category10(); + for (i = j = 0, len = distinct_vals.length; j < len; i = ++j) { + value = distinct_vals[i]; + this_color_dict[value] = color(i); + } + } else { + console.log("distinct_values:", distinct_vals); + if (_.every(distinct_vals, (function(_this) { + return function(d) { + if (isNaN(d)) { + return false; + } else { + return true; + } + }; + })(this))) { + color_range = d3.scale.linear().domain([this.min_val, this.max_val]).range([0, 255]); + for (i = l = 0, len1 = distinct_vals.length; l < len1; i = ++l) { + value = distinct_vals[i]; + console.log("color_range(value):", parseInt(color_range(value))); + this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0); + } + } + } + this.attr_color_dict[key] = this_color_dict; + this.is_discrete[key] = discrete; + this.minimum_values[key] = this.min_val; + results.push(this.maximum_values[key] = this.max_val); + } + return results; + }; + + Bar_Chart.prototype.get_distinct_attr_vals = function() { + var attribute, j, len, ref, results, sample; + this.distinct_attr_vals = {}; + ref = this.sample_attr_vals; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + sample = ref[j]; + results.push((function() { + var ref1, results1; + results1 = []; + for (attribute in sample) { + if (!this.distinct_attr_vals[attribute]) { + this.distinct_attr_vals[attribute] = []; + } + if (ref1 = sample[attribute], indexOf.call(this.distinct_attr_vals[attribute], ref1) < 0) { + results1.push(this.distinct_attr_vals[attribute].push(sample[attribute])); + } else { + results1.push(void 0); + } + } + return results1; + }).call(this)); + } + return results; + }; + + Bar_Chart.prototype.add_legend = function() { + if (this.is_discrete[this.attribute_name]) { + return this.add_legend_discrete(); + } else { + return this.add_legend_continuous(); + } + }; + + Bar_Chart.prototype.remove_legend = function() { + $(".legend").remove(); + return $("#legend-left,#legend-right,#legend-colors").empty(); + }; + + Bar_Chart.prototype.add_legend_continuous = function() { + var svg_html; + $('#legend-left').html(this.minimum_values[this.attribute_name]); + $('#legend-right').html(this.maximum_values[this.attribute_name]); + svg_html = '<svg height="15" width="120"> <rect x="0" width="20" height="15" style="fill: rgb(0, 0, 0);"></rect> <rect x="20" width="20" height="15" style="fill: rgb(50, 0, 0);"></rect> <rect x="40" width="20" height="15" style="fill: rgb(100, 0, 0);"></rect> <rect x="60" width="20" height="15" style="fill: rgb(150, 0, 0);"></rect> <rect x="80" width="20" height="15" style="fill: rgb(200, 0, 0);"></rect> <rect x="100" width="20" height="15" style="fill: rgb(255, 0, 0);"></rect> </svg>'; + console.log("svg_html:", svg_html); + return $('#legend-colors').html(svg_html); + }; + + Bar_Chart.prototype.add_legend_discrete = function() { + var legend_span; + legend_span = d3.select('#bar_chart_legend').append('div').style('word-wrap', 'break-word').attr('class', 'legend').selectAll('span').data(this.distinct_attr_vals[this.attribute_name]).enter().append('span').style({ + 'word-wrap': 'normal', + 'display': 'inline-block' + }); + legend_span.append('span').style("background-color", (function(_this) { + return function(d) { + return _this.attr_color_dict[_this.attribute_name][d]; + }; + })(this)).style({ + 'display': 'inline-block', + 'width': '15px', + 'height': '15px', + 'margin': '0px 5px 0px 15px' + }); + return legend_span.append('span').text((function(_this) { + return function(d) { + return d; + }; + })(this)).style('font-size', '20px'); + }; + + Bar_Chart.prototype.open_trait_selection = function() { + return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { + return function() { + $.colorbox({ + inline: true, + href: "#collections_holder" + }); + return $('a.collection_name').attr('onClick', 'return false'); + }; + })(this)); + }; + + Bar_Chart.prototype.color_by_trait = function(trait_sample_data) { + var distinct_values, trimmed_samples; + console.log("BXD1:", trait_sample_data["BXD1"]); + console.log("trait_sample_data:", trait_sample_data); + trimmed_samples = this.trim_values(trait_sample_data); + distinct_values = {}; + distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples); + this.trait_color_dict = this.get_trait_color_dict(trimmed_samples, distinct_values); + console.log("TRAIT_COLOR_DICT:", this.trait_color_dict); + return this.rebuild_bar_graph(); + //return console.log("SAMPLES:", this.samples); + }; + + Bar_Chart.prototype.trim_values = function(trait_sample_data) { + var j, len, ref, sample, trimmed_samples; + trimmed_samples = {}; + ref = this.sample_lists['samples_all']; + for (j = 0, len = ref.length; j < len; j++) { + sample = ref[j]['name']; + if (sample in trait_sample_data) { + trimmed_samples[sample] = trait_sample_data[sample]; + } + } + console.log("trimmed_samples:", trimmed_samples); + return trimmed_samples; + }; + + Bar_Chart.prototype.get_distinct_values = function(samples) { + var distinct_values; + distinct_values = _.uniq(_.values(samples)); + console.log("distinct_values:", distinct_values); + return distinct_values; + }; + + Bar_Chart.prototype.get_trait_color_dict = function(samples, vals) { + var color, color_range, distinct_vals, i, j, k, key, len, len1, results, sample, this_color_dict, value; + trait_color_dict = {}; + console.log("vals:", vals); + for (key in vals) { + if (!hasProp.call(vals, key)) continue; + distinct_vals = vals[key]; + this_color_dict = {}; + this.min_val = d3.min(distinct_vals); + this.max_val = d3.max(distinct_vals); + if (distinct_vals.length < 10) { + color = d3.scale.category10(); + for (i = j = 0, len = distinct_vals.length; j < len; i = ++j) { + value = distinct_vals[i]; + this_color_dict[value] = color(i); + } + } else { + console.log("distinct_values:", distinct_vals); + if (_.every(distinct_vals, (function(_this) { + return function(d) { + if (isNaN(d)) { + return false; + } else { + return true; + } + }; + })(this))) { + color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]); + for (i = k = 0, len1 = distinct_vals.length; k < len1; i = ++k) { + value = distinct_vals[i]; + //console.log("color_range(value):", parseInt(color_range(value))); + this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0); + } + } + } + } + results = []; + console.log("SAMPLES:", samples) + for (sample in samples) { + if (!hasProp.call(samples, sample)) continue; + value = samples[sample]; + trait_color_dict[sample] = this_color_dict[value]; + //results.push(this.trait_color_dict[sample] = this_color_dict[value]); + } + return trait_color_dict; + }; + + return Bar_Chart; + + })(); + + root.Bar_Chart = Bar_Chart; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/box.js b/gn2/wqflask/static/new/javascript/box.js new file mode 100644 index 00000000..aae80f05 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/box.js @@ -0,0 +1,307 @@ +//Taken from http://bl.ocks.org/mbostock/4061502
+
+(function() {
+
+// Inspired by http://informationandvisualization.de/blog/box-plot
+d3.box = function() {
+ var width = 1,
+ height = 1,
+ duration = 0,
+ domain = null,
+ value = Number,
+ whiskers = boxWhiskers,
+ quartiles = boxQuartiles,
+ tickFormat = null;
+
+ // For each small multiple…
+ function box(g) {
+ g.each(function(d, i) {
+ console.log("d:", d)
+ console.log("domain:", domain)
+ d = d.map(value).sort(d3.ascending);
+ var g = d3.select(this),
+ n = d.length,
+ min = d[0],
+ max = d[n - 1];
+
+ // Compute quartiles. Must return exactly 3 elements.
+ var quartileData = d.quartiles = quartiles(d);
+
+ // Compute whiskers. Must return exactly 2 elements, or null.
+ var whiskerIndices = whiskers && whiskers.call(this, d, i),
+ whiskerData = whiskerIndices && whiskerIndices.map(function(i) { return d[i]; });
+
+ // Compute outliers. If no whiskers are specified, all data are "outliers".
+ // We compute the outliers as indices, so that we can join across transitions!
+ var outlierIndices = whiskerIndices
+ ? d3.range(0, whiskerIndices[0]).concat(d3.range(whiskerIndices[1] + 1, n))
+ : d3.range(n);
+
+ // Compute the new x-scale.
+ var x1 = d3.scale.linear()
+ .domain(domain && domain.call(this, d, i) || [min, max])
+ .range([height, 0]);
+
+ // Retrieve the old x-scale, if this is an update.
+ var x0 = this.__chart__ || d3.scale.linear()
+ .domain([0, Infinity])
+ .range(x1.range());
+
+ // Stash the new scale.
+ this.__chart__ = x1;
+
+ // Note: the box, median, and box tick elements are fixed in number,
+ // so we only have to handle enter and update. In contrast, the outliers
+ // and other elements are variable, so we need to exit them! Variable
+ // elements also fade in and out.
+
+ // Update center line: the vertical line spanning the whiskers.
+ var center = g.selectAll("line.center")
+ .data(whiskerData ? [whiskerData] : []);
+
+ center.enter().insert("line", "rect")
+ .attr("class", "center")
+ .attr("x1", width / 2)
+ .attr("y1", function(d) { return x0(d[0]); })
+ .attr("x2", width / 2)
+ .attr("y2", function(d) { return x0(d[1]); })
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .style("opacity", 1)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); });
+
+ center.transition()
+ .duration(duration)
+ .style("opacity", 1)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); });
+
+ center.exit().transition()
+ .duration(duration)
+ .style("opacity", 1e-6)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); })
+ .remove();
+
+ // Update innerquartile box.
+ var box = g.selectAll("rect.box")
+ .data([quartileData]);
+
+ box.enter().append("rect")
+ .attr("class", "box")
+ .attr("x", 0)
+ .attr("y", function(d) { return x0(d[2]); })
+ .attr("width", width)
+ .attr("height", function(d) { return x0(d[0]) - x0(d[2]); })
+ .transition()
+ .duration(duration)
+ .attr("y", function(d) { return x1(d[2]); })
+ .attr("height", function(d) { return x1(d[0]) - x1(d[2]); });
+
+ box.transition()
+ .duration(duration)
+ .attr("y", function(d) { return x1(d[2]); })
+ .attr("height", function(d) { return x1(d[0]) - x1(d[2]); });
+
+ // Update median line.
+ var medianLine = g.selectAll("line.median")
+ .data([quartileData[1]]);
+
+ medianLine.enter().append("line")
+ .attr("class", "median")
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", width)
+ .attr("y2", x0)
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ medianLine.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ // Update whiskers.
+ var whisker = g.selectAll("line.whisker")
+ .data(whiskerData || []);
+
+ whisker.enter().insert("line", "circle, text")
+ .attr("class", "whisker")
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", width)
+ .attr("y2", x0)
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1);
+
+ whisker.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1);
+
+ whisker.exit().transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1e-6)
+ .remove();
+
+ // Update outliers.
+ var outlier = g.selectAll("circle.outlier")
+ .data(outlierIndices, Number);
+
+ outlier.enter().insert("circle", "text")
+ .attr("class", "outlier")
+ .attr("r", 5)
+ .attr("cx", width / 2)
+ .attr("cy", function(i) { return x0(d[i]); })
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1);
+
+ outlier.transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1);
+
+ outlier.exit().transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1e-6)
+ .remove();
+
+ // Compute the tick format.
+ var format = tickFormat || x1.tickFormat(8);
+
+ // Update box ticks.
+ var boxTick = g.selectAll("text.box")
+ .data(quartileData);
+
+ console.log("quartileData:", quartileData);
+
+ boxTick.enter().append("text")
+ .attr("class", "box")
+ .attr("dy", ".3em")
+ .attr("dx", function(d, i) { return i & 1 ? 6 : -6 })
+ .attr("x", function(d, i) { return i & 1 ? width : 0 })
+ .attr("y", x0)
+ .attr("text-anchor", function(d, i) { return i & 1 ? "start" : "end"; })
+ .text(format)
+ .transition()
+ .duration(duration)
+ .attr("y", x1);
+
+ boxTick.transition()
+ .duration(duration)
+ .text(format)
+ .attr("y", x1);
+
+ // Update whisker ticks. These are handled separately from the box
+ // ticks because they may or may not exist, and we want don't want
+ // to join box ticks pre-transition with whisker ticks post-.
+ var whiskerTick = g.selectAll("text.whisker")
+ .data(whiskerData || []);
+
+ whiskerTick.enter().append("text")
+ .attr("class", "whisker")
+ .attr("dy", ".3em")
+ .attr("dx", 6)
+ .attr("x", width)
+ .attr("y", x0)
+ .text(format)
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("y", x1)
+ .style("opacity", 1);
+
+ whiskerTick.transition()
+ .duration(duration)
+ .text(format)
+ .attr("y", x1)
+ .style("opacity", 1);
+
+ whiskerTick.exit().transition()
+ .duration(duration)
+ .attr("y", x1)
+ .style("opacity", 1e-6)
+ .remove();
+ });
+ d3.timer.flush();
+ }
+
+ box.width = function(x) {
+ if (!arguments.length) return width;
+ width = x;
+ return box;
+ };
+
+ box.height = function(x) {
+ if (!arguments.length) return height;
+ height = x;
+ return box;
+ };
+
+ box.tickFormat = function(x) {
+ if (!arguments.length) return tickFormat;
+ tickFormat = x;
+ return box;
+ };
+
+ box.duration = function(x) {
+ if (!arguments.length) return duration;
+ duration = x;
+ return box;
+ };
+
+ box.domain = function(x) {
+ if (!arguments.length) return domain;
+ domain = x == null ? x : d3.functor(x);
+ return box;
+ };
+
+ box.value = function(x) {
+ if (!arguments.length) return value;
+ value = x;
+ return box;
+ };
+
+ box.whiskers = function(x) {
+ if (!arguments.length) return whiskers;
+ whiskers = x;
+ return box;
+ };
+
+ box.quartiles = function(x) {
+ if (!arguments.length) return quartiles;
+ quartiles = x;
+ return box;
+ };
+
+ return box;
+};
+
+function boxWhiskers(d) {
+ return [0, d.length - 1];
+}
+
+function boxQuartiles(d) {
+ return [
+ d3.quantile(d, .25),
+ d3.quantile(d, .5),
+ d3.quantile(d, .75)
+ ];
+}
+
+})();
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/box_plot.js b/gn2/wqflask/static/new/javascript/box_plot.js new file mode 100644 index 00000000..566a8eb8 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/box_plot.js @@ -0,0 +1,80 @@ +// Generated by CoffeeScript 1.8.0 +var Box_Plot, root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +Box_Plot = (function() { + function Box_Plot(sample_list, sample_group) { + this.sample_list = sample_list; + this.sample_group = sample_group; + this.get_samples(); + this.margin = { + top: 10, + right: 50, + bottom: 20, + left: 50 + }; + this.plot_width = 200 - this.margin.left - this.margin.right; + this.plot_height = 500 - this.margin.top - this.margin.bottom; + this.min = d3.min(this.sample_vals); + this.max = d3.max(this.sample_vals); + this.svg = this.create_svg(); + this.enter_data(); + } + + Box_Plot.prototype.get_samples = function() { + var sample; + return this.sample_vals = (function() { + var _i, _len, _ref, _results; + _ref = this.sample_list; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + if (sample.value !== null) { + _results.push(sample.value); + } + } + return _results; + }).call(this); + }; + + Box_Plot.prototype.create_svg = function() { + var svg; + svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width - 30).height(this.plot_height - 30).domain([this.min, this.max]); + return svg; + }; + + Box_Plot.prototype.enter_data = function() { + return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg); + }; + + Box_Plot.prototype.inter_quartile_range = function(k) { + return (function(_this) { + return function(d, i) { + var inter_quartile_range, j, q1, q3; + console.log("iqr d:", d); + q1 = d.quartiles[0]; + q3 = d.quartiles[2]; + inter_quartile_range = (q3 - q1) * k; + console.log("iqr:", inter_quartile_range); + i = 0; + j = d.length; + console.log("d[-1]:", d[1]); + console.log("q1 - iqr:", q1 - inter_quartile_range); + while (d[i] < q1 - inter_quartile_range) { + i++; + } + while (d[j] > q3 + inter_quartile_range) { + j--; + } + console.log("[i, j]", [i, j]); + return [i, j]; + }; + })(this); + }; + + return Box_Plot; + +})(); + +root.Box_Plot = Box_Plot; diff --git a/gn2/wqflask/static/new/javascript/chr_lod_chart.js b/gn2/wqflask/static/new/javascript/chr_lod_chart.js new file mode 100644 index 00000000..c6cbd01b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/chr_lod_chart.js @@ -0,0 +1,297 @@ +// Generated by CoffeeScript 1.9.2 +var Chr_Lod_Chart; + +Chr_Lod_Chart = (function() { + function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) { + this.plot_height = plot_height; + this.plot_width = plot_width; + this.chr = chr; + this.manhattanPlot = manhattanPlot; + this.mappingScale = mappingScale; + this.qtl_results = js_data.qtl_results; + console.log("qtl_results are:", this.qtl_results); + console.log("chr is:", this.chr); + this.get_max_chr(); + this.filter_qtl_results(); + console.log("filtered results:", this.these_results); + this.get_qtl_count(); + this.x_coords = []; + this.y_coords = []; + this.marker_names = []; + console.time('Create coordinates'); + this.create_coordinates(); + console.log("@x_coords: ", this.x_coords); + console.log("@y_coords: ", this.y_coords); + console.timeEnd('Create coordinates'); + this.x_buffer = this.plot_width / 30; + this.y_buffer = this.plot_height / 20; + this.x_max = d3.max(this.x_coords); + this.y_max = d3.max(this.y_coords) * 1.2; + this.y_threshold = this.get_lod_threshold(); + this.svg = this.create_svg(); + this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); + console.log("coordinates:", this.plot_coordinates); + this.plot_height -= this.y_buffer; + this.create_scales(); + console.time('Create graph'); + this.create_graph(); + console.timeEnd('Create graph'); + } + + Chr_Lod_Chart.prototype.get_max_chr = function() { + var key, results; + this.max_chr = 0; + results = []; + for (key in js_data.chromosomes) { + console.log("key is:", key); + if (parseInt(key) > this.max_chr) { + results.push(this.max_chr = parseInt(key)); + } else { + results.push(void 0); + } + } + return results; + }; + + Chr_Lod_Chart.prototype.filter_qtl_results = function() { + var i, len, ref, result, results, this_chr; + this.these_results = []; + this_chr = 100; + ref = this.qtl_results; + results = []; + for (i = 0, len = ref.length; i < len; i++) { + result = ref[i]; + if (result.chr === "X") { + this_chr = this.max_chr; + } else { + this_chr = result.chr; + } + if (this_chr > parseInt(this.chr[0])) { + break; + } + if (parseInt(this_chr) === parseInt(this.chr[0])) { + results.push(this.these_results.push(result)); + } else { + results.push(void 0); + } + } + return results; + }; + + Chr_Lod_Chart.prototype.get_qtl_count = function() { + var high_qtl_count, i, len, ref, result; + high_qtl_count = 0; + ref = this.these_results; + for (i = 0, len = ref.length; i < len; i++) { + result = ref[i]; + if (result.lod_score > 1) { + high_qtl_count += 1; + } + } + console.log("high_qtl_count:", high_qtl_count); + return this.y_axis_filter = 2; + }; + + Chr_Lod_Chart.prototype.create_coordinates = function() { + var i, len, ref, result, results; + ref = this.these_results; + console.log("THESE_RESULTS:", ref) + results = []; + for (i = 0, len = ref.length; i < len; i++) { + result = ref[i]; + this.x_coords.push(parseFloat(result.Mb)); + if (js_data.result_score_type == "LOD") { + this.y_coords.push(result.lod_score); + } + else { + console.log("LRS VALUE:", result['lrs_value']) + this.y_coords.push(result['lrs_value']); + } + results.push(this.marker_names.push(result.name)); + } + return results; + }; + + Chr_Lod_Chart.prototype.create_svg = function() { + var svg; + svg = d3.select("#topchart").append("svg").attr("class", "chr_manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g"); + return svg; + }; + + Chr_Lod_Chart.prototype.create_scales = function() { + if (this.mappingScale == "morgan") { + max_pos = 0 + for (i = 0, len = this.these_results.length; i < len; i++) { + marker = this.these_results[i] + if (parseFloat(marker['Mb']) > max_pos){ + max_pos = parseFloat(marker.Mb) + } + } + this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]); + } + else { + this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); + } + return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); + }; + + Chr_Lod_Chart.prototype.get_lod_threshold = function() { + if (this.y_max / 2 > 2) { + return this.y_max / 2; + } else { + return 2; + } + }; + + Chr_Lod_Chart.prototype.create_graph = function() { + this.add_border(); + this.add_x_axis(); + this.add_y_axis(); + this.add_title(); + this.add_back_button(); + if (this.manhattanPlot) { + return this.add_plot_points(); + } else { + return this.add_path(); + } + }; + + Chr_Lod_Chart.prototype.add_border = function() { + var border_coords; + border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]]; + return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) { + return function(d) { + return d[0]; + }; + })(this)).attr("y2", (function(_this) { + return function(d) { + return d[1]; + }; + })(this)).attr("x1", (function(_this) { + return function(d) { + return d[2]; + }; + })(this)).attr("x2", (function(_this) { + return function(d) { + return d[3]; + }; + })(this)).style("stroke", "#000"); + }; + + Chr_Lod_Chart.prototype.add_x_axis = function() { + this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20); + this.xAxis.tickFormat((function(_this) { + return function(d) { + d3.format("d"); + return d; + }; + })(this)); + return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) { + return function(d) { + return "translate(-12,0) rotate(-90)"; + }; + })(this)); + }; + + Chr_Lod_Chart.prototype.add_y_axis = function() { + this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis); + }; + + Chr_Lod_Chart.prototype.add_title = function() { + return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) { + return function(d) { + return (_this.plot_width + _this.x_buffer) / 2; + }; + })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black"); + }; + + Chr_Lod_Chart.prototype.add_back_button = function() { + return $("#return_to_full_view").show().click((function(_this) { + return function() { + return _this.return_to_full_view(); + }; + })(this)); + }; + + Chr_Lod_Chart.prototype.add_path = function() { + var line_function, line_graph; + line_function = d3.svg.line().x((function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).y((function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).interpolate("linear"); + return line_graph = this.svg.append("path").attr("d", line_function(this.plot_coordinates)).attr("stroke", "blue").attr("stroke-width", 1).attr("fill", "none"); + }; + + Chr_Lod_Chart.prototype.add_plot_points = function() { + return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).attr("cy", (function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).attr("r", (function(_this) { + return function(d) { + return 2; + }; + })(this)).attr("fill", (function(_this) { + return function(d) { + return "black"; + }; + })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) { + return function(d) { + return "point_" + String(d[2]); + }; + })(this)).classed("circle", true).on("mouseover", (function(_this) { + return function(d) { + var this_id; + console.log("d3.event is:", d3.event); + console.log("d is:", d); + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); + }; + })(this)).on("mouseout", (function(_this) { + return function(d) { + var this_id; + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { + return 2; + }).attr("fill", function(d) { + return "black"; + }).attr("stroke", "black").attr("stroke-width", "1"); + }; + })(this)).append("svg:title").text((function(_this) { + return function(d) { + return d[2]; + }; + })(this)); + }; + + Chr_Lod_Chart.prototype.return_to_full_view = function() { + $("#return_to_full_view").hide(); + $('#topchart').remove(); + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + return create_lod_chart(); + }; + + Chr_Lod_Chart.prototype.show_marker_in_table = function(marker_info) { + var marker_name; + console.log("in show_marker_in_table"); + + /* Searches for the select marker in the results table below */ + if (marker_info) { + marker_name = marker_info[2]; + return $("#qtl_results_filter").find("input:first").val(marker_name).change(); + } + }; + + return Chr_Lod_Chart; + +})(); diff --git a/gn2/wqflask/static/new/javascript/chr_manhattan_plot.js b/gn2/wqflask/static/new/javascript/chr_manhattan_plot.js new file mode 100644 index 00000000..c661edc7 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/chr_manhattan_plot.js @@ -0,0 +1,273 @@ +// Generated by CoffeeScript 1.8.0 +var Chr_Manhattan_Plot; + +Chr_Manhattan_Plot = (function() { + function Chr_Manhattan_Plot(plot_height, plot_width, chr, manhattanPlot) { + this.plot_height = plot_height; + this.plot_width = plot_width; + this.chr = chr; + this.qtl_results = js_data.qtl_results; + console.log("qtl_results are:", this.qtl_results); + console.log("chr is:", this.chr); + this.get_max_chr(); + this.filter_qtl_results(); + console.log("filtered results:", this.these_results); + this.get_qtl_count(); + this.x_coords = []; + this.y_coords = []; + this.marker_names = []; + console.time('Create coordinates'); + this.create_coordinates(); + console.log("@x_coords: ", this.x_coords); + console.log("@y_coords: ", this.y_coords); + console.timeEnd('Create coordinates'); + this.x_buffer = this.plot_width / 30; + this.y_buffer = this.plot_height / 20; + this.x_max = d3.max(this.x_coords); + this.y_max = d3.max(this.y_coords) * 1.2; + this.y_threshold = this.get_lod_threshold(); + this.svg = this.create_svg(); + this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); + console.log("coordinates:", this.plot_coordinates); + this.plot_height -= this.y_buffer; + this.create_scales(); + console.time('Create graph'); + this.create_graph(); + console.timeEnd('Create graph'); + } + + Chr_Manhattan_Plot.prototype.get_max_chr = function() { + var key, _results; + this.max_chr = 0; + _results = []; + for (key in js_data.chromosomes) { + console.log("key is:", key); + if (parseInt(key) > this.max_chr) { + _results.push(this.max_chr = parseInt(key)); + } else { + _results.push(void 0); + } + } + return _results; + }; + + Chr_Manhattan_Plot.prototype.filter_qtl_results = function() { + var result, this_chr, _i, _len, _ref, _results; + this.these_results = []; + this_chr = 100; + _ref = this.qtl_results; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + if (result.chr === "X") { + this_chr = this.max_chr; + } else { + this_chr = result.chr; + } + console.log("this_chr is:", this_chr); + console.log("@chr[0] is:", parseInt(this.chr[0])); + if (this_chr > parseInt(this.chr[0])) { + break; + } + if (parseInt(this_chr) === parseInt(this.chr[0])) { + _results.push(this.these_results.push(result)); + } else { + _results.push(void 0); + } + } + return _results; + }; + + Chr_Manhattan_Plot.prototype.get_qtl_count = function() { + var high_qtl_count, result, _i, _len, _ref; + high_qtl_count = 0; + _ref = this.these_results; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + if (result.lod_score > 1) { + high_qtl_count += 1; + } + } + console.log("high_qtl_count:", high_qtl_count); + return this.y_axis_filter = 2; + }; + + Chr_Manhattan_Plot.prototype.create_coordinates = function() { + var result, _i, _len, _ref, _results; + _ref = this.these_results; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + this.x_coords.push(parseFloat(result.Mb)); + this.y_coords.push(result.lod_score); + _results.push(this.marker_names.push(result.name)); + } + return _results; + }; + + Chr_Manhattan_Plot.prototype.create_svg = function() { + var svg; + svg = d3.select("#topchart").append("svg").attr("class", "chr_manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g"); + return svg; + }; + + Chr_Manhattan_Plot.prototype.create_scales = function() { + this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); + return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); + }; + + Chr_Manhattan_Plot.prototype.get_lod_threshold = function() { + if (this.y_max / 2 > 2) { + return this.y_max / 2; + } else { + return 2; + } + }; + + Chr_Manhattan_Plot.prototype.create_graph = function() { + this.add_border(); + this.add_x_axis(); + this.add_y_axis(); + this.add_title(); + this.add_back_button(); + if (manhattanPlot) { + return this.add_plot_points(); + } else { + return this.add_path(); + } + }; + + Chr_Manhattan_Plot.prototype.add_border = function() { + var border_coords; + border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]]; + return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) { + return function(d) { + return d[0]; + }; + })(this)).attr("y2", (function(_this) { + return function(d) { + return d[1]; + }; + })(this)).attr("x1", (function(_this) { + return function(d) { + return d[2]; + }; + })(this)).attr("x2", (function(_this) { + return function(d) { + return d[3]; + }; + })(this)).style("stroke", "#000"); + }; + + Chr_Manhattan_Plot.prototype.add_x_axis = function() { + this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20); + this.xAxis.tickFormat((function(_this) { + return function(d) { + d3.format("d"); + return d; + }; + })(this)); + return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) { + return function(d) { + return "translate(-12,0) rotate(-90)"; + }; + })(this)); + }; + + Chr_Manhattan_Plot.prototype.add_y_axis = function() { + this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis); + }; + + Chr_Manhattan_Plot.prototype.add_title = function() { + return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) { + return function(d) { + return (_this.plot_width + _this.x_buffer) / 2; + }; + })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black"); + }; + + Chr_Manhattan_Plot.prototype.add_back_button = function() { + return this.svg.append("text").attr("class", "back").text("Return to full view").attr("x", this.x_buffer * 2).attr("y", this.y_buffer / 2).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", this.return_to_full_view); + }; + + Chr_Manhattan_Plot.prototype.add_path = function() { + var line_function, line_graph; + line_function = d3.svg.line().x((function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).y((function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).interpolate("linear"); + return line_graph = this.svg.append("path").attr("d", line_function(this.plot_coordinates)).attr("stroke", "blue").attr("stroke-width", 1).attr("fill", "none"); + }; + + Chr_Manhattan_Plot.prototype.add_plot_points = function() { + return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).attr("cy", (function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).attr("r", (function(_this) { + return function(d) { + return 2; + }; + })(this)).attr("fill", (function(_this) { + return function(d) { + return "black"; + }; + })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) { + return function(d) { + return "point_" + String(d[2]); + }; + })(this)).classed("circle", true).on("mouseover", (function(_this) { + return function(d) { + var this_id; + console.log("d3.event is:", d3.event); + console.log("d is:", d); + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); + }; + })(this)).on("mouseout", (function(_this) { + return function(d) { + var this_id; + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { + return 2; + }).attr("fill", function(d) { + return "black"; + }).attr("stroke", "black").attr("stroke-width", "1"); + }; + })(this)).append("svg:title").text((function(_this) { + return function(d) { + return d[2]; + }; + })(this)); + }; + + Chr_Manhattan_Plot.prototype.return_to_full_view = function() { + $('#topchart').remove(); + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + return create_manhattan_plot(); + }; + + Chr_Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) { + var marker_name; + console.log("in show_marker_in_table"); + + /* Searches for the select marker in the results table below */ + if (marker_info) { + marker_name = marker_info[2]; + return $("#qtl_results_filter").find("input:first").val(marker_name).change(); + } + }; + + return Chr_Manhattan_Plot; + +})(); diff --git a/gn2/wqflask/static/new/javascript/colorbrewer.js b/gn2/wqflask/static/new/javascript/colorbrewer.js new file mode 100644 index 00000000..2efa9632 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/colorbrewer.js @@ -0,0 +1,302 @@ +// This product includes color specifications and designs developed by Cynthia Brewer (http://colorbrewer.org/).
+var colorbrewer = {YlGn: {
+3: ["#f7fcb9","#addd8e","#31a354"],
+4: ["#ffffcc","#c2e699","#78c679","#238443"],
+5: ["#ffffcc","#c2e699","#78c679","#31a354","#006837"],
+6: ["#ffffcc","#d9f0a3","#addd8e","#78c679","#31a354","#006837"],
+7: ["#ffffcc","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#005a32"],
+8: ["#ffffe5","#f7fcb9","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#005a32"],
+9: ["#ffffe5","#f7fcb9","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#006837","#004529"]
+},YlGnBu: {
+3: ["#edf8b1","#7fcdbb","#2c7fb8"],
+4: ["#ffffcc","#a1dab4","#41b6c4","#225ea8"],
+5: ["#ffffcc","#a1dab4","#41b6c4","#2c7fb8","#253494"],
+6: ["#ffffcc","#c7e9b4","#7fcdbb","#41b6c4","#2c7fb8","#253494"],
+7: ["#ffffcc","#c7e9b4","#7fcdbb","#41b6c4","#1d91c0","#225ea8","#0c2c84"],
+8: ["#ffffd9","#edf8b1","#c7e9b4","#7fcdbb","#41b6c4","#1d91c0","#225ea8","#0c2c84"],
+9: ["#ffffd9","#edf8b1","#c7e9b4","#7fcdbb","#41b6c4","#1d91c0","#225ea8","#253494","#081d58"]
+},GnBu: {
+3: ["#e0f3db","#a8ddb5","#43a2ca"],
+4: ["#f0f9e8","#bae4bc","#7bccc4","#2b8cbe"],
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+},RdYlGn: {
+3: ["#fc8d59","#ffffbf","#91cf60"],
+4: ["#d7191c","#fdae61","#a6d96a","#1a9641"],
+5: ["#d7191c","#fdae61","#ffffbf","#a6d96a","#1a9641"],
+6: ["#d73027","#fc8d59","#fee08b","#d9ef8b","#91cf60","#1a9850"],
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+},Accent: {
+3: ["#7fc97f","#beaed4","#fdc086"],
+4: ["#7fc97f","#beaed4","#fdc086","#ffff99"],
+5: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0"],
+6: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"],
+7: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f","#bf5b17"],
+8: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f","#bf5b17","#666666"]
+},Dark2: {
+3: ["#1b9e77","#d95f02","#7570b3"],
+4: ["#1b9e77","#d95f02","#7570b3","#e7298a"],
+5: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e"],
+6: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02"],
+7: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02","#a6761d"],
+8: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02","#a6761d","#666666"]
+},Paired: {
+3: ["#a6cee3","#1f78b4","#b2df8a"],
+4: ["#a6cee3","#1f78b4","#b2df8a","#33a02c"],
+5: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99"],
+6: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c"],
+7: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f"],
+8: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00"],
+9: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6"],
+10: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a"],
+11: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a","#ffff99"],
+12: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a","#ffff99","#b15928"]
+},Pastel1: {
+3: ["#fbb4ae","#b3cde3","#ccebc5"],
+4: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4"],
+5: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6"],
+6: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc"],
+7: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd"],
+8: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd","#fddaec"],
+9: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd","#fddaec","#f2f2f2"]
+},Pastel2: {
+3: ["#b3e2cd","#fdcdac","#cbd5e8"],
+4: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4"],
+5: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9"],
+6: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9","#fff2ae"],
+7: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9","#fff2ae","#f1e2cc"],
+8: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9","#fff2ae","#f1e2cc","#cccccc"]
+},Set1: {
+3: ["#e41a1c","#377eb8","#4daf4a"],
+4: ["#e41a1c","#377eb8","#4daf4a","#984ea3"],
+5: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00"],
+6: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33"],
+7: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628"],
+8: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628","#f781bf"],
+9: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628","#f781bf","#999999"]
+},Set2: {
+3: ["#66c2a5","#fc8d62","#8da0cb"],
+4: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3"],
+5: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854"],
+6: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854","#ffd92f"],
+7: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854","#ffd92f","#e5c494"],
+8: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854","#ffd92f","#e5c494","#b3b3b3"]
+},Set3: {
+3: ["#8dd3c7","#ffffb3","#bebada"],
+4: ["#8dd3c7","#ffffb3","#bebada","#fb8072"],
+5: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3"],
+6: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462"],
+7: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69"],
+8: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5"],
+9: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9"],
+10: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9","#bc80bd"],
+11: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9","#bc80bd","#ccebc5"],
+12: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9","#bc80bd","#ccebc5","#ffed6f"]
+}};
diff --git a/gn2/wqflask/static/new/javascript/compare_traits_scatterplot.js b/gn2/wqflask/static/new/javascript/compare_traits_scatterplot.js new file mode 100644 index 00000000..5c0ef16c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/compare_traits_scatterplot.js @@ -0,0 +1,121 @@ +// Generated by CoffeeScript 1.8.0 +var root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +root.create_scatterplot = function(json_ids, json_data) { + var data, h, halfh, halfw, indID, margin, mychart, totalh, totalw, w; + console.log("TESTING2"); + h = 400; + w = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + halfw = w + margin.left + margin.right; + totalw = halfw * 2; + mychart = scatterplot().xvar(0).yvar(1).xlab("X").ylab("Y").height(h).width(w).margin(margin); + data = json_data; + indID = json_ids; + d3.select("div#comparison_scatterplot").datum({ + data: data, + indID: indID + }).call(mychart); + return mychart.pointsSelect().on("mouseover", function(d) { + return d3.select(this).attr("r", mychart.pointsize() * 3); + }).on("mouseout", function(d) { + return d3.select(this).attr("r", mychart.pointsize()); + }); +}; + +root.create_scatterplots = function(trait_names, json_ids, json_data) { + var brush, brushend, brushmove, brushstart, chart, data, h, halfh, halfw, i, indID, margin, mychart, num_traits, svg, totalh, totalw, w, xscale, xshift, xvar, yscale, yshift, yvar, _i, _j, _k, _ref, _ref1, _ref2, _results; + console.log("json_data:", json_data); + console.log("trait_names:", trait_names); + num_traits = json_data.length; + console.log("num_traits:", num_traits); + h = 300; + w = 400; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * (num_traits - 1); + halfw = w + margin.left + margin.right; + totalw = halfw; + xvar = []; + yvar = []; + xshift = []; + yshift = []; + for (i = _i = 0, _ref = num_traits - 1; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) { + xvar.push(i); + yvar.push(0); + xshift.push(0); + yshift.push(halfh * i); + } + console.log("xvar:", xvar); + console.log("yvar:", yvar); + svg = d3.select("div#comparison_scatterplot").append("svg").attr("height", totalh).attr("width", totalw); + mychart = []; + chart = []; + for (i = _j = 1, _ref1 = num_traits - 1; 1 <= _ref1 ? _j <= _ref1 : _j >= _ref1; i = 1 <= _ref1 ? ++_j : --_j) { + mychart[i - 1] = scatterplot().xvar(xvar[i]).yvar(yvar[i]).nxticks(6).height(h).width(w).margin(margin).pointsize(4).xlab("" + trait_names[i - 1]).ylab("" + trait_names[0]).title("" + trait_names[0] + " vs. " + trait_names[i - 1]); + data = json_data; + indID = json_ids; + chart[i - 1] = svg.append("g").attr("id", "chart" + (i - 1)).attr("transform", "translate(" + xshift[i] + "," + yshift[i - 1] + ")"); + chart[i - 1].datum({ + data: data, + indID: indID + }).call(mychart[i - 1]); + } + brush = []; + brushstart = function(i) { + return function() { + var j, _k, _ref2; + for (j = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; j = 0 <= _ref2 ? ++_k : --_k) { + if (j !== i) { + chart[j].call(brush[j].clear()); + } + } + return svg.selectAll("circle").attr("opacity", 0.6).classed("selected", false); + }; + }; + brushmove = function(i) { + return function() { + var e; + svg.selectAll("circle").classed("selected", false); + e = brush[i].extent(); + return chart[i].selectAll("circle").classed("selected", function(d, j) { + var circ, cx, cy, selected; + circ = d3.select(this); + cx = circ.attr("cx"); + cy = circ.attr("cy"); + selected = e[0][0] <= cx && cx <= e[1][0] && e[0][1] <= cy && cy <= e[1][1]; + if (selected) { + svg.selectAll("circle.pt" + j).classed("selected", true); + } + return selected; + }); + }; + }; + brushend = function() { + return svg.selectAll("circle").attr("opacity", 1); + }; + xscale = d3.scale.linear().domain([margin.left, margin.left + w]).range([margin.left, margin.left + w]); + yscale = d3.scale.linear().domain([margin.top, margin.top + h]).range([margin.top, margin.top + h]); + _results = []; + for (i = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; i = 0 <= _ref2 ? ++_k : --_k) { + brush[i] = d3.svg.brush().x(xscale).y(yscale).on("brushstart", brushstart(i)).on("brush", brushmove(i)).on("brushend", brushend); + _results.push(chart[i].call(brush[i])); + } + return _results; +}; diff --git a/gn2/wqflask/static/new/javascript/comparison_bar_chart.js b/gn2/wqflask/static/new/javascript/comparison_bar_chart.js new file mode 100644 index 00000000..5e73807c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/comparison_bar_chart.js @@ -0,0 +1,25 @@ +generate_traces = function() { + traces = []; + for (i = 0, _len = js_data.traits.length; i < _len; i++) { + this_trace = { + x: js_data.samples, + y: js_data.sample_data[i], + name: js_data.traits[i], + type: 'bar', + bargap: 20 + } + + traces.push(this_trace) + } + + return traces +} + +create_bar_chart = function() { + var data = generate_traces() + var layout = {barmode: 'group', bargap: 5}; + + Plotly.newPlot('comp_bar_chart', data, layout); +} + +create_bar_chart();
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/corr_matrix.js b/gn2/wqflask/static/new/javascript/corr_matrix.js new file mode 100644 index 00000000..ad0fc8b8 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/corr_matrix.js @@ -0,0 +1,159 @@ +// Generated by CoffeeScript 1.8.0 +var iplotCorr, root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +iplotCorr = function(data, chartOpts) { + var cells, chartdivid, colorScale, corXscale, corYscale, corZscale, corcolors, corr, corr_tip, corrplot, cortitle, drawScatter, height, i, j, margin, nGroup, ncorrX, ncorrY, nind, nvar, pixel_height, pixel_width, rectcolor, scat_tip, scatcolors, scatterplot, scattitle, svg, totalh, totalw, width, zlim, _ref, _ref1, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9; + height = (_ref = chartOpts != null ? chartOpts.height : void 0) != null ? _ref : 450; + width = (_ref1 = chartOpts != null ? chartOpts.width : void 0) != null ? _ref1 : height; + margin = (_ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref2 : { + left: 70, + top: 40, + right: 5, + bottom: 70, + inner: 5 + }; + corcolors = (_ref3 = chartOpts != null ? chartOpts.corcolors : void 0) != null ? _ref3 : ["darkslateblue", "white", "crimson"]; + zlim = (_ref4 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref4 : [-1, 0, 1]; + rectcolor = (_ref5 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? _ref5 : d3.rgb(230, 230, 230); + cortitle = (_ref6 = chartOpts != null ? chartOpts.cortitle : void 0) != null ? _ref6 : ""; + scattitle = (_ref7 = chartOpts != null ? chartOpts.scattitle : void 0) != null ? _ref7 : ""; + scatcolors = (_ref8 = chartOpts != null ? chartOpts.scatcolors : void 0) != null ? _ref8 : null; + chartdivid = (_ref9 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref9 : 'chart'; + totalh = height + margin.top + margin.bottom; + totalw = (width + margin.left + margin.right) * 2; + svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw); + corrplot = svg.append("g").attr("id", "corplot").attr("transform", "translate(" + margin.left + "," + margin.top + ")"); + scatterplot = svg.append("g").attr("id", "scatterplot").attr("transform", "translate(" + (margin.left * 2 + margin.right + width) + "," + margin.top + ")"); + nind = data.indID.length; + nvar = data["var"].length; + ncorrX = data.cols.length; + ncorrY = data.rows.length; + corXscale = d3.scale.ordinal().domain(d3.range(ncorrX)).rangeBands([0, width]); + corYscale = d3.scale.ordinal().domain(d3.range(ncorrY)).rangeBands([0, height]); + corZscale = d3.scale.linear().domain(zlim).range(corcolors); + pixel_width = corXscale(1) - corXscale(0); + pixel_height = corYscale(0) - corYscale(1); + corr = []; + for (i in data.corr) { + for (j in data.corr[i]) { + corr.push({ + row: i, + col: j, + value: data.corr[i][j] + }); + } + corrplot.append("text").attr("class", "corrlabel_y").attr("y", corYscale(i) - pixel_height / 2).attr("x", -margin.left * 0.1).text(data["var"][data.rows[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "end"); + //corrplot.append("text").attr("class", "corrlabel_x").attr("x", corXscale(i) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + + } + scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none"); + corr_tip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return d3.format(".2f")(d.value); + }).direction('e').offset([0, 10]); + corrplot.call(corr_tip); + + cells = corrplot.selectAll("empty").data(corr).enter().append("rect").attr("class", "cell").attr("x", function(d) { + return corXscale(d.col); + }).attr("y", function(d) { + return corYscale(d.row); + }).attr("width", corXscale.rangeBand()).attr("height", corYscale.rangeBand()).attr("fill", function(d) { + return corZscale(d.value); + }).attr("stroke", "none").attr("stroke-width", 2).on("mouseover", function(d) { + d3.select(this).attr("stroke", "black"); + corr_tip.show(d); + //corrplot.append("text").attr("class", "corrlabel").attr("x", corXscale(d.col) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[d.col]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + //return corrplot.append("text").attr("class", "corrlabel_x").attr("y", corYscale(d.row) + pixel_height / 2).attr("x", -margin.left * 0.1).text(data["var"][data.rows[d.row]]).attr("dominant-baseline", "middle").attr("text-anchor", "end"); + return corrplot.append("text").attr("class", "corrlabel_x").attr("x", corXscale(d.col) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[d.col]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + }).on("mouseout", function(d) { + corr_tip.hide(d); + d3.selectAll("text.corrlabel_x").remove(); + return d3.select(this).attr("stroke", "none"); + }).on("click", function(d) { + return drawScatter(d.col, d.row); + }); + nGroup = d3.max(data.group); + if (!(scatcolors != null) || scatcolors.length < nGroup) { + if (nGroup === 1) { + scatcolors = [d3.rgb(150, 150, 150)]; + } else if (nGroup <= 3) { + scatcolors = ["crimson", "green", "darkslateblue"]; + } else { + if (nGroup <= 10) { + colorScale = d3.scale.category10(); + } else { + colorScale = d3.scale.category20(); + } + scatcolors = (function() { + var _results; + _results = []; + for (i in d3.range(nGroup)) { + _results.push(colorScale(i)); + } + return _results; + })(); + } + } + scat_tip = d3.tip().attr('class', 'd3-tip').html(function(d, i) { + return data.indID[i]; + }).direction('e').offset([0, 10]); + scatterplot.call(scat_tip); + drawScatter = function(i, j) { + var xScale, xticks, yScale, yticks; + d3.selectAll("circle.points").remove(); + d3.selectAll("text.axes").remove(); + d3.selectAll("line.axes").remove(); + console.log("data.dat:", data.dat); + console.log("data.cols:", data.cols); + xScale = d3.scale.linear().domain(d3.extent(data.dat[data.cols[i]])).range([margin.inner, width - margin.inner]); + yScale = d3.scale.linear().domain(d3.extent(data.dat[data.rows[j]])).range([height - margin.inner, margin.inner]); + scatterplot.append("text").attr("id", "xaxis").attr("class", "axes").attr("x", width / 2).attr("y", height + margin.bottom * 0.7).text(data["var"][data.cols[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("fill", "slateblue"); + scatterplot.append("text").attr("id", "yaxis").attr("class", "axes").attr("x", -margin.left * 0.8).attr("y", height / 2).text(data["var"][data.rows[j]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("transform", "rotate(270," + (-margin.left * 0.8) + "," + (height / 2) + ")").attr("fill", "slateblue"); + xticks = xScale.ticks(5); + yticks = yScale.ticks(5); + scatterplot.selectAll("empty").data(xticks).enter().append("text").attr("class", "axes").text(function(d) { + return formatAxis(xticks)(d); + }).attr("x", function(d) { + return xScale(d); + }).attr("y", height + margin.bottom * 0.3).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + scatterplot.selectAll("empty").data(yticks).enter().append("text").attr("class", "axes").text(function(d) { + return formatAxis(yticks)(d); + }).attr("x", -margin.left * 0.1).attr("y", function(d) { + return yScale(d); + }).attr("dominant-baseline", "middle").attr("text-anchor", "end"); + scatterplot.selectAll("empty").data(xticks).enter().append("line").attr("class", "axes").attr("x1", function(d) { + return xScale(d); + }).attr("x2", function(d) { + return xScale(d); + }).attr("y1", 0).attr("y2", height).attr("stroke", "white").attr("stroke-width", 1); + scatterplot.selectAll("empty").data(yticks).enter().append("line").attr("class", "axes").attr("y1", function(d) { + return yScale(d); + }).attr("y2", function(d) { + return yScale(d); + }).attr("x1", 0).attr("x2", width).attr("stroke", "white").attr("stroke-width", 1); + return scatterplot.selectAll("empty").data(d3.range(nind)).enter().append("circle").attr("class", "points").attr("cx", function(d) { + return xScale(data.dat[data.cols[i]][d]); + }).attr("cy", function(d) { + return yScale(data.dat[data.rows[j]][d]); + }).attr("r", function(d) { + var x, y; + x = data.dat[data.cols[i]][d]; + y = data.dat[data.rows[j]][d]; + if ((x != "") && (y != "")) { + return 3; + } else { + return null; + } + }).attr("stroke", "black").attr("stroke-width", 1).attr("fill", function(d) { + return scatcolors[data.group[d] - 1]; + }).on("mouseover", scat_tip.show).on("mouseout", scat_tip.hide); + }; + corrplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none"); + scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none"); + corrplot.append("text").text(cortitle).attr("id", "corrtitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + scatterplot.append("text").text(scattitle).attr("id", "scattitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + return d3.select("div#caption").style("opacity", 1); +}; + +root.corr_matrix = iplotCorr; diff --git a/gn2/wqflask/static/new/javascript/corr_scatter_plot.js b/gn2/wqflask/static/new/javascript/corr_scatter_plot.js new file mode 100644 index 00000000..553423cf --- /dev/null +++ b/gn2/wqflask/static/new/javascript/corr_scatter_plot.js @@ -0,0 +1,73 @@ +// Generated by CoffeeScript 1.8.0 +var Scatter_Plot, root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +Scatter_Plot = (function() { + function Scatter_Plot() { + var chart, data, g, height, i, main, margin, maxx, maxy, minx, miny, sample1, sample2, samplename, samples_1, samples_2, text, width, x, xAxis, y, yAxis; + data = new Array(); + samples_1 = js_data.samples_1; + samples_2 = js_data.samples_2; + i = 0; + for (samplename in samples_1) { + sample1 = samples_1[samplename]; + sample2 = samples_2[samplename]; + data[i++] = [sample1.value, sample2.value]; + } + margin = { + top: 100, + right: 15, + bottom: 60, + left: 60 + }; + width = js_data.width - margin.left - margin.right; + height = js_data.height - margin.top - margin.bottom; + minx = d3.min(data, function(d) { + return d[0]; + }) * 0.95; + maxx = d3.max(data, function(d) { + return d[0]; + }) * 1.05; + miny = d3.min(data, function(d) { + return d[1]; + }) * 0.95; + maxy = d3.max(data, function(d) { + return d[1]; + }) * 1.05; + x = d3.scale.linear().domain([minx, maxx]).range([0, width]); + y = d3.scale.linear().domain([miny, maxy]).range([height, 0]); + chart = d3.select("#scatter_plot").append("svg:svg").attr("width", width + margin.right + margin.left).attr("height", height + margin.top + margin.bottom).attr("class", "chart"); + main = chart.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")").attr("width", width).attr("height", height).attr("class", "main"); + xAxis = d3.svg.axis().scale(x).orient("bottom"); + main.append("g").attr("transform", "translate(0," + height + ")").attr("class", "main axis date").call(xAxis); + yAxis = d3.svg.axis().scale(y).orient("left"); + main.append("g").attr("transform", "translate(0,0)").attr("class", "main axis date").call(yAxis); + g = main.append("svg:g"); + g.selectAll("scatter-dots").data(data).enter().append("svg:circle").attr("cx", function(d) { + return x(d[0]); + }).attr("cy", function(d) { + return y(d[1]); + }).attr("fill", js_data.circle_color).attr("r", js_data.circle_radius); + main.append("line").attr("x1", x(minx)).attr("y1", y(js_data.slope * minx + js_data.intercept)).attr("x2", x(maxx * 0.995)).attr("y2", y(js_data.slope * maxx * 0.995 + js_data.intercept)).style("stroke", js_data.line_color).style("stroke-width", js_data.line_width); + chart.append("text").attr("x", width / 2).attr("y", margin.top / 2 - 25).text("Sample Correlation Scatterplot"); + text = ""; + text += "N=" + js_data.num_overlap; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 - 5).text(text); + text = ""; + text += "r=" + js_data.r_value + "\t"; + text += "p(r)=" + js_data.p_value; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 15).text(text); + text = ""; + text += "slope=" + js_data.slope + "\t"; + text += "intercept=" + js_data.intercept; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 35).text(text); + chart.append("text").attr("x", width / 2).attr("y", height + margin.top + 35).text(js_data.trait_1); + chart.append("text").attr("x", 20).attr("y", height / 2 + margin.top + 30).attr("transform", "rotate(-90 20," + (height / 2 + margin.top + 30) + ")").text(js_data.trait_2); + } + + return Scatter_Plot; + +})(); + +root.Scatter_Plot = Scatter_Plot; diff --git a/gn2/wqflask/static/new/javascript/create_corr_matrix.js b/gn2/wqflask/static/new/javascript/create_corr_matrix.js new file mode 100644 index 00000000..c0c39fbc --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_corr_matrix.js @@ -0,0 +1,94 @@ +var neg_color_scale = chroma.scale(['#91bfdb', '#ffffff']).domain([-1, -0.4]); +var pos_color_scale = chroma.scale(['#ffffff', '#fc8d59']).domain([0.4, 1]) +$('.corr_cell').each( function () { + corr_value = parseFloat($(this).find('span.corr_value').text()) + if (corr_value >= 0.5){ + $(this).css('background-color', pos_color_scale(parseFloat(corr_value))._rgb) + } + else if (corr_value <= -0.5) { + $(this).css('background-color', neg_color_scale(parseFloat(corr_value))._rgb) + } + else { + $(this).css('background-color', 'white') + } +}); + +$('#short_labels').click( function (){ + if ($('.short_check').css("display") == "none"){ + $('.short_check').css("display", "inline-block") + } else { + $('.short_check').css("display", "none") + } + $('.shortName').each( function() { + if ($(this).css("display") == "none"){ + $(this).css("display", "block"); + } + else { + $(this).css("display", "none"); + } + }); +}); + +$('#long_labels').click( function (){ + if ($('.long_check').css("display") == "none"){ + $('.long_check').css("display", "inline-block") + } else { + $('.long_check').css("display", "none") + } + $('.verboseName').each( function() { + if ($(this).css("display") == "none"){ + $(this).css("display", "block"); + } + else { + $(this).css("display", "none"); + } + }); +}); + +select_all = function() { + $(".trait_checkbox").each(function() { + $(this).prop('checked', true); + }); +}; + +deselect_all = function() { + $(".trait_checkbox").each(function() { + $(this).prop('checked', false); + }); +}; + +change_buttons = function() { + num_checked = $('.trait_checkbox:checked').length; + if (num_checked === 0) { + $("#add").prop("disabled", true); + } else { + $("#add").prop("disabled", false); + } +}; + +add = function() { + var traits; + traits = $("input[name=pca_trait]:checked").map(function() { + return $(this).val(); + }).get(); + + var traits_hash = md5(traits.toString()); + + $.ajax({ + type: "POST", + url: "/collections/store_trait_list", + data: { + hash: traits_hash, + traits: traits.toString() + } + }); + + return $.colorbox({ + href: "/collections/add?hash=" + traits_hash + }); +} + +$("#select_all").click(select_all); +$("#deselect_all").click(deselect_all); +$("#add").click(add); +$(".btn, .trait_checkbox").click(change_buttons); diff --git a/gn2/wqflask/static/new/javascript/create_datatable.js b/gn2/wqflask/static/new/javascript/create_datatable.js new file mode 100644 index 00000000..541dfdf5 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_datatable.js @@ -0,0 +1,117 @@ +create_table = function(tableId="trait_table", tableData = [], columnDefs = [], customSettings = {}) { + + loadDataTable(tableId=tableId, tableData=tableData, customSettings, firstRun=true) + + var widthChange = 0; // For storing the change in width so overall table width can be adjusted by that amount + function loadDataTable(tableId, tableData, customSettings, firstRun=false){ + if (!firstRun){ + columnDefs = setUserColumnsDefWidths(tableId, columnDefs); + } + + tableSettings = { + "drawCallback": function( settings ) { + $('#' + tableId + ' tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected") && event.target.tagName.toLowerCase() !== 'a'){ + $(this).removeClass("selected") + } else if (event.target.tagName.toLowerCase() !== 'a') { + $(this).addClass("selected") + } + change_buttons() + }); + }, + "columns": columnDefs, + "sDom": "iti", + "destroy": true, + "autoWidth": false, + "bSortClasses": false, + "scrollY": "100vh", + "scrollX": "100%", + "scrollCollapse": true, + "scroller": true, + "iDisplayLength": -1, + "initComplete": function (settings) { + // Add JQueryUI resizable functionality to each th in the ScrollHead table + $('#' + tableId + '_wrapper .dataTables_scrollHead thead th').resizable({ + handles: "e", + alsoResize: '#' + tableId + '_wrapper .dataTables_scrollHead table', //Not essential but makes the resizing smoother + resize: function( event, ui ) { + widthChange = ui.size.width - ui.originalSize.width; + }, + stop: function () { + saveColumnSettings(tableId, theTable); + loadDataTable(tableId, tableData, customSettings, firstRun=false); + } + }); + } + } + + if (tableData.length > 0){ + tableSettings["data"] = tableData + } + + // Replace default settings with custom settings or add custom settings if not already set in default settings + $.each(customSettings, function(key, value) { + tableSettings[key] = value + }); + + if (!firstRun){ + $('#' + tableId + '_container').css("width", String($('#' + tableId).width() + widthChange + 17) + "px"); // Change the container width by the change in width of the adjusted column, so the overall table size adjusts properly + + let checkedRows = getCheckedRows(tableId); + theTable = $('#' + tableId).DataTable(tableSettings); + if (checkedRows.length > 0){ + recheckRows(theTable, checkedRows); + } + } else { + theTable = $('#' + tableId).DataTable(tableSettings); + theTable.draw(); + $('#' + tableId + '_container').css("width", String($('#' + tableId).width() + 17) + "px"); + theTable.columns.adjust().draw(); + } + } + + theTable.on( 'order.dt search.dt draw.dt', function () { + theTable.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) { + cell.innerHTML = i+1; + } ); + } ).draw(); + + window.addEventListener('resize', function(){ + theTable.columns.adjust(); + }); + + $('#' + tableId + '_searchbox').on( 'keyup', function () { + theTable.search($(this).val()).draw(); + } ); + + $('.toggle-vis').on('click', function (e) { + e.preventDefault(); + + function toggleColumn(column) { + // Toggle column visibility + column.visible( ! column.visible() ); + if (column.visible()){ + $(this).removeClass("active"); + } else { + $(this).addClass("active"); + } + } + + // Get the column API object + var targetCols = $(this).attr('data-column').split(",") + for (let i = 0; i < targetCols.length; i++){ + var column = theTable.column( targetCols[i] ); + toggleColumn(column); + } + } ); + + $('#redraw').on('click', function (e) { + e.preventDefault(); + trait_table.columns().visible( true ); + $('.toggle-vis.active').removeClass('active'); + }); +} diff --git a/gn2/wqflask/static/new/javascript/create_heatmap.js b/gn2/wqflask/static/new/javascript/create_heatmap.js new file mode 100644 index 00000000..f3ae2a46 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_heatmap.js @@ -0,0 +1,14 @@ +// Generated by CoffeeScript 1.8.0 +var create_heatmap; + +create_heatmap = function() { + var data, h, mychart, w; + h = 500; + w = 1200; + mychart = lodheatmap().height(h).width(w); + data = js_data.json_data; + console.log("data:", data); + return d3.select("div#chart").datum(data).call(mychart); +}; + +create_heatmap(); diff --git a/gn2/wqflask/static/new/javascript/create_lodchart.js b/gn2/wqflask/static/new/javascript/create_lodchart.js new file mode 100644 index 00000000..778eed3a --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_lodchart.js @@ -0,0 +1,50 @@ +//var create_lod_chart; + +create_lod_chart = function() { + var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; + h = 500; + w = 1200; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + totalw = w + margin.left + margin.right; + if ('additive' in js_data) { + additive = js_data.additive; + } else { + additive = false; + } + console.log("js_data:", js_data); + mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot); + data = js_data.json_data; + d3.select("div#topchart").datum(data).call(mychart); + chrrect = mychart.chrSelect(); + chrrect.on("mouseover", function() { + return d3.select(this).attr("fill", "#E9CFEC"); + }).on("mouseout", function(d, i) { + return d3.select(this).attr("fill", function() { + if (i % 2) { + return "#F1F1F9"; + } + return "#FBFBFF"; + }); + }); + return mychart.markerSelect().on("click", function(d) { + var r; + r = d3.select(this).attr("r"); + return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); + }); +}; + +create_lod_chart() + +/* +$(function() { + return root.create_lod_chart = create_lod_chart; +}); +*/
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/create_manhattan_plot.js b/gn2/wqflask/static/new/javascript/create_manhattan_plot.js new file mode 100644 index 00000000..30af484d --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_manhattan_plot.js @@ -0,0 +1,68 @@ +// Generated by CoffeeScript 1.8.0 +var create_manhattan_plot; + +create_manhattan_plot = function() { + var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; + h = 500; + w = 1200; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + totalw = w + margin.left + margin.right; + console.log("js_data:", js_data); + mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab("LOD score").manhattanPlot(js_data.manhattan_plot); + data = js_data.json_data; + d3.select("div#topchart").datum(data).call(mychart); + chrrect = mychart.chrSelect(); + chrrect.on("mouseover", function() { + return d3.select(this).attr("fill", "#E9CFEC"); + }).on("mouseout", function(d, i) { + return d3.select(this).attr("fill", function() { + if (i % 2) { + return "#F1F1F9"; + } + return "#FBFBFF"; + }); + }); + return mychart.markerSelect().on("click", function(d) { + var r; + r = d3.select(this).attr("r"); + return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); + }); +}; + +create_manhattan_plot(); + +$("#export").click((function(_this) { + return function() { + var filename, form, svg, svg_xml; + svg = $("#topchart").find("svg")[0]; + svg_xml = (new XMLSerializer).serializeToString(svg); + console.log("svg_xml:", svg_xml); + filename = "manhattan_plot_" + js_data.this_trait; + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }; +})(this)); + +$("#export_pdf").click((function(_this) { + return function() { + var filename, form, svg, svg_xml; + svg = $("#topchart").find("svg")[0]; + svg_xml = (new XMLSerializer).serializeToString(svg); + console.log("svg_xml:", svg_xml); + filename = "manhattan_plot_" + js_data.this_trait; + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }; +})(this)); diff --git a/gn2/wqflask/static/new/javascript/ctl_graph.js b/gn2/wqflask/static/new/javascript/ctl_graph.js new file mode 100644 index 00000000..bd950592 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/ctl_graph.js @@ -0,0 +1,193 @@ +window.onload=function() { + // id of Cytoscape Web container div + //var div_id = "cytoscapeweb"; + + var cy = cytoscape({ + container: $('#cytoscapeweb'), // container to render in + + elements: elements_list, + + style: [ // the stylesheet for the graph + { + selector: 'node', + style: { + 'background-color': '#666', + 'label': 'data(symbol)', + 'font-size': 10 + } + }, + + { + selector: 'edge', + style: { + 'width': 'data(width)', + 'line-color': 'data(color)', + 'target-arrow-color': '#ccc', + 'target-arrow-shape': 'none', + 'font-size': 8, + 'curve-style': 'bezier' + } + } + ], + + zoom: 12, + layout: { name: 'circle', + fit: true, // whether to fit the viewport to the graph + padding: 30 // the padding on fit + //idealEdgeLength: function( edge ){ return edge.data['correlation']*10; }, + }, + + + zoomingEnabled: true, + userZoomingEnabled: true, + panningEnabled: true, + userPanningEnabled: true, + boxSelectionEnabled: false, + selectionType: 'single', + + // rendering options: + styleEnabled: true + }); + + var eles = cy.$() // var containing all elements, so elements can be restored after being removed + + var defaults = { + zoomFactor: 0.05, // zoom factor per zoom tick + zoomDelay: 45, // how many ms between zoom ticks + minZoom: 0.1, // min zoom level + maxZoom: 10, // max zoom level + fitPadding: 30, // padding when fitting + panSpeed: 10, // how many ms in between pan ticks + panDistance: 10, // max pan distance per tick + panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction) + panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed) + panInactiveArea: 8, // radius of inactive area in pan drag box + panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0 + zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution) + fitSelector: undefined, // selector of elements to fit + animateOnFit: function(){ // whether to animate on fit + return false; + }, + fitAnimationDuration: 1000, // duration of animation on fit + + // icon class names + sliderHandleIcon: 'fa fa-minus', + zoomInIcon: 'fa fa-plus', + zoomOutIcon: 'fa fa-minus', + resetIcon: 'fa fa-expand' + }; + + cy.panzoom( defaults ); + + function create_qtips(cy){ + cy.nodes().qtip({ + content: function(){ + gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().sid + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>' + ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>' + omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>' + qtip_content = gn_link + ncbi_link + omim_link + return qtip_content + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + + cy.edges().qtip({ + content: function(){ + edge_ID = '<b>Edge: ' + this.data().id + '</b><br>' + lod_score = 'LOD: ' + this.data().lod + '<br>' + return edge_ID + lod_score + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + } + + create_qtips(cy) + + $('#slide').change(function() { + eles.restore() + + console.log(eles) + + // nodes_to_restore = eles.filter("node[max_corr >= " + $(this).val() + "], edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]") + // nodes_to_restore.restore() + + // edges_to_restore = eles.filter("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]") + // edges_to_restore.restore() + + //cy.$("node[max_corr >= " + $(this).val() + "]").restore(); + //cy.$("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]").restore(); + + cy.$("node[max_corr < " + $(this).val() + "]").remove(); + cy.$("edge[correlation < " + $(this).val() + "][correlation > -" + $(this).val() + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + + }); + + $('#reset_graph').click(function() { + eles.restore() + $('#slide').val(0) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + + $('select[name=focus_select]').change(function() { + focus_trait = $(this).val() + + eles.restore() + cy.$('edge[source != "' + focus_trait + '"][target != "' + focus_trait + '"]').remove() + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + + $('select[name=layout_select]').change(function() { + layout_type = $(this).val() + console.log("LAYOUT:", layout_type) + cy.layout({ name: layout_type, + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + + $("a#image_link").click(function(e) { + var pngData = cy.png(); + + $(this).attr('href', pngData); + $(this).attr('download', 'network_graph.png'); + + console.log("TESTING:", image_link) + + }); + + +}; + + diff --git a/gn2/wqflask/static/new/javascript/curvechart.js b/gn2/wqflask/static/new/javascript/curvechart.js new file mode 100644 index 00000000..48bf6bf3 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/curvechart.js @@ -0,0 +1,353 @@ +// Generated by CoffeeScript 1.8.0 +var curvechart; + +curvechart = function() { + var axispos, chart, commonX, curvesSelect, height, margin, nxticks, nyticks, rectcolor, rotate_ylab, strokecolor, strokecolorhilit, strokewidth, strokewidthhilit, title, titlepos, width, xlab, xlim, xscale, xticks, ylab, ylim, yscale, yticks; + width = 800; + height = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + xlim = null; + ylim = null; + nxticks = 5; + xticks = null; + nyticks = 5; + yticks = null; + rectcolor = "#e6e6e6"; + strokecolor = null; + strokecolorhilit = null; + strokewidth = 2; + strokewidthhilit = 2; + title = ""; + xlab = "X"; + ylab = "Y"; + rotate_ylab = null; + yscale = d3.scale.linear(); + xscale = d3.scale.linear(); + curvesSelect = null; + commonX = true; + chart = function(selection) { + return selection.each(function(data) { + var curve, curves, g, gEnter, group, i, indID, indtip, j, lastpoint, ngroup, points, pointsg, svg, titlegrp, tmp, v, xaxis, xrange, xs, yaxis, yrange, ys, _i, _j, _len, _ref, _ref1, _ref2, _ref3, _results; + indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null; + indID = indID != null ? indID : (function() { + _results = []; + for (var _i = 1, _ref1 = data.data.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); } + return _results; + }).apply(this); + group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() { + var _results1; + _results1 = []; + for (i in data.data) { + _results1.push(1); + } + return _results1; + })(); + ngroup = d3.max(group); + group = (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = group.length; _j < _len; _j++) { + g = group[_j]; + _results1.push(g - 1); + } + return _results1; + })(); + strokecolor = strokecolor != null ? strokecolor : selectGroupColors(ngroup, "pastel"); + strokecolor = expand2vector(strokecolor, ngroup); + strokecolorhilit = strokecolorhilit != null ? strokecolorhilit : selectGroupColors(ngroup, "dark"); + strokecolorhilit = expand2vector(strokecolorhilit, ngroup); + if (commonX) { + data = (function() { + var _results1; + _results1 = []; + for (i in data.data) { + _results1.push({ + x: data.x, + y: data.data[i] + }); + } + return _results1; + })(); + } else { + data = data.data; + } + xlim = xlim != null ? xlim : d3.extent(pullVarAsArray(data, "x")); + ylim = ylim != null ? ylim : d3.extent(pullVarAsArray(data, "y")); + for (i in data) { + tmp = data[i]; + data[i] = []; + for (j in tmp.x) { + if (!((tmp.x[j] == null) || (tmp.y[j] == null))) { + data[i].push({ + x: tmp.x[j], + y: tmp.y[j] + }); + } + } + } + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "none"); + xrange = [margin.left + margin.inner, margin.left + width - margin.inner]; + yrange = [margin.top + height - margin.inner, margin.top + margin.inner]; + xscale.domain(xlim).range(xrange); + yscale.domain(ylim).range(yrange); + xs = d3.scale.linear().domain(xlim).range(xrange); + ys = d3.scale.linear().domain(ylim).range(yrange); + yticks = yticks != null ? yticks : ys.ticks(nyticks); + xticks = xticks != null ? xticks : xs.ticks(nxticks); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) { + return xscale(d); + }).attr("x2", function(d) { + return xscale(d); + }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) { + return xscale(d); + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return formatAxis(xticks)(d); + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab); + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + indtip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return indID[d]; + }).direction('e').offset([0, 10]); + svg.call(indtip); + curve = d3.svg.line().x(function(d) { + return xscale(d.x); + }).y(function(d) { + return yscale(d.y); + }); + curves = g.append("g").attr("id", "curves"); + curvesSelect = curves.selectAll("empty").data(d3.range(data.length)).enter().append("path").datum(function(d) { + return data[d]; + }).attr("d", curve).attr("class", function(d, i) { + return "path" + i; + }).attr("fill", "none").attr("stroke", function(d, i) { + return strokecolor[group[i]]; + }).attr("stroke-width", strokewidth).on("mouseover.panel", function(d, i) { + var circle; + d3.select(this).attr("stroke", strokecolorhilit[group[i]]).moveToFront(); + circle = d3.select("circle#hiddenpoint" + i); + return indtip.show(i, circle.node()); + }).on("mouseout.panel", function(d, i) { + d3.select(this).attr("stroke", strokecolor[group[i]]).moveToBack(); + return indtip.hide(); + }); + lastpoint = (function() { + var _results1; + _results1 = []; + for (i in data) { + _results1.push({ + x: null, + y: null + }); + } + return _results1; + })(); + for (i in data) { + _ref3 = data[i]; + for (_j = 0, _len = _ref3.length; _j < _len; _j++) { + v = _ref3[_j]; + if ((v.x != null) && (v.y != null)) { + lastpoint[i] = v; + } + } + } + pointsg = g.append("g").attr("id", "invisiblepoints"); + points = pointsg.selectAll("empty").data(lastpoint).enter().append("circle").attr("id", function(d, i) { + return "hiddenpoint" + i; + }).attr("cx", function(d) { + return xscale(d.x); + }).attr("cy", function(d) { + return yscale(d.y); + }).attr("r", 1).attr("opacity", 0); + return g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.xlim = function(value) { + if (!arguments.length) { + return xlim; + } + xlim = value; + return chart; + }; + chart.nxticks = function(value) { + if (!arguments.length) { + return nxticks; + } + nxticks = value; + return chart; + }; + chart.xticks = function(value) { + if (!arguments.length) { + return xticks; + } + xticks = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.strokecolor = function(value) { + if (!arguments.length) { + return strokecolor; + } + strokecolor = value; + return chart; + }; + chart.strokecolorhilit = function(value) { + if (!arguments.length) { + return strokecolorhilit; + } + strokecolorhilit = value; + return chart; + }; + chart.strokewidth = function(value) { + if (!arguments.length) { + return strokewidth; + } + strokewidth = value; + return chart; + }; + chart.strokewidthhilit = function(value) { + if (!arguments.length) { + return strokewidthhilit; + } + strokewidthhilit = value; + return chart; + }; + chart.commonX = function(value) { + if (!arguments.length) { + return commonX; + } + commonX = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.xscale = function() { + return xscale; + }; + chart.curvesSelect = function() { + return curvesSelect; + }; + return chart; +}; diff --git a/gn2/wqflask/static/new/javascript/d3panels.min.js b/gn2/wqflask/static/new/javascript/d3panels.min.js new file mode 100644 index 00000000..dfc10643 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/d3panels.min.js @@ -0,0 +1 @@ +!function(){var d3panels={version:"1.7.1"};"use strict";d3panels.formatAxis=function(d){var extra_digits=arguments.length>1&&arguments[1]!==undefined?arguments[1]:0;var gap,ndig;if(d[0]!=null){gap=d[1]-d[0]}else if(d.length>2){gap=d[2]-d[1]}else{gap=d[1]}ndig=Math.floor(d3panels.log10(Math.abs(gap)));if(ndig>0){ndig=0}ndig=Math.abs(ndig)+extra_digits;return function(val){if(val!=null&&val!=="NA"){return d3.format("."+ndig+"f")(val)}return"NA"}};d3panels.unique=function(x){var k,len,output,v;output={};for(k=0,len=x.length;k<len;k++){v=x[k];if(v!=null){output[v]=v}}output=function(){var results;results=[];for(v in output){results.push(output[v])}return results}();return d3panels.forceAsArray(output)};d3panels.pullVarAsArray=function(data,variable){var i,results;results=[];for(i in data){results.push(data[i][variable])}return results};d3panels.reorgByChr=function(uniquechr,chr,vector){var c,i,k,len,result;if(chr.length!==vector.length){d3panels.displayError("reorgByChr: chr.length ("+chr.length+") != vector.length ("+vector.length+")")}result={};for(i=k=0,len=uniquechr.length;k<len;i=++k){c=uniquechr[i];result[c]=function(){var results;results=[];for(i in vector){if(chr[i]===c){results.push(vector[i])}}return results}()}return result};d3panels.reorgLodData=function(data){var i;data.posByChr=d3panels.reorgByChr(data.chrname,data.chr,data.pos);data.lodByChr=d3panels.reorgByChr(data.chrname,data.chr,data.lod);if(data.poslabel!=null){data.poslabelByChr=d3panels.reorgByChr(data.chrname,data.chr,data.poslabel)}if(data.marker!=null){data.markerinfo=function(){var results;results=[];for(i in data.marker){if(data.marker[i]!==""){results.push({name:data.marker[i],chr:data.chr[i],pos:data.pos[i],lod:data.lod[i]})}}return results}()}return data};d3panels.calc_chrscales=function(plot_width,left_margin,gap,chr,start,end){var reverse=arguments.length>6&&arguments[6]!==undefined?arguments[6]:false;var chr_end_pixels,chr_length,chr_start_pixels,domain,i,k,n_chr,range,ref,right,tot_chr_length,tot_pixels,xscale;n_chr=chr.length;chr_length=function(){var results;results=[];for(i in end){results.push(end[i]-start[i])}return results}();tot_chr_length=chr_length.reduce(function(t,s){return t+s});tot_pixels=plot_width-gap*n_chr;chr_start_pixels=[left_margin+gap/2];chr_end_pixels=[left_margin+gap/2+tot_pixels/tot_chr_length*chr_length[0]];for(i=k=1,ref=n_chr-1;1<=ref?k<=ref:k>=ref;i=1<=ref?++k:--k){chr_start_pixels.push(chr_end_pixels[i-1]+gap);chr_end_pixels.push(chr_start_pixels[i]+tot_pixels/tot_chr_length*chr_length[i])}right=plot_width+left_margin*2;xscale={};for(i in chr){domain=[start[i],end[i]];range=[chr_start_pixels[i],chr_end_pixels[i]];if(reverse){domain.reverse();range=[right-range[1],right-range[0]]}xscale[chr[i]]=d3.scaleLinear().domain(domain).range(range)}return xscale};d3panels.selectGroupColors=function(ngroup,palette){var cat20,pastel1,pastel20,set1;if(ngroup===0){return[]}set1=["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628","#f781bf","#999999"];pastel1=["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd","#fddaec","#f2f2f2"];cat20=["#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2","#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"];pastel20=["#8fc7f4","#fed7f8","#ffbf8e","#fffbb8","#8ce08c","#d8ffca","#f68788","#ffd8d6","#d4a7fd","#f5f0f5","#cc968b","#f4dcd4","#f3b7f2","#f7f6f2","#bfbfbf","#f7f7f7","#fcfd82","#fbfbcd","#87feff","#defaf5"];if(palette==="dark"){if(ngroup===1){return["slateblue"]}if(ngroup===2){return["MediumVioletRed","slateblue"]}if(ngroup===3){return["MediumVioletRed","MediumSeaGreen","slateblue"]}if(ngroup<=9){return set1.slice(0,ngroup)}return cat20.slice(0,ngroup)}else{if(ngroup===1){return["#bebebe"]}if(ngroup===2){return["lightpink","lightblue"]}if(ngroup<=9){return pastel1.slice(0,ngroup)}return pastel20.slice(0,ngroup)}};d3panels.expand2vector=function(input,n){var i;if(input==null){return input}if(Array.isArray(input)&&input.length>=n){return input}if(!Array.isArray(input)){input=[input]}if(input.length>1&&n>1){input=function(){var results;results=[];for(i in d3.range(n)){results.push(input[i%input.length])}return results}()}if(input.length===1&&n>1){input=function(){var results;results=[];for(i in d3.range(n)){results.push(input[0])}return results}()}return input};d3panels.median=function(x){var n,xv;if(x==null){return null}x=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];if(xv!=null){results.push(xv)}}return results}();n=x.length;if(!(n>0)){return null}x.sort(function(a,b){return a-b});if(n%2===1){return x[(n-1)/2]}return(x[n/2]+x[n/2-1])/2};d3panels.pad_vector=function(x){var pad=arguments.length>1&&arguments[1]!==undefined?arguments[1]:null;if(pad==null){return[x[0]-(x[1]-x[0])].concat(x).concat([x[x.length-1]+(x[x.length-1]-x[x.length-2])])}return[x[0]-pad].concat(x).concat(x[x.length-1]+pad)};d3panels.calc_midpoints=function(x){var i,k,ref,results;results=[];for(i=k=0,ref=x.length-2;0<=ref?k<=ref:k>=ref;i=0<=ref?++k:--k){results.push((x[i]+x[i+1])/2)}return results};d3panels.calc_cell_rect=function(cells,xmid,ymid){var bottom,cell,k,left,len,results,right,top;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];left=xmid[cell.xindex];right=xmid[1+cell.xindex];top=ymid[cell.yindex];bottom=ymid[1+cell.yindex];cell.left=d3.min([left,right]);cell.width=Math.abs(right-left);cell.top=d3.min([top,bottom]);results.push(cell.height=Math.abs(bottom-top))}return results};d3panels.calc_chrcell_rect=function(cells,xmid,ymid){var bottom,cell,k,left,len,results,right,top;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];left=xmid[cell.chr][cell.posindex];right=xmid[cell.chr][1+cell.posindex];top=ymid[cell.lodindex];bottom=ymid[1+cell.lodindex];cell.left=d3.min([left,right]);cell.width=Math.abs(right-left);cell.top=d3.min([top,bottom]);results.push(cell.height=Math.abs(bottom-top))}return results};d3panels.calc_2dchrcell_rect=function(cells,xmid,ymid){var bottom,cell,k,left,len,results,right,top;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];left=xmid[cell.chrx][cell.xindexByChr];right=xmid[cell.chrx][1+cell.xindexByChr];top=ymid[cell.chry][cell.yindexByChr];bottom=ymid[cell.chry][1+cell.yindexByChr];cell.left=d3.min([left,right]);cell.width=Math.abs(right-left);cell.top=d3.min([top,bottom]);results.push(cell.height=Math.abs(bottom-top))}return results};d3panels.maxdiff=function(x){var d,i,k,ref,result;if(x.length<2){return null}result=x[1]-x[0];if(x.length<3){return result}for(i=k=2,ref=x.length;2<=ref?k<ref:k>ref;i=2<=ref?++k:--k){d=x[i]-x[i-1];if(d>result){result=d}}return result};d3panels.matrixMin=function(mat){var i,j,result;result=mat[0][0];for(i in mat){for(j in mat[i]){if(!(result!=null)||result>mat[i][j]&&mat[i][j]!=null){result=mat[i][j]}}}return result};d3panels.matrixMax=function(mat){var i,j,result;result=mat[0][0];for(i in mat){for(j in mat[i]){if(!(result!=null)||result<mat[i][j]&&mat[i][j]!=null){result=mat[i][j]}}}return result};d3panels.matrixMaxAbs=function(mat){var i,j,result;result=Math.abs(mat[0][0]);for(i in mat){for(j in mat[i]){if(!(result!=null)||result<Math.abs(mat[i][j])&&mat[i][j]!=null){result=Math.abs(mat[i][j])}}}return result};d3panels.matrixExtent=function(mat){return[d3panels.matrixMin(mat),d3panels.matrixMax(mat)]};d3panels.forceAsArray=function(x){if(x==null){return x}if(Array.isArray(x)){return x}return[x]};d3panels.missing2null=function(vec){var missingvalues=arguments.length>1&&arguments[1]!==undefined?arguments[1]:["NA",""];return vec.map(function(value){if(missingvalues.indexOf(value)>-1){return null}else{return value}})};d3panels.displayError=function(message){var divid=arguments.length>1&&arguments[1]!==undefined?arguments[1]:null;var div;div="div.error";if(divid!=null){div+="#"+divid}if(d3.select(div).empty()){d3.select("body").insert("div",":first-child").attr("class","error")}return d3.select(div).append("p").text(message)};d3panels.sumArray=function(vec){var x;vec=function(){var k,len,results;results=[];for(k=0,len=vec.length;k<len;k++){x=vec[k];if(x!=null){results.push(x)}}return results}();if(!(vec.length>0)){return null}return vec.reduce(function(a,b){return a*1+b*1})};d3panels.calc_crosstab=function(data){var col,cs,i,k,l,ncol,nrow,ref,ref1,result,row,rs;nrow=data.ycat.length;ncol=data.xcat.length;result=function(){var k,ref,results;results=[];for(row=k=0,ref=nrow;0<=ref?k<=ref:k>=ref;row=0<=ref?++k:--k){results.push(function(){var l,ref1,results1;results1=[];for(col=l=0,ref1=ncol;0<=ref1?l<=ref1:l>=ref1;col=0<=ref1?++l:--l){results1.push(0)}return results1}())}return results}();for(i in data.x){result[data.y[i]][data.x[i]]+=1}rs=d3panels.rowSums(result);cs=d3panels.colSums(result);for(i=k=0,ref=ncol;0<=ref?k<ref:k>ref;i=0<=ref?++k:--k){result[nrow][i]=cs[i]}for(i=l=0,ref1=nrow;0<=ref1?l<ref1:l>ref1;i=0<=ref1?++l:--l){result[i][ncol]=rs[i]}result[nrow][ncol]=d3panels.sumArray(rs);return result};d3panels.rowSums=function(mat){var k,len,results,x;results=[];for(k=0,len=mat.length;k<len;k++){x=mat[k];results.push(d3panels.sumArray(x))}return results};d3panels.transpose=function(mat){var i,j,k,ref,results;results=[];for(j=k=0,ref=mat[0].length;0<=ref?k<ref:k>ref;j=0<=ref?++k:--k){results.push(function(){var l,ref1,results1;results1=[];for(i=l=0,ref1=mat.length;0<=ref1?l<ref1:l>ref1;i=0<=ref1?++l:--l){results1.push(mat[i][j])}return results1}())}return results};d3panels.colSums=function(mat){return d3panels.rowSums(d3panels.transpose(mat))};d3panels.log2=function(x){if(x==null){return x}return Math.log(x)/Math.log(2)};d3panels.log10=function(x){if(x==null){return x}return Math.log(x)/Math.log(10)};d3panels.abs=function(x){if(x==null){return x}return Math.abs(x)};d3panels.mean_by_group=function(g,y){var i,means,n;means={};n={};for(i in g){if(n[g[i]]!=null){if(y[i]!=null){means[g[i]]+=y[i]}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){means[g[i]]=y[i]}if(y[i]!=null){n[g[i]]=1}}}for(i in means){means[i]/=n[i]}return means};d3panels.sd_by_group=function(g,y){var dev,i,means,n,sds;means=d3panels.mean_by_group(g,y);sds={};n={};for(i in g){dev=y[i]-means[g[i]];if(n[g[i]]!=null){if(y[i]!=null){sds[g[i]]+=dev*dev}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){sds[g[i]]=dev*dev}if(y[i]!=null){n[g[i]]=1}}}for(i in sds){sds[i]=n[i]<2?null:Math.sqrt(sds[i]/(n[i]-1))}return sds};d3panels.count_groups=function(g,y){var i,n;n={};for(i in g){if(n[g[i]]!=null){if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){n[g[i]]=1}}}return n};d3panels.ci_by_group=function(g,y){var m=arguments.length>2&&arguments[2]!==undefined?arguments[2]:2;var ci,dev,i,means,n,sds;means=d3panels.mean_by_group(g,y);sds={};n={};for(i in g){dev=y[i]-means[g[i]];if(n[g[i]]!=null){if(y[i]!=null){sds[g[i]]+=dev*dev}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){sds[g[i]]=dev*dev}if(y[i]!=null){n[g[i]]=1}}}for(i in sds){sds[i]=n[i]<2?null:Math.sqrt(sds[i]/(n[i]-1))}ci={};for(i in means){ci[i]={mean:means[i],low:n[i]>0?means[i]-m*sds[i]/Math.sqrt(n[i]):means[i],high:n[i]>0?means[i]+m*sds[i]/Math.sqrt(n[i]):means[i]}}return ci};d3panels.pad_ylim=function(ylim){var p=arguments.length>1&&arguments[1]!==undefined?arguments[1]:.025;var d;d=ylim[1]-ylim[0];return[ylim[0]-d*p,ylim[1]+d*p]};d3panels.add_chrname_start_end=function(data){var c,i,k,l,len,len1,ref,ref1,these_pos;if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(data.chrstart==null){data.chrstart=[];ref=data.chrname;for(k=0,len=ref.length;k<len;k++){c=ref[k];these_pos=function(){var results;results=[];for(i in data.chr){if(data.chr[i]===c){results.push(data.pos[i])}}return results}();data.chrstart.push(d3.min(these_pos))}}if(data.chrend==null){data.chrend=[];ref1=data.chrname;for(l=0,len1=ref1.length;l<len1;l++){c=ref1[l];these_pos=function(){var results;results=[];for(i in data.chr){if(data.chr[i]===c){results.push(data.pos[i])}}return results}();data.chrend.push(d3.max(these_pos))}}data.start=d3panels.forceAsArray(data.start);data.end=d3panels.forceAsArray(data.end);return data};d3panels.calc_breaks=function(number,low,high){var d,i,results;if(low>=high){d3panels.displayError("calc_breaks: should have low < high");if(low>high){var _ref=[high,low];low=_ref[0];high=_ref[1]}if(low===high){low-=.5;high+=.5}}if(number<2){d3panels.displayError("calc_breaks: number should be >= 2");number=2}d=(high-low)/(number-1);results=[];for(i in d3.range(number)){results.push(low+d*i)}return results};d3panels.calc_freq=function(values,breaks){var return_counts=arguments.length>2&&arguments[2]!==undefined?arguments[2]:false;var br,i,k,len,n,ref,result,v,z;v=values.slice(0);v.sort(function(a,b){return+a-b});br=breaks.slice(0);br.sort(function(a,b){return+a-b});br[0]-=1e-6;br[br.length-1]+=1e-6;result=function(){var k,len,ref,results;ref=d3.range(br.length-1);results=[];for(k=0,len=ref.length;k<len;k++){i=ref[k];results.push(0)}return results}();n=v.length;v=function(){var k,len,results;results=[];for(k=0,len=v.length;k<len;k++){z=v[k];if(z>br[0]&&z<br[br.length-1]){results.push(z)}}return results}();if(v.length<n){d3panels.displayError("calc_freq: values out of range of breaks")}n=v.length;ref=d3.range(br.length-1);for(k=0,len=ref.length;k<len;k++){i=ref[k];result[i]=function(){var l,len1,results;results=[];for(l=0,len1=v.length;l<len1;l++){z=v[l];if(z>=br[i]&&z<br[i+1]){results.push(z)}}return results}().length;if(!return_counts){result[i]/=n*(br[i+1]-br[i])}}return result};d3panels.calc_hist_path=function(freq,breaks){var i,result;if(freq.length!==breaks.length-1){d3panels.displayError("freq.length ("+freq.length+") should be breaks.length - 1 ("+(breaks.length-1)+")")}result=[{x:breaks[0],y:0}];for(i in freq){result.push({x:breaks[i],y:freq[i]});result.push({x:breaks[+i+1],y:freq[i]})}result.push({x:breaks[breaks.length-1],y:0});return result};d3panels.index_of_nearest=function(d,vec){var abs_diff;abs_diff=vec.map(function(val){return Math.abs(val-d)});return abs_diff.indexOf(d3.min(abs_diff))};d3panels.check_listarg_v_default=function(arg,defaults){var key;for(key in defaults){if(arg[key]==null){arg[key]=defaults[key]}}return arg};d3panels.object_position=function(object){var obj,x,y;obj=object.node().getBoundingClientRect();x=obj.left/2+obj.right/2;y=obj.top/2+obj.bottom/2;return{x:x,y:y}};"use strict";d3panels.lod2dheatmap=function(chartOpts){var cellSelect,cells,celltip,chart,chrGap,colors,equalCells,height,hilitcolor,margin,nullcolor,oneAtTop,ref,ref1,ref10,ref11,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,width,xscale,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:800;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:60};chrGap=(ref3=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref3:6;equalCells=(ref4=chartOpts!=null?chartOpts.equalCells:void 0)!=null?ref4:false;oneAtTop=(ref5=chartOpts!=null?chartOpts.oneAtTop:void 0)!=null?ref5:false;colors=(ref6=chartOpts!=null?chartOpts.colors:void 0)!=null?ref6:["slateblue","white","crimson"];nullcolor=(ref7=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref7:"#e6e6e6";zlim=(ref8=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref8:null;zthresh=(ref9=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref9:null;hilitcolor=(ref10=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref10:"black";tipclass=(ref11=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref11:"tooltip";xscale=null;yscale=null;zscale=null;celltip=null;cells=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cellg,chr,i,indexWithinChr,j,k,l,len,len1,len2,m,myframe,n_pos,posByChr,ref12,ref13,ref14,tooltipfunc,x,xmid_scaled,y,ymid_scaled,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});if(data.chr==null){d3panels.displayError("lod2dheatmap: data.chr is missing")}if(data.pos==null){d3panels.displayError("lod2dheatmap: data.pos is missing")}if(data.lod==null){d3panels.displayError("lod2dheatmap: data.lod is missing")}n_pos=data.chr.length;if(data.pos.length!==n_pos){d3panels.displayError("lod2dheatmap: data.pos.length ("+data.pos.length+") != data.chr.length ("+n_pos+")")}if(data.lod.length!==n_pos){d3panels.displayError("lod2dheatmap: data.lod.length ("+data.lod.length+") != data.chr.length ("+n_pos+")")}for(i in data.lod){if(data.lod[i].length!==n_pos){d3panels.displayError("lod2dheatmap: data.lod["+i+"].length ("+data.lod[i].length+") != data.chr.length ("+n_pos+")")}}if(data.poslabel!=null){if(data.poslabel.length!==n_pos){d3panels.displayError("lod2dheatmap: data.poslabel.length ("+data.poslabel.length+") != data.chr.length ("+n_pos+")")}}else{data.poslabel=function(){var results;results=[];for(i in data.chr){results.push(data.chr[i]+"@"+d3panels.formatAxis(data.pos)(data.pos[i]))}return results}()}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(equalCells){data.pos=[];ref12=data.chrname;for(k=0,len=ref12.length;k<len;k++){chr=ref12[k];data.pos=data.pos.concat(function(){var results;results=[];for(i in data.chr){if(data.chr[i]===chr){results.push(+i)}}return results}())}}data=d3panels.add_chrname_start_end(data);if(equalCells){chrGap=(width-margin.left-margin.right-2*data.chrname.length)/data.chr.length+2}chartOpts.chrGap=chrGap;chartOpts.width=width;chartOpts.height=height;chartOpts.margin=margin;myframe=d3panels.chr2dpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();posByChr=d3panels.reorgByChr(data.chrname,data.chr,data.pos);xmid_scaled={};ymid_scaled={};ref13=data.chrname;for(l=0,len1=ref13.length;l<len1;l++){chr=ref13[l];xmid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref14,results;ref14=posByChr[chr];results=[];for(m=0,len2=ref14.length;m<len2;m++){x=ref14[m];results.push(xscale[chr](x))}return results}(),chrGap-2));ymid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref14,results;ref14=posByChr[chr];results=[];for(m=0,len2=ref14.length;m<len2;m++){y=ref14[m];results.push(yscale[chr](y))}return results}(),oneAtTop?chrGap-2:2-chrGap))}zmin=d3panels.matrixMin(data.lod);zmax=d3panels.matrixMaxAbs(data.lod);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("lod2dheatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;indexWithinChr=[];ref14=data.chrname;for(m=0,len2=ref14.length;m<len2;m++){chr=ref14[m];indexWithinChr=indexWithinChr.concat(function(){var results;results=[];for(i in posByChr[chr]){results.push(+i)}return results}())}cells=[];for(i in data.chr){for(j in data.chr){if(Math.abs(data.lod[i][j])>=zthresh){cells.push({lod:data.lod[i][j],chrx:data.chr[i],chry:data.chr[j],poslabelx:data.poslabel[i],poslabely:data.poslabel[j],xindex:i,yindex:j,xindexByChr:indexWithinChr[i],yindexByChr:indexWithinChr[j]})}}}d3panels.calc_2dchrcell_rect(cells,xmid_scaled,ymid_scaled);cellg=svg.append("g").attr("id","cells");cellSelect=cellg.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return d.left}).attr("y",function(d){return d.top}).attr("width",function(d){return d.width}).attr("height",function(d){return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.lod!=null){return zscale(d.lod)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").on("mouseover",function(d){return d3.select(this).attr("stroke",hilitcolor).raise()}).on("mouseout",function(){return d3.select(this).attr("stroke","none")});tooltipfunc=function tooltipfunc(d){var z;z=d3.format(".2f")(Math.abs(d.lod));return"("+d.poslabelx+","+d.poslabely+") → "+z};return celltip=d3panels.tooltip_create(d3.select("body"),cellg.selectAll("rect"),{tipclass:tipclass},tooltipfunc)};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return zscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.panelframe=function(chartOpts){var axispos,box,boxcolor,boxwidth,chart,height,margin,nxticks,nyticks,plot_height,plot_width,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,ref18,ref19,ref2,ref20,ref21,ref22,ref23,ref24,ref25,ref26,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,v_over_h,width,xNA,xNA_size,xlab,xlabels,xlim,xlineOpts,xlines,xscale,xscale_wnull,xticklab,xticks,yNA,yNA_size,ylab,ylabels,ylim,ylineOpts,ylines,yscale,yscale_wnull,yticklab,yticks;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40,inner:3};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:"X";ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"Y";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;xNA=(ref9=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref9:false;yNA=(ref10=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref10:false;xNA_size=(ref11=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref11:{width:20,gap:10};yNA_size=(ref12=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref12:{width:20,gap:10};xlim=(ref13=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref13:[0,1];ylim=(ref14=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref14:[0,1];nxticks=(ref15=chartOpts!=null?chartOpts.nxticks:void 0)!=null?ref15:5;xticks=(ref16=chartOpts!=null?chartOpts.xticks:void 0)!=null?ref16:null;xticklab=(ref17=chartOpts!=null?chartOpts.xticklab:void 0)!=null?ref17:null;nyticks=(ref18=chartOpts!=null?chartOpts.nyticks:void 0)!=null?ref18:5;yticks=(ref19=chartOpts!=null?chartOpts.yticks:void 0)!=null?ref19:null;yticklab=(ref20=chartOpts!=null?chartOpts.yticklab:void 0)!=null?ref20:null;rectcolor=(ref21=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref21:"#e6e6e6";boxcolor=(ref22=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref22:"black";boxwidth=(ref23=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref23:2;xlineOpts=(ref24=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref24:{color:"white",width:2};ylineOpts=(ref25=chartOpts!=null?chartOpts.ylineOpts:void 0)!=null?ref25:{color:"white",width:2};v_over_h=(ref26=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref26:false;xscale=null;yscale=null;xNA=xNA;yNA=yNA;xlines=null;ylines=null;xlabels=null;ylabels=null;plot_width=null;plot_height=null;box=null;svg=null;xscale_wnull=null;yscale_wnull=null;chart=function chart(selection){var boxes,boxes2include,d,g,i,inner_height,inner_width,xNA_xpos,xaxis,xrange,yNA_ypos,yaxis,ylabpos_x,ylabpos_y,yrange;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40,inner:3});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});xNA_size=d3panels.check_listarg_v_default(xNA_size,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA_size,{width:20,gap:10});xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"white",width:2});ylineOpts=d3panels.check_listarg_v_default(ylineOpts,{color:"white",width:2});svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");if(!xNA){xNA_size={width:0,gap:0}}if(!yNA){yNA_size={width:0,gap:0}}plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);inner_width=width-(margin.right+margin.left+xNA_size.width+xNA_size.gap);inner_height=height-(margin.top+margin.bottom+yNA_size.width+yNA_size.gap);boxes={left:[margin.left+xNA_size.width+xNA_size.gap,margin.left,margin.left,margin.left+xNA_size.width+xNA_size.gap],width:[inner_width,xNA_size.width,xNA_size.width,inner_width],top:[margin.top,margin.top,height-(margin.bottom+yNA_size.width),height-(margin.bottom+yNA_size.width)],height:[inner_height,inner_height,yNA_size.width,yNA_size.width]};xNA_xpos=xNA?margin.left+xNA_size.width/2:-5e4;yNA_ypos=yNA?height-margin.bottom-yNA_size.width/2:-5e4;xrange=[boxes.left[0],boxes.left[0]+boxes.width[0]];yrange=[boxes.top[0]+boxes.height[0],boxes.top[0]];for(i in boxes.left){if(boxes.width[i]>0&&boxes.height[i]>0){g.append("rect").attr("x",boxes.left[i]).attr("y",boxes.top[i]).attr("height",boxes.height[i]).attr("width",boxes.width[i]).attr("fill",rectcolor).attr("stroke","none").attr("shape-rendering","crispEdges")}}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1;if(v_over_h){yaxis=g.append("g").attr("class","y axis");xaxis=g.append("g").attr("class","x axis")}else{xaxis=g.append("g").attr("class","x axis");yaxis=g.append("g").attr("class","y axis")}xaxis.append("text").attr("class","title").text(xlab).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(ylab).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");xscale=d3.scaleLinear().domain(xlim).range([xrange[0]+margin.inner,xrange[1]-margin.inner]);yscale=d3.scaleLinear().domain(ylim).range([yrange[0]-margin.inner,yrange[1]+margin.inner]);xscale_wnull=function xscale_wnull(val){if(val==null){return xNA_xpos}return xscale(val)};yscale_wnull=function yscale_wnull(val){if(val==null){return yNA_ypos}return yscale(val)};xticks=xticks!=null?xticks:xscale.ticks(nxticks);if(xticklab!=null&&xticklab.length!==xticks.length){d3panels.displayError("panelframe: xticklab.length ("+xticklab.length+") != xticks.length ("+xticks.length+")")}if(!(xticklab!=null&&xticklab.length===xticks.length)){xticklab=function(){var j,len,results;results=[];for(j=0,len=xticks.length;j<len;j++){d=xticks[j];results.push(d3panels.formatAxis(xticks)(d))}return results}()}if(xNA){xticks=[null].concat(xticks)}if(xNA){xticklab=["NA"].concat(xticklab)}yticks=yticks!=null?yticks:yscale.ticks(nyticks);if(yticklab!=null&&yticklab.length!==yticks.length){d3panels.displayError("panelframe: yticklab.length ("+yticklab.length+") != yticks.length ("+yticks.length+")")}if(!(yticklab!=null&&yticklab.length===yticks.length)){yticklab=function(){var j,len,results;results=[];for(j=0,len=yticks.length;j<len;j++){d=yticks[j];results.push(d3panels.formatAxis(yticks)(d))}return results}()}if(yNA){yticks=[null].concat(yticks)}if(yNA){yticklab=["NA"].concat(yticklab)}ylines=yaxis.append("g").attr("id","ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1",function(d){return yscale_wnull(d)}).attr("y2",function(d){return yscale_wnull(d)}).attr("x1",function(d,i){if(i<yticks.length){return xrange[0]}return margin.left}).attr("x2",function(d,i){if(i<yticks.length){return xrange[1]}return margin.left+xNA_size.width}).attr("fill","none").attr("stroke",ylineOpts.color).attr("stroke-width",ylineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");xlines=xaxis.append("g").attr("id","xlines").selectAll("empty").data(xticks.concat(xticks)).enter().append("line").attr("x1",function(d){return xscale_wnull(d)}).attr("x2",function(d){return xscale_wnull(d)}).attr("y1",function(d,i){if(i<xticks.length){return yrange[0]}return height-margin.bottom}).attr("y2",function(d,i){if(i<xticks.length){return yrange[1]}return height-margin.bottom-yNA_size.width}).attr("fill","none").attr("stroke",xlineOpts.color).attr("stroke-width",xlineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(xticklab).enter().append("text").attr("x",function(d,i){return xscale_wnull(xticks[i])}).attr("y",height-margin.bottom+axispos.xlabel).text(function(d){return d});ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y",function(d,i){return yscale_wnull(yticks[i])}).attr("x",margin.left-axispos.ylabel).text(function(d){return d});boxes2include=function(){var results;results=[];for(i in boxes.left){if(boxes.width[i]>0&&boxes.height[i]>0){results.push(i)}}return results}();box=svg.append("g").attr("id","box");return box.selectAll("empty").data(boxes2include).enter().append("rect").attr("x",function(i){return boxes.left[i]}).attr("y",function(i){return boxes.top[i]}).attr("height",function(i){return boxes.height[i]}).attr("width",function(i){return boxes.width[i]}).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale_wnull};chart.yscale=function(){return yscale_wnull};chart.xNA=function(){return xNA};chart.yNA=function(){return yNA};chart.xlines=function(){return xlines};chart.ylines=function(){return ylines};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.chrpanelframe=function(chartOpts){var altrectcolor,axispos,box,boxcolor,boxwidth,chart,chrGap,chrSelect,chrlinecolor,chrlines,chrlinewidth,height,horizontal,margin,nyticks,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,ref18,ref19,ref2,ref20,ref21,ref22,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,width,xlab,xlabels,xlineOpts,xscale,ylab,ylabels,ylim,ylineOpts,yscale,yticklab,yticks;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:null;ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"LOD score";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;ylim=(ref9=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref9:[0,1];nyticks=(ref10=chartOpts!=null?chartOpts.nyticks:void 0)!=null?ref10:5;yticks=(ref11=chartOpts!=null?chartOpts.yticks:void 0)!=null?ref11:null;yticklab=(ref12=chartOpts!=null?chartOpts.yticklab:void 0)!=null?ref12:null;rectcolor=(ref13=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref13:"#e6e6e6";altrectcolor=(ref14=chartOpts!=null?chartOpts.altrectcolor:void 0)!=null?ref14:"#d4d4d4";chrlinecolor=(ref15=chartOpts!=null?chartOpts.chrlinecolor:void 0)!=null?ref15:"";chrlinewidth=(ref16=chartOpts!=null?chartOpts.chrlinewidth:void 0)!=null?ref16:2;boxcolor=(ref17=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref17:"black";boxwidth=(ref18=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref18:2;xlineOpts=(ref19=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref19:{color:"#d4d4d4",width:2};ylineOpts=(ref20=chartOpts!=null?chartOpts.ylineOpts:void 0)!=null?ref20:{color:"white",width:2};chrGap=(ref21=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref21:6;horizontal=(ref22=chartOpts.horizontal)!=null?ref22:false;xscale=null;yscale=null;xlabels=null;ylabels=null;chrSelect=null;chrlines=null;box=null;svg=null;chart=function chart(selection,data){var c,d,g,plot_height,plot_width,thechr,xaxis,xlines,xticks,yaxis,ylabpos_x,ylabpos_y,ylines;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"white",width:2});ylineOpts=d3panels.check_listarg_v_default(ylineOpts,{color:"white",width:2});if(data.chr==null){d3panels.displayError("chrpanelframe: data.chr is missing")}if(data.end==null){d3panels.displayError("chrpanelframe: data.end is missing")}if(xlab==null){xlab=data.chr.length===1?"Position":"Chromosome"}svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);if(!(data!=null?data.start:void 0)){data.start=function(){var j,len,ref23,results;ref23=data.chr;results=[];for(j=0,len=ref23.length;j<len;j++){c=ref23[j];results.push(0)}return results}()}if(data.chr.length!==data.start.length){d3panels.displayError("chrpanelframe: data.start.length ("+data.start.length+") != data.chr.length ("+data.chr.length+")")}if(data.chr.length!==data.end.length){d3panels.displayError("chrpanelframe: data.end.length ("+data.end.length+") != data.chr.length ("+data.chr.length+")")}if(horizontal){xscale=d3panels.calc_chrscales(plot_height,margin.top,chrGap,data.chr,data.start,data.end);yscale=d3.scaleLinear().domain(ylim.reverse()).range([plot_width+margin.left,margin.left])}else{xscale=d3panels.calc_chrscales(plot_width,margin.left,chrGap,data.chr,data.start,data.end);yscale=d3.scaleLinear().domain(ylim).range([plot_height+margin.top,margin.top])}g.append("rect").attr("x",margin.left).attr("width",plot_width).attr("y",margin.top).attr("height",plot_height).attr("fill",rectcolor).attr("shape-rendering","crispEdges");if(altrectcolor!==""){chrSelect=g.append("g").selectAll("empty").data(data.chr).enter().append("rect").attr("x",function(d,i){if(horizontal){return margin.left}return xscale[d](data.start[i])-chrGap/2}).attr("width",function(d,i){if(horizontal){return plot_width}return xscale[d](data.end[i])-xscale[d](data.start[i])+chrGap}).attr("y",function(d,i){if(horizontal){return xscale[d](data.start[i])-chrGap/2}return margin.top}).attr("height",function(d,i){if(horizontal){return xscale[d](data.end[i])-xscale[d](data.start[i])+chrGap}return plot_height}).attr("fill",function(d,i){if(i%2===0){return rectcolor}return altrectcolor}).attr("shape-rendering","crispEdges")}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);if(horizontal){rotate_ylab=rotate_ylab!=null?rotate_ylab:xlab.length>1}else{rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1}xaxis=g.append("g").attr("class",function(){if(horizontal){return"y axis"}return"x axis"});yaxis=g.append("g").attr("class",function(){if(horizontal){return"x axis"}return"y axis"});xaxis.append("text").attr("class","title").text(function(){if(horizontal){return ylab}return xlab}).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(function(){if(horizontal){return xlab}return ylab}).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");if(data.chr.length>1){xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x",function(d,i){if(horizontal){return margin.left-axispos.ylabel}return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}).attr("y",function(d,i){if(horizontal){return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}return height-margin.bottom+axispos.xlabel}).text(function(d){return d})}else{thechr=data.chr[0];xticks=xscale[thechr].ticks(5);xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(xticks).enter().append("text").attr("x",function(d){if(horizontal){return margin.left-axispos.ylabel}return xscale[thechr](d)}).attr("y",function(d,i){if(horizontal){return xscale[thechr](d)}return height-margin.bottom+axispos.xlabel}).text(function(d){return d});xlines=xaxis.append("g").attr("id","xlines").selectAll("empty").data(xticks).enter().append("line").attr("x1",function(d){if(horizontal){return margin.left}return xscale[thechr](d)}).attr("x2",function(d){if(horizontal){return margin.left+plot_width}return xscale[thechr](d)}).attr("y1",function(d,i){if(horizontal){return xscale[thechr](d)}return margin.top}).attr("y2",function(d,i){if(horizontal){return xscale[thechr](d)}return plot_height+margin.top}).attr("fill","none").attr("stroke",xlineOpts.color).attr("stroke-width",xlineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none")}yticks=yticks!=null?yticks:yscale.ticks(nyticks);if(yticklab!=null&&yticklab.length!==yticks.length){displayError("chrpanelframe: yticklab.length ("+yticklab.length+") != yticks.length ("+yticks.length+")")}if(!(yticklab!=null&&yticklab.length===yticks.length)){yticklab=function(){var j,len,results;results=[];for(j=0,len=yticks.length;j<len;j++){d=yticks[j];results.push(d3panels.formatAxis(yticks)(d))}return results}()}ylines=yaxis.append("g").attr("id","ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1",function(d){if(horizontal){return margin.top}return yscale(d)}).attr("y2",function(d){if(horizontal){return margin.top+plot_height}return yscale(d)}).attr("x1",function(d,i){if(horizontal){return yscale(d)}return margin.left}).attr("x2",function(d,i){if(horizontal){return yscale(d)}return plot_width+margin.left}).attr("fill","none").attr("stroke",ylineOpts.color).attr("stroke-width",ylineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y",function(d,i){if(horizontal){return height-margin.bottom+axispos.xlabel}return yscale(yticks[i])}).attr("x",function(d,i){if(horizontal){return yscale(yticks[i])}return margin.left-axispos.ylabel}).text(function(d){return d});if(chrlinecolor!==""&&data.chr.length>1){chrlines=svg.append("g").attr("id","chrlines");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("x1",function(d,i){if(horizontal){return margin.left}return xscale[d](data.end[i])+chrGap/2}).attr("x2",function(d,i){if(horizontal){return margin.left+plot_width}return xscale[d](data.end[i])+chrGap/2}).attr("y1",function(d,i){if(horizontal){return xscale[d](data.end[i])+chrGap/2}return margin.top}).attr("y2",function(d,i){if(horizontal){return xscale[d](data.end[i])+chrGap/2}return margin.top+plot_height}).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges")}return box=svg.append("rect").attr("class","box").attr("x",margin.left).attr("y",margin.top).attr("height",plot_height).attr("width",plot_width).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.chrSelect=function(){return chrSelect};chart.chrlines=function(){return chrlines};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.chr2dpanelframe=function(chartOpts){var altrectcolor,axispos,box,boxcolor,boxwidth,chart,chrGap,chrSelect,chrlinecolor,chrlines,chrlinewidth,height,margin,oneAtTop,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,width,xlab,xlabels,xscale,ylab,ylabels,yscale;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:800;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:60};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:"Chromosome";ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"Chromosome";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;rectcolor=(ref9=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref9:"#e6e6e6";altrectcolor=(ref10=chartOpts!=null?chartOpts.altrectcolor:void 0)!=null?ref10:"#d4d4d4";chrlinecolor=(ref11=chartOpts!=null?chartOpts.chrlinecolor:void 0)!=null?ref11:"";chrlinewidth=(ref12=chartOpts!=null?chartOpts.chrlinewidth:void 0)!=null?ref12:2;boxcolor=(ref13=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref13:"black";boxwidth=(ref14=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref14:2;chrGap=(ref15=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref15:6;oneAtTop=(ref16=chartOpts!=null?chartOpts.oneAtTop:void 0)!=null?ref16:false;xscale=null;yscale=null;xlabels=null;ylabels=null;chrSelect=null;chrlines=null;box=null;svg=null;chart=function chart(selection,data){var c,chrRect,chrx,chry,g,j,k,len,len1,plot_height,plot_width,ref17,ref18,x,xaxis,y,yaxis,ylabpos_x,ylabpos_y;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});if(data.chr==null){d3panels.displayError("chr2dpanelframe: data.chr is missing")}if(data.end==null){d3panels.displayError("chr2dpanelframe: data.end is missing")}svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);if(!(data!=null?data.start:void 0)){data.start=function(){var j,len,ref17,results;ref17=data.chr;results=[];for(j=0,len=ref17.length;j<len;j++){c=ref17[j];results.push(0)}return results}()}if(data.chr.length!==data.start.length){d3panels.displayError("chr2dpanelframe: data.start.length ("+data.start.length+") != data.chr.length ("+data.chr.length+")")}if(data.chr.length!==data.end.length){d3panels.displayError("chr2dpanelframe: data.end.length ("+data.end.length+") != data.chr.length ("+data.chr.length+")")}xscale=d3panels.calc_chrscales(plot_width,margin.left,chrGap,data.chr,data.start,data.end);yscale=d3panels.calc_chrscales(plot_height,margin.top,chrGap,data.chr,data.start,data.end,!oneAtTop);g.append("rect").attr("x",margin.left).attr("width",plot_width).attr("y",margin.top).attr("height",plot_height).attr("fill",rectcolor).attr("shape-rendering","crispEdges");chrRect=[];ref17=data.chr;for(x=j=0,len=ref17.length;j<len;x=++j){chrx=ref17[x];ref18=data.chr;for(y=k=0,len1=ref18.length;k<len1;y=++k){chry=ref18[y];chrRect.push({chrx:chrx,xi:x,chry:chry,yi:y,odd:(x+y)%2})}}if(altrectcolor!==""){chrSelect=g.append("g").selectAll("empty").data(chrRect).enter().append("rect").attr("x",function(d){return xscale[d.chrx](data.start[d.xi])-chrGap/2}).attr("width",function(d){return xscale[d.chrx](data.end[d.xi])-xscale[d.chrx](data.start[d.xi])+chrGap}).attr("y",function(d){if(oneAtTop){return yscale[d.chry](data.start[d.yi])-chrGap/2}return yscale[d.chry](data.end[d.yi])-chrGap/2}).attr("height",function(d){if(oneAtTop){return yscale[d.chry](data.end[d.yi])-yscale[d.chry](data.start[d.yi])+chrGap}return yscale[d.chry](data.start[d.yi])-yscale[d.chry](data.end[d.yi])+chrGap}).attr("fill",function(d,i){if(!d.odd){return rectcolor}return altrectcolor}).attr("shape-rendering","crispEdges")}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1;xaxis=g.append("g").attr("class","x axis");yaxis=g.append("g").attr("class","y axis");xaxis.append("text").attr("class","title").text(function(){return xlab}).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(function(){return ylab}).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x",function(d,i){return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}).attr("y",height-margin.bottom+axispos.xlabel).text(function(d){return d});ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(data.chr).enter().append("text").attr("y",function(d,i){return(yscale[d](data.start[i])+yscale[d](data.end[i]))/2}).attr("x",margin.left-axispos.ylabel).text(function(d){return d});if(chrlinecolor!==""&&data.chr.length>1){chrlines=svg.append("g").attr("id","chrlines");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("x1",function(d,i){return xscale[d](data.end[i])+chrGap/2}).attr("x2",function(d,i){return xscale[d](data.end[i])+chrGap/2}).attr("y1",margin.top).attr("y2",margin.top+plot_height).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("y1",function(d,i){if(oneAtTop){return yscale[d](data.end[i])+chrGap/2}return yscale[d](data.end[i])-chrGap/2}).attr("y2",function(d,i){if(oneAtTop){return yscale[d](data.end[i])+chrGap/2}return yscale[d](data.end[i])-chrGap/2}).attr("x1",margin.left).attr("x2",margin.left+plot_width).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges")}return box=svg.append("rect").attr("class","box").attr("x",margin.left).attr("y",margin.top).attr("height",plot_height).attr("width",plot_width).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.chrSelect=function(){return chrSelect};chart.chrlines=function(){return chrlines};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.cichart=function(chartOpts){var chart,horizontal,ref,ref1,ref10,ref11,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,segcolor,segments,segstrokewidth,segwidth,svg,tip,tipclass,v_over_h,vertsegcolor,xcatlabels,xlab,xlineOpts,xscale,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xcatlabels=(ref=chartOpts!=null?chartOpts.xcatlabels:void 0)!=null?ref:null;segwidth=(ref1=chartOpts!=null?chartOpts.segwidth:void 0)!=null?ref1:.4;segcolor=(ref2=chartOpts!=null?chartOpts.segcolor:void 0)!=null?ref2:"slateblue";segstrokewidth=(ref3=chartOpts!=null?chartOpts.segstrokewidth:void 0)!=null?ref3:"3";vertsegcolor=(ref4=chartOpts!=null?chartOpts.vertsegcolor:void 0)!=null?ref4:"slateblue";xlab=(ref5=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref5:"Group";ylab=(ref6=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref6:"Response";ylim=(ref7=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref7:null;xlineOpts=(ref8=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref8:{color:"#CDCDCD",width:5};horizontal=(ref9=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref9:false;v_over_h=(ref10=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref10:horizontal;tipclass=(ref11=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref11:"tooltip";xscale=null;yscale=null;segments=null;tip=null;svg=null;chart=function chart(selection,data){var direction,high,i,low,mean,myframe,ncat,segmentGroup,tipfunc,xlim,xticks,xval,yval;xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"#CDCDCD",width:5});if(data.mean==null){d3panels.displayError("cichart: data.mean is missing")}if(data.low==null){d3panels.displayError("cichart: data.low is missing")}if(data.high==null){d3panels.displayError("cichart: data.high is missing")}mean=data.mean;low=data.low;high=data.high;ncat=mean.length;if(ncat!==low.length){d3panels.displayError("cichart: low.length ["+low.length+"] != mean.length ["+ncat+"]")}if(ncat!==high.length){d3panels.displayError("cichart: high.length ["+high.length+"] != mean.length ["+ncat+"]")}xticks=function(){var results;results=[];for(i in mean){results.push(+i+1)}return results}();xcatlabels=xcatlabels!=null?xcatlabels:xticks;if(xcatlabels.length!==mean.length){d3panels.displayError("cichart: xcatlabels.length ["+xcatlabels.length+"] != mean.length ["+ncat+"]")}ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(low.concat(high)));xlim=[.5,mean.length+.5];segcolor=d3panels.expand2vector(d3panels.forceAsArray(segcolor),mean.length);vertsegcolor=d3panels.expand2vector(d3panels.forceAsArray(vertsegcolor),mean.length);if(horizontal){chartOpts.ylim=xlim.reverse();chartOpts.xlim=ylim;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.yNA=chartOpts.xNA;chartOpts.xNA=chartOpts.yNA;chartOpts.yticks=xticks;chartOpts.yticklab=xcatlabels;chartOpts.v_over_h=v_over_h}else{chartOpts.ylim=ylim;chartOpts.xlim=xlim;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.ylineOpts=chartOpts.ylineOpts;chartOpts.xlineOpts=xlineOpts;chartOpts.xticks=xticks;chartOpts.xticklab=xcatlabels;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();segmentGroup=svg.append("g").attr("id","segments");segments=segmentGroup.selectAll("empty").data(low).enter().append("line").attr("x1",function(d,i){if(!horizontal){return xscale(i+1)}return xscale(d)}).attr("x2",function(d,i){if(!horizontal){return xscale(i+1)}return xscale(high[i])}).attr("y1",function(d,i){if(!horizontal){return yscale(d)}return yscale(i+1)}).attr("y2",function(d,i){if(!horizontal){return yscale(high[i])}return yscale(i+1)}).attr("fill","none").attr("stroke",function(d,i){return vertsegcolor[i]}).attr("stroke-width",segstrokewidth).attr("shape-rendering","crispEdges");yval=mean.concat(low,high);xval=function(){var results;results=[];for(i in yval){results.push(+(i%ncat)+1)}return results}();segments=segmentGroup.selectAll("empty").data(yval).enter().append("line").attr("x1",function(d,i){if(horizontal){return xscale(d)}else{if(i<ncat){return xscale(xval[i]-segwidth/2)}return xscale(xval[i]-segwidth/3)}}).attr("x2",function(d,i){if(horizontal){return xscale(d)}else{if(i<ncat){return xscale(xval[i]+segwidth/2)}return xscale(xval[i]+segwidth/3)}}).attr("y1",function(d,i){if(horizontal){if(i<ncat){return yscale(xval[i]-segwidth/2)}return yscale(xval[i]-segwidth/3)}else{return yscale(d)}}).attr("y2",function(d,i){if(horizontal){if(i<ncat){return yscale(xval[i]+segwidth/2)}return yscale(xval[i]+segwidth/3)}else{return yscale(d)}}).attr("fill","none").attr("stroke",function(d,i){return segcolor[i%mean.length]}).attr("stroke-width",segstrokewidth).attr("shape-rendering","crispEdges");direction=horizontal?"north":"east";tipfunc=function tipfunc(d,i){var f,index;index=i%mean.length;f=d3panels.formatAxis([low[index],mean[index]],1);return f(mean[index])+" ("+f(low[index])+" - "+f(high[index])+")"};tip=d3panels.tooltip_create(d3.select("body"),segments,{direction:direction,tipclass:tipclass},tipfunc);return myframe.box().raise()};chart.yscale=function(){return yscale};chart.xscale=function(){return xscale};chart.segments=function(){return segments};chart.tip=function(){return tip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(tip);return null};return chart};"use strict";d3panels.crosstab=function(chartOpts){var bordercolor,cellPad,chart,colrect,fontsize,height,hilitcolor,margin,rectcolor,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rowrect,svg,title,titlepos,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:600;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:300;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:80,right:40,bottom:20};cellPad=(ref3=chartOpts!=null?chartOpts.cellPad:void 0)!=null?ref3:null;titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:50;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";fontsize=(ref6=chartOpts!=null?chartOpts.fontsize:void 0)!=null?ref6:null;rectcolor=(ref7=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref7:"#e6e6e6";hilitcolor=(ref8=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref8:"#e9cfec";bordercolor=(ref9=chartOpts!=null?chartOpts.bordercolor:void 0)!=null?ref9:"black";rowrect=null;colrect=null;svg=null;chart=function chart(selection,data){var borders,cell,cellHeight,cellWidth,cells,collab,denom,i,j,k,l,n,ncol,nrow,plot_height,plot_width,rect,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,rowlab,tab,titles,values,xscale,xv,yscale,yv;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});if(data.x==null){d3panels.displayError("crosstab: data.x is missing")}if(data.y==null){d3panels.displayError("crosstab: data.y is missing")}n=data.x.length;if(data.y.length!==n){d3panels.displayError("crosstab: data.x.length ["+data.x.length+"] != data.y.length ["+data.y.length+"]")}data.xcat=(ref10=data!=null?data.xcat:void 0)!=null?ref10:function(){var k,len,ref11,results;ref11=d3.range(d3.max(data.x));results=[];for(k=0,len=ref11.length;k<len;k++){xv=ref11[k];results.push(xv+1)}return results}();data.ycat=(ref11=data!=null?data.ycat:void 0)!=null?ref11:function(){var k,len,ref12,results;ref12=d3.range(d3.max(data.y));results=[];for(k=0,len=ref12.length;k<len;k++){yv=ref12[k];results.push(yv+1)}return results}();ncol=data.xcat.length;if(d3.max(data.x)>ncol||d3.min(data.x)<=0){d3panels.displayError("crosstab: data.x should be in range 1-"+ncol+" [was "+d3.min(data.x)+" - "+d3.max(data.x)+"]")}nrow=data.ycat.length;if(d3.max(data.y)>nrow||d3.min(data.y)<=0){d3panels.displayError("crosstab: data.y should be in range 1-"+nrow+" [was "+d3.min(data.y)+" - "+d3.max(data.y)+"]")}data.x=function(){var k,len,ref12,results;ref12=data.x;results=[];for(k=0,len=ref12.length;k<len;k++){xv=ref12[k];results.push(xv-1)}return results}();data.y=function(){var k,len,ref12,results;ref12=data.y;results=[];for(k=0,len=ref12.length;k<len;k++){yv=ref12[k];results.push(yv-1)}return results}();tab=d3panels.calc_crosstab(data);data.xlabel=(ref12=data!=null?data.xlabel:void 0)!=null?ref12:"";data.ylabel=(ref13=data!=null?data.ylabel:void 0)!=null?ref13:"";cells=[];for(i=k=0,ref14=nrow;0<=ref14?k<=ref14:k>=ref14;i=0<=ref14?++k:--k){for(j=l=0,ref15=ncol;0<=ref15?l<=ref15:l>=ref15;j=0<=ref15?++l:--l){cell={value:tab[i][j],row:i,col:j,shaded:false,rowpercent:"",colpercent:""};if(i<nrow-1&&(j<ncol-1||j===ncol)){cell.shaded=true}if(j<ncol-1&&(i<nrow-1||i===nrow)){cell.shaded=true}if(i<nrow-1){denom=tab[nrow][j]-tab[nrow-1][j];cell.colpercent=denom>0?Math.round(100*tab[i][j]/denom)+"%":"—"}else if(i===nrow-1){denom=tab[nrow][j];cell.colpercent=denom>0?"("+Math.round(100*tab[i][j]/denom)+"%)":"—"}else{cell.colpercent=cell.value}if(j<ncol-1){denom=tab[i][ncol]-tab[i][ncol-1];cell.rowpercent=denom>0?Math.round(100*tab[i][j]/denom)+"%":"—"}else if(j===ncol-1){denom=tab[i][ncol];cell.rowpercent=denom>0?"("+Math.round(100*tab[i][j]/denom)+"%)":"—"}else{cell.rowpercent=cell.value}cells.push(cell)}}plot_width=width-margin.left-margin.right;plot_height=height-margin.top-margin.bottom;cellWidth=plot_width/(ncol+2);cellHeight=plot_height/(nrow+2);fontsize=fontsize!=null?fontsize:cellHeight*.5;cellPad=cellPad!=null?cellPad:cellWidth*.1;xscale=d3.scaleBand().domain(function(){var results=[];for(var m=0,ref16=ncol+1;0<=ref16?m<=ref16:m>=ref16;0<=ref16?m++:m--){results.push(m)}return results}.apply(this)).range([margin.left,width-margin.right]);yscale=d3.scaleBand().domain(function(){var results=[];for(var m=0,ref17=nrow+1;0<=ref17?m<=ref17:m>=ref17;0<=ref17?m++:m--){results.push(m)}return results}.apply(this)).range([margin.top,height-margin.bottom]);svg=selection.append("svg").attr("width",width).attr("height",height).attr("class","d3panels");rect=svg.append("g").attr("id","value_rect");rect.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return xscale(d.col+1)}).attr("y",function(d){return yscale(d.row+1)}).attr("width",cellWidth).attr("height",cellHeight).attr("fill",function(d){if(d.shaded){return rectcolor}else{return"none"}}).attr("stroke",function(d){if(d.shaded){return rectcolor}else{return"none"}}).attr("stroke-width",0).style("pointer-events","none").attr("shape-rendering","crispEdges");values=svg.append("g").attr("id","values");values.selectAll("empty").data(cells).enter().append("text").attr("x",function(d){return xscale(d.col+1)+cellWidth-cellPad}).attr("y",function(d){return yscale(d.row+1)+cellHeight/2}).text(function(d){return d.value}).attr("class",function(d){return"crosstab row"+d.row+" col"+d.col}).style("font-size",fontsize).style("pointer-events","none");colrect=svg.append("g").attr("id","colrect");colrect.selectAll("empty").data(data.xcat.concat("Total")).enter().append("rect").attr("x",function(d,i){return xscale(i+1)}).attr("y",yscale(0)).attr("width",cellWidth).attr("height",cellHeight).attr("fill","white").attr("stroke","white").attr("shape-rendering","crispEdges").on("mouseover",function(d,i){d3.select(this).attr("fill",hilitcolor).attr("stroke",hilitcolor);return values.selectAll(".col"+i).text(function(d){return d.colpercent})}).on("mouseout",function(d,i){d3.select(this).attr("fill","white").attr("stroke","white");return values.selectAll("text.col"+i).text(function(d){return d.value})});collab=svg.append("g").attr("id","collab");collab.selectAll("empty").data(data.xcat.concat("Total")).enter().append("text").attr("x",function(d,i){return xscale(i+1)+cellWidth-cellPad}).attr("y",yscale(0)+cellHeight/2).text(function(d){return d}).attr("class","crosstab").style("font-size",fontsize).style("pointer-events","none");rowrect=svg.append("g").attr("id","rowrect");rowrect.selectAll("empty").data(data.ycat.concat("Total")).enter().append("rect").attr("x",xscale(0)).attr("y",function(d,i){return yscale(i+1)}).attr("width",cellWidth).attr("height",cellHeight).attr("fill","white").attr("stroke","white").attr("shape-rendering","crispEdges").on("mouseover",function(d,i){d3.select(this).attr("fill",hilitcolor).attr("stroke",hilitcolor);return values.selectAll(".row"+i).text(function(d){return d.rowpercent})}).on("mouseout",function(d,i){d3.select(this).attr("fill","white").attr("stroke","white");return values.selectAll(".row"+i).text(function(d){return d.value})});rowlab=svg.append("g").attr("id","rowlab");rowlab.selectAll("empty").data(data.ycat.concat("Total")).enter().append("text").attr("x",xscale(0)+cellWidth-cellPad).attr("y",function(d,i){return yscale(i+1)+cellHeight/2}).text(function(d){return d}).attr("class","crosstab").style("font-size",fontsize).style("pointer-events","none");borders=svg.append("g").attr("id","borders");borders.append("rect").attr("x",xscale(1)).attr("y",yscale(1)).attr("width",cellWidth*ncol).attr("height",cellHeight*nrow).attr("fill","none").attr("stroke",bordercolor).attr("stroke-width",2).style("pointer-events","none").attr("shape-rendering","crispEdges");borders.append("rect").attr("x",xscale(ncol+1)).attr("y",yscale(nrow+1)).attr("width",cellWidth).attr("height",cellHeight).attr("fill","none").attr("stroke",bordercolor).attr("stroke-width",2).style("pointer-events","none").attr("shape-rendering","crispEdges");titles=svg.append("g").attr("id","titles");titles.append("text").attr("class","crosstabtitle").attr("x",margin.left+(ncol+1)*cellWidth/2).attr("y",margin.top-cellHeight/2).text(data.xlabel).style("font-size",fontsize).style("font-weight","bold");titles.append("text").attr("class","crosstab").attr("x",xscale(0)+cellWidth-cellPad).attr("y",yscale(0)+cellHeight/2).text(data.ylabel).style("font-size",fontsize).style("font-weight","bold");return titles.append("text").attr("class","crosstabtitle").attr("x",margin.left+(width-margin.left-margin.right)/2).attr("y",margin.top-titlepos).text(title).style("font-size",fontsize)};chart.rowrect=function(){return rowrect};chart.colrect=function(){return colrect};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.curvechart=function(chartOpts){var chart,curves,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref2,ref3,ref4,ref5,ref6,svg,tipclass,xlim,xscale,ylim,yscale;if(chartOpts==null){chartOpts={}}xlim=(ref=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref:null;ylim=(ref1=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref1:null;linecolor=(ref2=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref2:null;linecolorhilit=(ref3=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref3:null;linewidth=(ref4=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref4:2;linewidthhilit=(ref5=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref5:2;tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";xscale=null;yscale=null;curves=null;indtip=null;svg=null;chart=function chart(selection,data){var add_curves,i,j,myframe,n_ind,ref7,x,y;if(data.x==null){d3panels.displayError("curvechart: data.x is missing")}if(data.y==null){d3panels.displayError("curvechart: data.y is missing")}x=data.x;y=data.y;n_ind=y.length;if(x.length===1&&y.length>1){for(j=i=2,ref7=n_ind;2<=ref7?i<=ref7:i>=ref7;j=2<=ref7?++i:--i){x.push(x[0])}}if(x.length!==n_ind){d3panels.displayError("curvechart: data.x.length ("+x.length+") != data.y.length ("+n_ind+")")}xlim=xlim!=null?xlim:d3panels.matrixExtent(x);ylim=ylim!=null?ylim:d3panels.matrixExtent(y);chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();add_curves=d3panels.add_curves({linecolor:linecolor,linecolorhilit:linecolorhilit,linewidth:linewidth,linewidthhilit:linewidthhilit,tipclass:tipclass});add_curves(myframe,data);curves=add_curves.curves();indtip=add_curves.indtip();return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";var indexOf=[].indexOf;d3panels.dotchart=function(chartOpts){var chart,horizontal,indtip,jitter,pointcolor,points,pointsize,pointstroke,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,v_over_h,xNA,xNA_size,xcategories,xcatlabels,xlab,xlineOpts,xscale,yNA,yNA_size,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xcategories=(ref=chartOpts!=null?chartOpts.xcategories:void 0)!=null?ref:null;xcatlabels=(ref1=chartOpts!=null?chartOpts.xcatlabels:void 0)!=null?ref1:null;xNA=(ref2=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref2:{handle:true,force:false};yNA=(ref3=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref3:{handle:true,force:false};xNA_size=(ref4=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref4:{width:20,gap:10};yNA_size=(ref5=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref5:{width:20,gap:10};ylim=(ref6=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref6:null;xlab=(ref7=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref7:"Group";ylab=(ref8=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref8:"Response";xlineOpts=(ref9=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref9:{color:"#cdcdcd",width:5};pointcolor=(ref10=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref10:null;pointstroke=(ref11=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref11:"black";pointsize=(ref12=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref12:3;jitter=(ref13=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref13:"beeswarm";tipclass=(ref14=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref14:"tooltip";horizontal=(ref15=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref15:false;v_over_h=(ref16=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref16:horizontal;xscale=null;yscale=null;xNA=xNA;yNA=yNA;points=null;indtip=null;svg=null;chart=function chart(selection,data){var force,g,group,i,indID,jitter_width,myframe,ngroup,pointGroup,ref17,ref18,ref19,ref20,scaledPoints,u,x,xlim,xv,y;xNA=d3panels.check_listarg_v_default(xNA,{handle:true,force:false});yNA=d3panels.check_listarg_v_default(yNA,{handle:true,force:false});xNA_size=d3panels.check_listarg_v_default(xNA,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA,{width:20,gap:10});if(data.x==null){d3panels.displayError("dotchart: data.x is missing")}if(data.y==null){d3panels.displayError("dotchart: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);indID=(ref17=data!=null?data.indID:void 0)!=null?ref17:function(){var results=[];for(var j=1,ref18=x.length;1<=ref18?j<=ref18:j>=ref18;1<=ref18?j++:j--){results.push(j)}return results}.apply(this);if(x.length!==y.length){d3panels.displayError("dotchart: length(x) ["+x.length+"] != length(y) ["+y.length+"]")}if(indID.length!==x.length){d3panels.displayError("dotchart: length(indID) ["+indID.length+"] != length(x) ["+x.length+"]")}group=(ref19=data!=null?data.group:void 0)!=null?ref19:function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){i=x[j];results.push(1)}return results}();group=d3panels.expand2vector(group,x.length);ngroup=d3.max(group);group=function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("dotchart: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==x.length){d3panels.displayError("dotchart: group.length ("+group.length+") != x.length ("+x.length+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}xcategories=xcategories!=null?xcategories:d3panels.unique(x);xcategories=d3panels.forceAsArray(xcategories);xcatlabels=xcatlabels!=null?xcatlabels:xcategories;xcatlabels=d3panels.forceAsArray(xcatlabels);if(xcatlabels.length!==xcategories.length){d3panels.displayError("dotchart: xcatlabels.length ["+xcatlabels.length+"] != xcategories.length ["+xcategories.length+"]")}if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){xv=x[j];results.push(xv!=null&&!(indexOf.call(xcategories,xv)>=0))}return results}())>0){d3panels.displayError("dotchart: Some x values not in xcategories");console.log("xcategories:");console.log(xcategories);console.log("x:");console.log(x);for(i in x){if(x[i]!=null&&!(ref20=x[i],indexOf.call(xcategories,ref20)>=0)){x[i]=null}}}ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(y));xlim=[d3.min(xcategories)-.5,d3.max(xcategories)+.5];xNA.handle=xNA.force||xNA.handle&&!x.every(function(v){return v!=null});yNA.handle=yNA.force||yNA.handle&&!y.every(function(v){return v!=null});if(horizontal){chartOpts.ylim=xlim.reverse();chartOpts.xlim=ylim;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.yNA=xNA.handle;chartOpts.xNA=yNA.handle;chartOpts.xNA_size=yNA_size;chartOpts.yNA_size=xNA_size;chartOpts.yticks=xcategories;chartOpts.yticklab=xcatlabels;chartOpts.v_over_h=v_over_h}else{chartOpts.ylim=ylim;chartOpts.xlim=xlim;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.ylineOpts=chartOpts.ylineOpts;chartOpts.xlineOpts=xlineOpts;chartOpts.xNA=xNA.handle;chartOpts.yNA=yNA.handle;chartOpts.xNA_size=xNA_size;chartOpts.yNA_size=yNA_size;chartOpts.xticks=xcategories;chartOpts.xticklab=xcatlabels;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();if(horizontal){scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(y[i]),y:yscale(x[i])})}return results}()}else{scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(x[i]),y:yscale(y[i])})}return results}()}pointGroup=svg.append("g").attr("id","points");points=pointGroup.selectAll("empty").data(scaledPoints).enter().append("circle").attr("class",function(d,i){return"pt"+i}).attr("r",pointsize).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width","1").attr("cx",function(d){return d.x}).attr("cy",function(d){return d.y});indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]});if(jitter==="random"){jitter_width=.2;u=function(){var results;results=[];for(i in scaledPoints){results.push((Math.random()-.5)*jitter_width)}return results}();if(horizontal){points.attr("cy",function(d,i){if(x[i]!=null){return yscale(x[i]+u[i])}return yscale(x[i])+u[i]/jitter_width*xNA_size.width/2})}else{points.attr("cx",function(d,i){if(x[i]!=null){return xscale(x[i]+u[i])}return xscale(x[i])+u[i]/jitter_width*xNA_size.width/2})}}else if(jitter==="beeswarm"){if(horizontal){d3.range(scaledPoints.length).map(function(i){return scaledPoints[i].fx=scaledPoints[i].x});force=d3.forceSimulation(scaledPoints).force("y",d3.forceY(function(d){return d.y})).force("collide",d3.forceCollide(pointsize*1.1)).stop()}else{d3.range(scaledPoints.length).map(function(i){return scaledPoints[i].fy=scaledPoints[i].y});force=d3.forceSimulation(scaledPoints).force("x",d3.forceX(function(d){return d.x})).force("collide",d3.forceCollide(pointsize*1.1)).stop()}(function(){var results=[];for(var j=0;j<=30;j++){results.push(j)}return results}).apply(this).map(function(d){force.tick();return points.attr("cx",function(d){return d.x}).attr("cy",function(d){return d.y})})}else if(jitter!=="none"){d3panels.displayError('dotchart: jitter should be "beeswarm", "random", or "none"')}return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xNA=function(){return xNA.handle};chart.yNA=function(){return yNA.handle};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.heatmap=function(chartOpts){var cellSelect,cells,celltip,chart,colors,hilitcolor,margin,nullcolor,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,ref8,svg,tipclass,xlim,xscale,ylim,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}margin=(ref=chartOpts!=null?chartOpts.margin:void 0)!=null?ref:{left:60,top:40,right:40,bottom:40,inner:0};xlim=(ref1=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref1:null;ylim=(ref2=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref2:null;nullcolor=(ref3=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref3:"#e6e6e6";colors=(ref4=chartOpts!=null?chartOpts.colors:void 0)!=null?ref4:["slateblue","white","crimson"];zlim=(ref5=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref5:null;zthresh=(ref6=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref6:null;hilitcolor=(ref7=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref7:"black";tipclass=(ref8=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref8:"tooltip";xscale=null;yscale=null;zscale=null;cells=null;celltip=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cell,cellrect,i,j,myframe,nx,ny,ref10,ref9,tooltipfunc,xlabels,xmid,xmid_scaled,xv,ylabels,ymid,ymid_scaled,yv,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40,inner:0});if(!(data.x!=null||data.xcat!=null)){d3panels.displayError("heatmap: data.x is missing")}if(!(data.y!=null||data.ycat!=null)){d3panels.displayError("heatmap: data.y is missing")}if(data.z==null){d3panels.displayError("heatmap: data.z is missing")}if(data.xcat!=null){data.x=function(){var results;results=[];for(i in data.xcat){results.push(+i)}return results}();xlim=xlim!=null?xlim:[-.5,data.x.length-.5];chartOpts.xticks=data.x;chartOpts.xlineOpts={color:"none",width:0};chartOpts.xlab=(ref9=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref9:""}if(data.ycat!=null){data.y=function(){var results;results=[];for(i in data.ycat){results.push(+i)}return results}();ylim=ylim!=null?ylim:[-.5,data.x.length-.5];chartOpts.yticks=data.y;chartOpts.ylineOpts={color:"none",width:0};chartOpts.ylab=(ref10=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref10:""}nx=data.x.length;ny=data.y.length;if(data.z.length!==nx){d3panels.displayError("heatmap: data.x.length ("+nx+") != data.z.length ("+data.z.length+")")}for(i in data.z){if(data.z[i].length!==ny){d3panels.displayError("heatmap: data.y.length ("+ny+") != data.z["+i+"].length ("+data.z[i].length+")")}}cells=[];for(i in data.z){for(j in data.z[i]){cells.push({x:data.x[i],y:data.y[j],z:data.z[i][j],xindex:+i,yindex:+j})}}xmid=d3panels.calc_midpoints(d3panels.pad_vector(data.x));ymid=d3panels.calc_midpoints(d3panels.pad_vector(data.y));xlim=xlim!=null?xlim:d3.extent(xmid);ylim=ylim!=null?ylim:d3.extent(ymid);zmin=d3panels.matrixMin(data.z);zmax=d3panels.matrixMaxAbs(data.z);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("heatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;cells=function(){var k,len,results;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];if(Math.abs(cell.z)>=zthresh){results.push(cell)}}return results}();chartOpts.margin=margin;chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();xlabels=myframe.xlabels();ylabels=myframe.ylabels();xmid_scaled=function(){var k,len,results;results=[];for(k=0,len=xmid.length;k<len;k++){xv=xmid[k];results.push(xscale(xv))}return results}();ymid_scaled=function(){var k,len,results;results=[];for(k=0,len=ymid.length;k<len;k++){yv=ymid[k];results.push(yscale(yv))}return results}();d3panels.calc_cell_rect(cells,xmid_scaled,ymid_scaled);cellrect=svg.append("g").attr("id","cells");cellSelect=cellrect.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return d.left}).attr("y",function(d){return d.top}).attr("width",function(d){return d.width}).attr("height",function(d){return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.z!=null){return zscale(d.z)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").attr("shape-rendering","crispEdges").on("mouseover",function(d){d3.select(this).attr("stroke",hilitcolor).raise();if(data.xcat!=null){svg.select("text#xlab"+d.x).attr("opacity",1)}if(data.ycat!=null){return svg.select("text#ylab"+d.y).attr("opacity",1)}}).on("mouseout",function(d){d3.select(this).attr("stroke","none");if(data.xcat!=null){svg.select("text#xlab"+d.x).attr("opacity",0)}if(data.ycat!=null){return svg.select("text#ylab"+d.y).attr("opacity",0)}});tooltipfunc=function tooltipfunc(d,i){var x,y,z;x=d3panels.formatAxis(data.x)(d.x);y=d3panels.formatAxis(data.y)(d.y);z=d3panels.formatAxis([0,zmax/100])(d.z);if(data.xcat!=null&&data.ycat!=null){return""+z}if(data.xcat!=null){return"("+y+") → "+z}if(data.ycat!=null){return"("+x+") → "+z}return"("+x+", "+y+") → "+z};celltip=d3panels.tooltip_create(d3.select("body"),cellrect.selectAll("rect"),{tipclass:tipclass},tooltipfunc);if(data.xcat!=null){xlabels.text(function(d,i){return data.xcat[i]}).attr("opacity",0).attr("id",function(d,i){return"xlab"+data.x[i]})}if(data.ycat!=null){ylabels.text(function(d,i){return data.ycat[i]}).attr("opacity",0).attr("id",function(d,i){return"ylab"+data.y[i]})}return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return zscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.lodchart=function(chartOpts){var chart,chrSelect,linecolor,linewidth,markerSelect,markertip,pointcolor,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,ref5,ref6,_svg,tipclass,_xscale,ylim,_yscale;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:"darkslateblue";linewidth=(ref1=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref1:2;pointcolor=(ref2=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref2:"#e9cfec";pointsize=(ref3=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref3:0;pointstroke=(ref4=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref4:"black";ylim=(ref5=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref5:null;tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";_xscale=null;_yscale=null;chrSelect=null;markerSelect=null;markertip=null;_svg=null;chart=function chart(selection,data){var add2chart,i,myframe,self_chart;if(data.chr==null){d3panels.displayError("lodchart: data.chr is missing")}if(data.pos==null){d3panels.displayError("lodchart: data.pos is missing")}if(data.lod==null){d3panels.displayError("lodchart: data.lod is missing")}if(data.marker==null){d3panels.displayError("lodchart: data.marker is missing")}if(data.pos.length!==data.chr.length){d3panels.displayError("lodchart: data.pos.length ("+data.pos.length+") != data.chr.length ("+data.chr.length+")")}if(data.lod.length!==data.chr.length){d3panels.displayError("lodchart: data.lod.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}if(data.marker==null){data.marker=[function(){var results;results=[];for(i in data.chr){results.push("")}return results}()]}if(data.marker.length!==data.chr.length){d3panels.displayError("lodchart: data.marker.length ("+data.marker.length+") != data.chr.length ("+data.chr.length+")")}data=d3panels.add_chrname_start_end(data);data=d3panels.reorgLodData(data);chartOpts.ylim=ylim!=null?ylim:[0,d3.max(data.lod)*1.05];myframe=d3panels.chrpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});_svg=myframe.svg();_xscale=myframe.xscale();_yscale=myframe.yscale();chrSelect=myframe.chrSelect();self_chart={svg:function svg(){return _svg},xscale:function xscale(){return _xscale},yscale:function yscale(){return _yscale}};add2chart=d3panels.add_lodcurve(chartOpts);add2chart(self_chart,data);markerSelect=add2chart.markerSelect();markertip=add2chart.markertip();return myframe.box().raise()};chart.xscale=function(){return _xscale};chart.yscale=function(){return _yscale};chart.chrSelect=function(){return chrSelect};chart.markerSelect=function(){return markerSelect};chart.markertip=function(){return markertip};chart.svg=function(){return _svg};chart.remove=function(){_svg.remove();d3panels.tooltip_destroy(markertip);return null};return chart};"use strict";d3panels.add_lodcurve=function(chartOpts){var chart,g,horizontal,linecolor,linedash,linewidth,markerSelect,markertip,pointcolor,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,tipclass;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:"darkslateblue";linewidth=(ref1=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref1:2;linedash=(ref2=chartOpts!=null?chartOpts.linedash:void 0)!=null?ref2:"";pointcolor=(ref3=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref3:"#e9cfec";pointsize=(ref4=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref4:0;pointstroke=(ref5=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref5:"black";tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";horizontal=(ref7=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref7:false;markerSelect=null;markertip=null;g=null;chart=function chart(prevchart,data){var bigpointsize,chr,curves,hiddenpoints,i,j,len,lodcurve,markerpoints,ref8,svg,xscale,yscale;if(data.chr==null){d3panels.displayError("add_lodcurve: data.chr is missing")}if(data.pos==null){d3panels.displayError("add_lodcurve: data.pos is missing")}if(data.lod==null){d3panels.displayError("add_lodcurve: data.lod is missing")}if(data.marker==null){d3panels.displayError("add_lodcurve: data.marker is missing")}if(data.pos.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.pos.length ("+data.pos.length+") != data.chr.length ("+data.chr.length+")")}if(data.lod.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.lod.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}if(data.marker==null){data.marker=[function(){var results;results=[];for(i in data.chr){results.push("")}return results}()]}if(data.marker.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.marker.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}data=d3panels.add_chrname_start_end(data);if(!(data.posByChr!=null&&data.lodByChr!=null&&data.markerinfo!=null)){data=d3panels.reorgLodData(data)}svg=prevchart.svg();g=svg.append("g").attr("id","lod_curve");xscale=prevchart.xscale();yscale=prevchart.yscale();lodcurve=function lodcurve(chr){return d3.line().x(function(d,i){if(horizontal){return yscale(data.lodByChr[chr][i])}return xscale[chr](d)}).y(function(d,i){if(horizontal){return xscale[chr](d)}return yscale(data.lodByChr[chr][i])})};if(linewidth>0){curves=g.append("g").attr("id","curves");ref8=data.chrname;for(j=0,len=ref8.length;j<len;j++){chr=ref8[j];curves.append("path").datum(data.posByChr[chr]).attr("d",lodcurve(chr)).attr("stroke",linecolor).attr("fill","none").attr("stroke-width",linewidth).attr("stroke-dasharray",linedash).style("pointer-events","none")}}if(pointsize>0){markerpoints=g.append("g").attr("id","markerpoints_visible");markerpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx",function(d){if(horizontal){return yscale(d.lod)}return xscale[d.chr](d.pos)}).attr("cy",function(d){if(horizontal){return xscale[d.chr](d.pos)}return yscale(d.lod)}).attr("r",function(d){if(d.lod!=null){return pointsize}else{return null}}).attr("fill",pointcolor).attr("stroke",pointstroke).attr("pointer-events","hidden")}hiddenpoints=g.append("g").attr("id","markerpoints_hidden");bigpointsize=d3.max([2*pointsize,3]);markerSelect=hiddenpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx",function(d){if(horizontal){return yscale(d.lod)}return xscale[d.chr](d.pos)}).attr("cy",function(d){if(horizontal){return xscale[d.chr](d.pos)}return yscale(d.lod)}).attr("id",function(d){return d.name}).attr("r",function(d){if(d.lod!=null){return bigpointsize}else{return null}}).attr("opacity",0).attr("fill",pointcolor).attr("stroke",pointstroke).attr("stroke-width","1").on("mouseover",function(d){return d3.select(this).attr("opacity",1)}).on("mouseout",function(){return d3.select(this).attr("opacity",0)});return markertip=d3panels.tooltip_create(d3.select("body"),markerSelect,{tipclass:tipclass},function(d,i){return[d.name," LOD = "+d3.format(".2f")(d.lod)]})};chart.markerSelect=function(){return markerSelect};chart.markertip=function(){return markertip};chart.remove=function(){g.remove();d3panels.tooltip_destroy(markertip);return null};return chart};"use strict";d3panels.add_curves=function(chartOpts){var chart,curveGroup,curves,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref2,ref3,ref4,tipclass;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:null;linecolorhilit=(ref1=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref1:null;linewidth=(ref2=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref2:2;linewidthhilit=(ref3=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref3:2;tipclass=(ref4=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref4:"tooltip";curves=null;indtip=null;curveGroup=null;chart=function chart(prevchart,data){var curvefunc,dataByPoint,g,group,i,indID,j,k,n_ind,ngroup,ref5,ref6,ref7,svg,x,xscale,y,yscale;if(data.x==null){d3panels.displayError("add_curves: data.x is missing")}if(data.y==null){d3panels.displayError("add_curves: data.y is missing")}x=function(){var k,len,ref5,results;ref5=data.x;results=[];for(k=0,len=ref5.length;k<len;k++){x=ref5[k];results.push(d3panels.missing2null(x))}return results}();y=function(){var k,len,ref5,results;ref5=data.y;results=[];for(k=0,len=ref5.length;k<len;k++){y=ref5[k];results.push(d3panels.missing2null(y))}return results}();n_ind=y.length;if(x.length===1&&y.length>1){for(j=k=2,ref5=n_ind;2<=ref5?k<=ref5:k>=ref5;j=2<=ref5?++k:--k){x.push(x[0])}}if(x.length!==n_ind){d3panels.displayError("add_curves: data.x.length ("+x.length+") != data.y.length ("+n_ind+")")}indID=(ref6=data!=null?data.indID:void 0)!=null?ref6:function(){var results=[];for(var l=1;1<=n_ind?l<=n_ind:l>=n_ind;1<=n_ind?l++:l--){results.push(l)}return results}.apply(this);if(indID.length!==n_ind){d3panels.displayError("add_curves: data.indID.length ("+indID.length+") != data.y.length ("+n_ind+")")}group=(ref7=data!=null?data.group:void 0)!=null?ref7:function(){var results;results=[];for(i in y){results.push(1)}return results}();group=d3panels.expand2vector(group,n_ind);ngroup=d3.max(group);group=function(){var l,len,results;results=[];for(l=0,len=group.length;l<len;l++){g=group[l];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var l,len,results;results=[];for(l=0,len=group.length;l<len;l++){g=group[l];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_curves: group values out of range");console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==n_ind){d3panels.displayError("add_curves: data.group.length ("+group.length+") != data.y.length ("+n_ind+")")}for(i in y){if(x[i].length!==y[i].length){d3panels.displayError("add_curves: length(x) ("+x[i].length+") != length(y) ("+y[i].length+") for individual "+indID[i]+" (index "+(i+1)+")")}}linecolor=linecolor!=null?linecolor:d3panels.selectGroupColors(ngroup,"pastel");linecolor=d3panels.expand2vector(linecolor,ngroup);linecolorhilit=linecolorhilit!=null?linecolorhilit:d3panels.selectGroupColors(ngroup,"dark");linecolorhilit=d3panels.expand2vector(linecolorhilit,ngroup);svg=prevchart.svg();xscale=prevchart.xscale();yscale=prevchart.yscale();dataByPoint=[];for(i in y){dataByPoint.push(function(){var results;results=[];for(j in y[i]){if(x[i][j]!=null&&y[i][j]!=null){results.push({x:x[i][j],y:y[i][j]})}}return results}())}curvefunc=d3.line().x(function(d){return xscale(d.x)}).y(function(d){return yscale(d.y)});curveGroup=svg.append("g").attr("id","curves");curves=curveGroup.selectAll("empty").data(d3.range(n_ind)).enter().append("path").datum(function(d){return dataByPoint[d]}).attr("d",curvefunc).attr("class",function(d,i){return"path"+i}).attr("fill","none").attr("stroke",function(d,i){return linecolor[group[i]]}).attr("stroke-width",linewidth).on("mouseover.panel",function(d,i){return d3.select(this).attr("stroke",linecolorhilit[group[i]]).attr("stroke-width",linewidthhilit).raise()}).on("mouseout.panel",function(d,i){return d3.select(this).attr("stroke",linecolor[group[i]]).attr("stroke-width",linewidth)});indtip=d3panels.tooltip_create(d3.select("body"),curves,{tipclass:tipclass},function(d,i){return indID[i]});return prevchart.box().raise()};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.remove=function(){curveGroup.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.add_points=function(chartOpts){var chart,indtip,jitter,pointGroup,pointcolor,points,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,tipclass;if(chartOpts==null){chartOpts={}}pointcolor=(ref=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref:null;pointsize=(ref1=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref1:3;pointstroke=(ref2=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref2:"black";jitter=(ref3=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref3:"beeswarm";tipclass=(ref4=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref4:"tooltip";points=null;indtip=null;pointGroup=null;chart=function chart(prevchart,data){var force,g,group,i,indID,ngroup,ref5,ref6,ref7,scaledPoints,svg,ux,uy,x,xscale,xwid,y,yscale,ywid;if(data.x==null){d3panels.displayError("add_points: data.x is missing")}if(data.y==null){d3panels.displayError("add_points: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);if(x.length!==y.length){d3panels.displayError("add_points: x.length ("+x.length+") != y.length ("+y.length+")")}indID=(ref5=data!=null?data.indID:void 0)!=null?ref5:null;indID=indID!=null?indID:function(){var results=[];for(var j=1,ref6=x.length;1<=ref6?j<=ref6:j>=ref6;1<=ref6?j++:j--){results.push(j)}return results}.apply(this);if(indID.length!==x.length){d3panels.displayError("add_points: indID.length ("+indID.length+") != x.length ("+x.length+")")}group=(ref7=data!=null?data.group:void 0)!=null?ref7:function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){i=x[j];results.push(1)}return results}();group=d3panels.expand2vector(group,x.length);ngroup=d3.max(group);group=function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_points: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==x.length){d3panels.displayError("add_points: group.length ("+group.length+") != x.length ("+x.length+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}svg=prevchart.svg();xscale=prevchart.xscale();yscale=prevchart.yscale();pointGroup=svg.append("g").attr("id","points");points=pointGroup.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx",function(d,i){return xscale(x[i])}).attr("cy",function(d,i){return yscale(y[i])}).attr("class",function(d,i){return"pt"+i}).attr("r",pointsize).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width","1");indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]});if(prevchart.xNA()||prevchart.yNA()){if(jitter==="random"){xwid=20-pointsize-2;xwid=xwid<=2?2:xwid;ywid=20-pointsize-2;ywid=ywid<=2?2:ywid;ux=function(){var results;results=[];for(i in x){results.push((Math.random()-.5)*xwid)}return results}();uy=function(){var results;results=[];for(i in x){results.push((Math.random()-.5)*ywid)}return results}();points.attr("cx",function(d,i){if(x[i]!=null){return xscale(x[i])}return xscale(x[i])+ux[i]}).attr("cy",function(d,i){if(y[i]!=null){return yscale(y[i])}return yscale(y[i])+uy[i]})}else if(jitter==="beeswarm"){scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(x[i]),y:yscale(y[i]),xnull:x[i]==null,ynull:y[i]==null})}return results}();d3.range(scaledPoints.length).map(function(i){if(!scaledPoints[i].xnull){scaledPoints[i].fx=scaledPoints[i].x}if(!scaledPoints[i].ynull){return scaledPoints[i].fy=scaledPoints[i].y}});force=d3.forceSimulation(scaledPoints).force("x",d3.forceX(function(d){return d.x})).force("y",d3.forceY(function(d){return d.y})).force("collide",d3.forceCollide(pointsize*1.1)).stop();(function(){var results=[];for(var j=0;j<=30;j++){results.push(j)}return results}).apply(this).map(function(d){force.tick();return points.attr("cx",function(d,i){return scaledPoints[i].x}).attr("cy",function(d,i){return scaledPoints[i].y})})}else if(jitter!=="none"){d3panels.displayError('add_points: jitter should be "beeswarm", "random", or "none"')}}return prevchart.box().raise()};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.remove=function(){pointGroup.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.lodheatmap=function(chartOpts){var cellSelect,cells,celltip,chart,chrGap,colors,equalCells,height,hilitcolor,horizontal,margin,nullcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,width,xlab,xscale,ylab,ylim,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40};colors=(ref3=chartOpts!=null?chartOpts.colors:void 0)!=null?ref3:["slateblue","white","crimson"];nullcolor=(ref4=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref4:"#e6e6e6";xlab=(ref5=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref5:null;ylab=(ref6=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref6:"";ylim=(ref7=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref7:null;zlim=(ref8=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref8:null;zthresh=(ref9=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref9:null;horizontal=(ref10=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref10:false;hilitcolor=(ref11=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref11:"black";chrGap=(ref12=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref12:6;equalCells=(ref13=chartOpts!=null?chartOpts.equalCells:void 0)!=null?ref13:false;tipclass=(ref14=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref14:"tooltip";xscale=null;yscale=null;zscale=null;cells=null;celltip=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cellg,celltipfunc,chr,direction,i,j,k,l,len,len1,len2,len3,len4,lod,m,myframe,n,n_lod,n_pos,o,pos,ref15,ref16,ref17,ref18,ref19,x,xmid_scaled,y,ylabels,ymid,ymid_scaled,yv,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40});if(data.chr==null){d3panels.displayError("lodheatmap: data.chr is missing")}if(data.pos==null){d3panels.displayError("lodheatmap: data.pos is missing")}if(data.lod==null){d3panels.displayError("lodheatmap: data.lod is missing")}if(data.ycat!=null){data.y=function(){var results;results=[];for(i in data.ycat){results.push(i+1)}return results}()}if(data.y==null){data.ycat=function(){var results;results=[];for(i in data.lod[0]){results.push(i+1)}return results}();data.y=function(){var results;results=[];for(i in data.lod[0]){results.push(i+1)}return results}()}data.y=function(){var k,len,ref15,results;ref15=data.y;results=[];for(k=0,len=ref15.length;k<len;k++){yv=ref15[k];results.push(+yv)}return results}();n_pos=data.chr.length;n_lod=data.y.length;if(n_pos!==data.pos.length){d3panels.displayError("lodheatmap: data.pos.length ("+data.pos.length+") != data.chr.length ("+n_pos+")")}if(n_pos!==data.lod.length){d3panels.displayError("lodheatmap: data.lod.length ("+data.lod.length+") != data.chr.length ("+n_pos+")")}for(i in data.lod){if(data.lod[i].length!==data.y.length){d3panels.displayError("lodheatmap: data.lod["+i+"].length ("+data.lod[i].length+") != data.y.length ("+n_lod+")")}}if(data.poslabel!=null){if(data.poslabel.length!==n_pos){d3panels.displayError("lodheatmap: data.poslabel.length ("+data.poslabel.length+") != data.chr.length ("+n_pos+")")}}else{data.poslabel=function(){var results;results=[];for(i in data.chr){results.push(data.chr[i]+"@"+d3panels.formatAxis(data.pos)(data.pos[i]))}return results}()}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(equalCells){data.pos=[];ref15=data.chrname;for(k=0,len=ref15.length;k<len;k++){chr=ref15[k];data.pos=data.pos.concat(function(){var results;results=[];for(i in data.chr){if(data.chr[i]===chr){results.push(+i)}}return results}())}}data=d3panels.add_chrname_start_end(data);if(equalCells){chrGap=(width-margin.left-margin.right-2*data.chrname.length)/data.chr.length+2}data=d3panels.reorgLodData(data);ymid=d3panels.calc_midpoints(d3panels.pad_vector(data.y));chartOpts.ylim=ylim!=null?ylim:d3.extent(ymid);chartOpts.horizontal=horizontal;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.chrGap=chrGap;chartOpts.width=width;chartOpts.height=height;chartOpts.margin=margin;if(data.ycat!=null){chartOpts.yticks=data.y;chartOpts.yticklab=data.ycat}myframe=d3panels.chrpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();ylabels=myframe.ylabels();ymid_scaled=function(){var l,len1,results;results=[];for(l=0,len1=ymid.length;l<len1;l++){y=ymid[l];results.push(yscale(y))}return results}();xmid_scaled={};ref16=data.chrname;for(l=0,len1=ref16.length;l<len1;l++){chr=ref16[l];xmid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref17,results;ref17=data.posByChr[chr];results=[];for(m=0,len2=ref17.length;m<len2;m++){x=ref17[m];results.push(xscale[chr](x))}return results}(),(chrGap-2)/2))}zmin=d3panels.matrixMin(data.lod);zmax=d3panels.matrixMaxAbs(data.lod);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("lodheatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;cells=[];ref17=data.chrname;for(m=0,len2=ref17.length;m<len2;m++){chr=ref17[m];ref18=data.posByChr[chr];for(i=n=0,len3=ref18.length;n<len3;i=++n){pos=ref18[i];ref19=data.lodByChr[chr][i];for(j=o=0,len4=ref19.length;o<len4;j=++o){lod=ref19[j];if(Math.abs(lod)>=zthresh){cells.push({lod:lod,chr:chr,pos:pos,poslabel:data.poslabelByChr[chr][i],posindex:+i,lodindex:+j})}}}}d3panels.calc_chrcell_rect(cells,xmid_scaled,ymid_scaled);cellg=svg.append("g").attr("id","cells");cellSelect=cellg.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){if(horizontal){return d.top}return d.left}).attr("y",function(d){if(horizontal){return d.left}return d.top}).attr("width",function(d){if(horizontal){return d.height}return d.width}).attr("height",function(d){if(horizontal){return d.width}return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.lod!=null){return zscale(d.lod)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").attr("shape-rendering","crispEdges").on("mouseover",function(d){d3.select(this).attr("stroke",hilitcolor).raise();if(data.ycat!=null){return svg.select("text#ylab"+d.lodindex).attr("opacity",1)}}).on("mouseout",function(d){d3.select(this).attr("stroke","none");if(data.ycat!=null){return svg.select("text#ylab"+d.lodindex).attr("opacity",0)}});if(data.ycat!=null){svg.selectAll("g#ylines").remove();ylabels.attr("opacity",0).attr("id",function(d,i){return"ylab"+i})}celltipfunc=function celltipfunc(d){var lodlabel,z;z=d3.format(".2f")(Math.abs(d.lod));lodlabel=data.ycat!=null?data.ycat[d.lodindex]:d3panels.formatAxis(data.y)(data.y[d.lodindex]);if(horizontal){return lodlabel+", "+d.poslabel+" → "+z}return d.poslabel+", "+lodlabel+" → "+z};direction=horizontal?"north":"east";celltip=d3panels.tooltip_create(d3.select("body"),cellg.selectAll("rect"),{direction:direction,tipclass:tipclass},celltipfunc);return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return yscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.mapchart=function(chartOpts){var chart,horizontal,linecolor,linecolorhilit,linewidth,markerSelect,martip,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,shiftStart,svg,tickwidth,tipclass,v_over_h,xlab,xlineOpts,xscale,ylab,yscale;if(chartOpts==null){chartOpts={}}tickwidth=(ref=chartOpts!=null?chartOpts.tickwidth:void 0)!=null?ref:10;linecolor=(ref1=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref1:"slateblue";linecolorhilit=(ref2=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref2:"Orchid";linewidth=(ref3=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref3:3;xlab=(ref4=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref4:"Chromosome";ylab=(ref5=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref5:"Position (cM)";xlineOpts=(ref6=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref6:{color:"#cdcdcd",width:5};horizontal=(ref7=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref7:false;v_over_h=(ref8=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref8:horizontal;shiftStart=(ref9=chartOpts!=null?chartOpts.shiftStart:void 0)!=null?ref9:false;tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;markerSelect=null;martip=null;svg=null;chart=function chart(selection,data){var chr,chrscale,direction,extentByChr,i,j,k,l,len,len1,markerpos,markers,minpos,myframe,n_chr,n_pos,pos,ref11,ref12,these_index,these_pos,tipfunc,x,xlim,xticklab,xticks,ylim;xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"#cdcdcd",width:5});if(data.chr==null){d3panels.displayError("mapchart: data.chr is missing")}if(data.pos==null){d3panels.displayError("mapchart: data.pos is missing")}if(data.marker==null){d3panels.displayError("mapchart: data.marker is missing")}n_pos=data.pos.length;if(data.chr.length!==n_pos){d3panels.displayError("mapchart: data.chr.length ("+data.chr.length+") != data.pos.length ("+n_pos+")")}if(data.marker.length!==n_pos){d3panels.displayError("mapchart: data.marker.length ("+data.marker.length+") != data.pos.length ("+n_pos+")")}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);data.adjpos=data.pos.slice(0);if(shiftStart){ref11=data.chrname;for(k=0,len=ref11.length;k<len;k++){chr=ref11[k];these_pos=function(){var results;results=[];for(i in data.pos){if(data.chr[i]===chr){results.push(data.pos[i])}}return results}();these_index=function(){var results;results=[];for(i in data.pos){if(data.chr[i]===chr){results.push(i)}}return results}();minpos=d3.min(these_pos);these_pos=function(){var l,len1,results;results=[];for(l=0,len1=these_pos.length;l<len1;l++){x=these_pos[l];results.push(x-minpos)}return results}();for(j in these_pos){data.adjpos[these_index[j]]=these_pos[j]}}}extentByChr={};ref12=data.chrname;for(l=0,len1=ref12.length;l<len1;l++){chr=ref12[l];pos=function(){var results;results=[];for(i in data.adjpos){if(data.chr[i]===chr){results.push(data.adjpos[i])}}return results}();extentByChr[chr]=d3.extent(pos)}ylim=ylim!=null?ylim:d3.extent(data.adjpos);n_chr=data.chrname.length;xlim=[.5,n_chr+.5];xticks=function(){var len2,m,ref13,results;ref13=d3.range(n_chr);results=[];for(m=0,len2=ref13.length;m<len2;m++){i=ref13[m];results.push(i+1)}return results}();xticklab=data.chrname;chartOpts.xNA=false;chartOpts.yNA=false;if(horizontal){chartOpts.xlim=ylim;chartOpts.ylim=xlim.reverse();chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xticks=chartOpts.yticks;chartOpts.yticks=xticks;chartOpts.nxticks=chartOpts.nyticks;chartOpts.xticklab=chartOpts.yticklab;chartOpts.yticklab=xticklab;chartOpts.v_over_h=v_over_h}else{chartOpts.xlim=xlim;chartOpts.ylim=ylim.reverse();chartOpts.xlineOpts=xlineOpts;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.xticks=xticks;chartOpts.xticklab=xticklab;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();chrscale=function chrscale(chr){var chrpos;chrpos=data.chrname.indexOf(chr)+1;if(!horizontal){return xscale(chrpos)}return yscale(chrpos)};svg.append("g").attr("id","chromosomes").selectAll("empty").data(data.chrname).enter().append("line").attr("x1",function(d){if(horizontal){return xscale(extentByChr[d][0])}return chrscale(d)}).attr("x2",function(d){if(horizontal){return xscale(extentByChr[d][1])}return chrscale(d)}).attr("y1",function(d){if(horizontal){return chrscale(d)}return yscale(extentByChr[d][0])}).attr("y2",function(d){if(horizontal){return chrscale(d)}return yscale(extentByChr[d][1])}).attr("fill","none").attr("stroke",linecolor).attr("stroke-width",linewidth).attr("shape-rendering","crispEdges").style("pointer-events","none");markerpos={};for(i in data.marker){markerpos[data.marker[i]]=d3.format(".1f")(data.pos[i])}markers=svg.append("g").attr("id","points");markerSelect=markers.selectAll("empty").data(data.marker).enter().append("line").attr("x1",function(d,i){if(horizontal){return xscale(data.adjpos[i])}return chrscale(data.chr[i])-tickwidth}).attr("x2",function(d,i){if(horizontal){return xscale(data.adjpos[i])}return chrscale(data.chr[i])+tickwidth}).attr("y1",function(d,i){if(horizontal){return chrscale(data.chr[i])-tickwidth}return yscale(data.adjpos[i])}).attr("y2",function(d,i){if(horizontal){return chrscale(data.chr[i])+tickwidth}return yscale(data.adjpos[i])}).attr("id",function(d){return d}).attr("fill","none").attr("stroke",linecolor).attr("stroke-width",linewidth).attr("shape-rendering","crispEdges").on("mouseover.paneltip",function(d){return d3.select(this).attr("stroke",linecolorhilit)}).on("mouseout.paneltip",function(){return d3.select(this).attr("stroke",linecolor)});tipfunc=function tipfunc(d,i){return d+" ("+markerpos[d]+")"};direction=horizontal?"north":"east";martip=d3panels.tooltip_create(d3.select("body"),markers.selectAll("line"),{direction:direction,tipclass:tipclass},tipfunc);return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.markerSelect=function(){return markerSelect};chart.martip=function(){return martip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(martip);return null};return chart};"use strict";d3panels.scatterplot=function(chartOpts){var chart,indtip,jitter,pointcolor,points,pointsize,pointstroke,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,xNA,xNA_size,xlim,xscale,yNA,yNA_size,ylim,yscale;if(chartOpts==null){chartOpts={}}xNA=(ref=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref:{handle:true,force:false};yNA=(ref1=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref1:{handle:true,force:false};xNA_size=(ref2=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref2:{width:20,gap:10};yNA_size=(ref3=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref3:{width:20,gap:10};xlim=(ref4=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref4:null;ylim=(ref5=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref5:null;pointcolor=(ref6=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref6:null;pointstroke=(ref7=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref7:"black";pointsize=(ref8=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref8:3;jitter=(ref9=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref9:"beeswarm";tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;xNA=xNA;yNA=yNA;points=null;indtip=null;svg=null;chart=function chart(selection,data){var addpts,myframe,x,y;xNA=d3panels.check_listarg_v_default(xNA,{handle:true,force:false});yNA=d3panels.check_listarg_v_default(yNA,{handle:true,force:false});xNA_size=d3panels.check_listarg_v_default(xNA,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA,{width:20,gap:10});if(data.x==null){d3panels.displayError("scatterplot: data.x is missing")}if(data.y==null){d3panels.displayError("scatterplot: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);if(x.length!==y.length){d3panels.displayError("scatterplot: x.length ("+x.length+") != y.length ("+y.length+")")}xNA.handle=xNA.force||xNA.handle&&!x.every(function(v){return v!=null});yNA.handle=yNA.force||yNA.handle&&!y.every(function(v){return v!=null});xlim=xlim!=null?xlim:d3panels.pad_ylim(d3.extent(x));ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(y));chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=xNA.handle;chartOpts.yNA=yNA.handle;chartOpts.xNA_size=xNA_size;chartOpts.yNA_size=yNA_size;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();addpts=d3panels.add_points({pointcolor:pointcolor,pointstroke:pointstroke,pointsize:pointsize,jitter:jitter,tipclass:tipclass});addpts(myframe,{x:x,y:y,indID:data.indID,group:data.group});points=addpts.points();return indtip=addpts.indtip()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xNA=function(){return xNA.handle};chart.yNA=function(){return yNA.handle};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.trichart=function(chartOpts){var boxcolor,boxwidth,chart,gridcolor,gridlines,gridwidth,height,indtip,labelpos,labels,margin,pointcolor,points,pointsize,pointstroke,pscale,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,title,titlepos,width,xscale,yscale;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:600;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:520;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:60,bottom:10};labelpos=(ref3=chartOpts!=null?chartOpts.labelpos:void 0)!=null?ref3:10;titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";labels=(ref6=chartOpts!=null?chartOpts.labels:void 0)!=null?ref6:["(1,0,0)","(0,1,0)","(0,0,1)"];rectcolor=(ref7=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref7:"#e6e6e6";boxcolor=(ref8=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref8:"black";boxwidth=(ref9=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref9:2;pointcolor=(ref10=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref10:null;pointstroke=(ref11=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref11:"black";pointsize=(ref12=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref12:3;gridlines=(ref13=chartOpts!=null?chartOpts.gridlines:void 0)!=null?ref13:0;gridcolor=(ref14=chartOpts!=null?chartOpts.gridcolor:void 0)!=null?ref14:"white";gridwidth=(ref15=chartOpts!=null?chartOpts.gridwidth:void 0)!=null?ref15:1;tipclass=(ref16=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref16:"tooltip";xscale=null;yscale=null;pscale=null;points=null;indtip=null;svg=null;chart=function chart(selection,data){var d,first,flag_length_not_3,flag_out_of_range,flag_sum_not_1,frame,framefunc,g,gr,group,i,indID,indices,j,len,n,ngroup,p,p1,p2,p3,p4,plot_height,plot_width,ref17,ref18,second,sum,v,vertices,vv,xlim,xy,ylim;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:60,bottom:10});if(data.p==null){d3panels.displayError("trichart: data.p is missing")}p=function(){var j,len,ref17,results;ref17=data.p;results=[];for(j=0,len=ref17.length;j<len;j++){v=ref17[j];results.push(d3panels.missing2null(v))}return results}();flag_length_not_3=false;flag_sum_not_1=false;flag_out_of_range=false;for(j=0,len=p.length;j<len;j++){v=p[j];if(v.length!==3){flag_length_not_3=true}sum=d3panels.sumArray(v);if(d3panels.abs(sum-1)>1e-6){flag_sum_not_1}if(d3panels.sumArray(function(){var k,len1,results;results=[];for(k=0,len1=v.length;k<len1;k++){vv=v[k];results.push(vv<0||vv>1)}return results}())>0){flag_out_of_range=true}}if(flag_length_not_3){d3panels.displayError("trichart: points not all of length 3")}if(flag_sum_not_1){d3panels.displayError("trichart: points not all summing to 1")}if(flag_out_of_range){d3panels.displayError("trichart: points not all in [0,1]")}n=p.length;indID=(ref17=data!=null?data.indID:void 0)!=null?ref17:function(){var results;results=[];for(i in p){results.push(+i+1)}return results}();if(indID.length!==n){d3panels.displayError("trichart: data.indID.length ("+indID.length+") != data.p.length ("+n+")")}group=(ref18=data!=null?data.group:void 0)!=null?ref18:function(){var results;results=[];for(i in p){results.push(1)}return results}();group=d3panels.expand2vector(group,n);ngroup=d3.max(group);group=function(){var k,len1,results;results=[];for(k=0,len1=group.length;k<len1;k++){g=group[k];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var k,len1,results;results=[];for(k=0,len1=group.length;k<len1;k++){g=group[k];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_points: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==n){d3panels.displayError("trichart: data.group.length ("+group.length+") != data.p.length ("+n+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}xlim=[0,2/Math.sqrt(3)];ylim=[0,1];plot_height=height-margin.top-margin.bottom;plot_width=width-margin.left-margin.right;if(plot_height>plot_width/xlim[1]){d=plot_height-plot_width/xlim[1];margin.top+=d/2;margin.bottom+=d/2;plot_height-=d}else{d=plot_width-plot_height*xlim[1];margin.left+=d/2;margin.right+=d/2;plot_width-=d}xscale=d3.scaleLinear().domain(xlim).range([margin.left,margin.left+plot_width]);yscale=d3.scaleLinear().domain(ylim).range([plot_height+margin.top,margin.top]);pscale=function pscale(p){sum=d3panels.sumArray(p);return{x:xscale((p[0]*2+p[1])/Math.sqrt(3)/sum),y:yscale(p[1]/sum)}};xy=function(){var k,len1,results;results=[];for(k=0,len1=p.length;k<len1;k++){v=p[k];results.push({x:(v[0]*2+v[1])/Math.sqrt(3),y:v[1]})}return results}();svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");frame=svg.append("g").attr("id","frame");vertices=[{x:xlim[0],y:ylim[0]},{x:xlim[1]/2,y:ylim[1]},{x:xlim[1],y:ylim[0]}];framefunc=d3.line().x(function(d){return xscale(vertices[d].x)}).y(function(d){return yscale(vertices[d].y)});indices=function(){var results;results=[];for(i in vertices){results.push(+i)}return results}().concat(0);frame.append("path").datum(indices).attr("d",framefunc).attr("fill",rectcolor).attr("stroke",boxcolor).attr("stroke-width",boxwidth);if(gridlines>0){gr=function(){var results=[];for(var k=1;1<=gridlines?k<=gridlines:k>=gridlines;1<=gridlines?k++:k--){results.push(k)}return results}.apply(this).map(function(i){return i/(gridlines+1)});p1=gr.map(function(x){return[x,0,1-x]});p2=gr.map(function(x){return[x,1-x,0]});p3=gr.map(function(x){return[0,1-x,x]});p4=gr.map(function(x){return[1-x,0,x]});first=p1.concat(p2).concat(p3);second=p2.concat(p3).concat(p4);g=frame.append("g").attr("class","gridlines").selectAll("empty").data(first).enter().append("line").attr("x1",function(d){return pscale(d).x}).attr("y1",function(d){return pscale(d).y}).attr("x2",function(d,i){return pscale(second[i]).x}).attr("y2",function(d,i){return pscale(second[i]).y}).attr("stroke",gridcolor).attr("stroke-width",gridwidth).attr("shape-rendering","crispEdges").style("pointer-events","none").attr("fill","none");frame.append("path").datum(indices).attr("d",framefunc).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth)}frame.append("g").attr("class","title").append("text").text(title).attr("x",plot_width/2+margin.left).attr("y",margin.top-titlepos);frame.append("g").attr("id","labels").selectAll("empty").data(vertices).enter().append("text").attr("x",function(d,i){return xscale(d.x)+[-1,+1,+1][i]*labelpos}).attr("y",function(d){return yscale(d.y)}).style("dominant-baseline","middle").style("text-anchor",function(d,i){return["end","start","start"][i]}).text(function(d,i){return labels[i]});points=svg.append("g").attr("id","points").selectAll("empty").data(p).enter().append("circle").attr("r",pointsize).attr("cx",function(d){return pscale(d).x}).attr("cy",function(d){return pscale(d).y}).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width",1);return indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]})};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.pscale=function(){return pscale};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.histchart=function(chartOpts){var chart,curves,density,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,tipclass,xlab,xlim,xscale,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xlim=(ref=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref:null;ylim=(ref1=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref1:null;xlab=(ref2=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref2:"";ylab=(ref3=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref3:"";rotate_ylab=(ref4=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref4:null;linecolor=(ref5=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref5:null;linecolorhilit=(ref6=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref6:null;linewidth=(ref7=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref7:2;linewidthhilit=(ref8=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref8:2;density=(ref9=chartOpts!=null?chartOpts.density:void 0)!=null?ref9:true;tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;curves=null;indtip=null;svg=null;chart=function chart(selection,data){var add_curves,breaks,brlim,d,f,freq,i,j,k,l,len,len1,maxn,maxpos,myframe,n_ind,p,path_data,path_x,path_y,pt,ref11,x,xv,xx;if(data.x==null){d3panels.displayError("histchart: data.x is missing")}x=data.x;data.group=function(){var results;results=[];for(i in x){results.push(+i+1)}return results}();n_ind=x.length;if(data.breaks==null){maxn=d3.max(function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];results.push(xv.length)}return results}());data.breaks=[2*Math.ceil(Math.sqrt(maxn)+1)]}breaks=d3panels.forceAsArray(data.breaks);xlim=xlim!=null?xlim:d3panels.matrixExtent(x);if(breaks.length===1){breaks=d3panels.calc_breaks(breaks[0],xlim[0],xlim[1])}brlim=[d3.min(breaks)-1e-6,d3.max(breaks)+1e-6];x=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xx=x[k];results.push(function(){var l,len1,results1;results1=[];for(l=0,len1=xx.length;l<len1;l++){xv=xx[l];if(xv>=brlim[0]&xv<=brlim[1]){results1.push(xv)}}return results1}())}return results}();freq=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];results.push(d3panels.calc_freq(xv,breaks,!density))}return results}();maxpos=[];for(k=0,len=freq.length;k<len;k++){f=freq[k];pt={x:breaks[1],y:f[0]};ref11=d3.range(f.length);for(l=0,len1=ref11.length;l<len1;l++){j=ref11[l];if(f[j]>pt.y){pt.y=f[j];pt.x=breaks[j+1]}}maxpos.push(pt)}ylim=ylim!=null?ylim:[0,d3panels.matrixMax(freq)*1.05];chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.rotate_ylab=rotate_ylab;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();path_data=function(){var len2,m,results;results=[];for(m=0,len2=freq.length;m<len2;m++){f=freq[m];results.push(d3panels.calc_hist_path(f,breaks))}return results}();path_x=function(){var len2,m,results;results=[];for(m=0,len2=path_data.length;m<len2;m++){p=path_data[m];results.push(function(){var len3,n,results1;results1=[];for(n=0,len3=p.length;n<len3;n++){d=p[n];results1.push(d.x)}return results1}())}return results}();path_y=function(){var len2,m,results;results=[];for(m=0,len2=path_data.length;m<len2;m++){p=path_data[m];results.push(function(){var len3,n,results1;results1=[];for(n=0,len3=p.length;n<len3;n++){d=p[n];results1.push(d.y)}return results1}())}return results}();add_curves=d3panels.add_curves({linecolor:linecolor,linecolorhilit:linecolorhilit,linewidth:linewidth,linewidthhilit:linewidthhilit,tipclass:tipclass});add_curves(myframe,{x:path_x,y:path_y,indID:data.indID,group:data.group});curves=add_curves.curves();indtip=add_curves.indtip();return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_dstroy(indtip);return null};return chart};"use strict";d3panels.slider=function(chartOpts){var buttoncolor,buttondotcolor,buttondotsize,buttonround,buttonsize,buttonstroke,_chart,height,margin,nticks,rectcolor,rectheight,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,slider_svg,stopindex,textsize,tickgap,tickheight,ticks,ticks_at_stops,value,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:80;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:25,right:25,inner:0,top:40,bottom:40};rectheight=(ref3=chartOpts!=null?chartOpts.rectheight:void 0)!=null?ref3:10;rectcolor=(ref4=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref4:"#ccc";buttonsize=(ref5=chartOpts!=null?chartOpts.buttonsize:void 0)!=null?ref5:rectheight*2;buttoncolor=(ref6=chartOpts!=null?chartOpts.buttoncolor:void 0)!=null?ref6:"#eee";buttonstroke=(ref7=chartOpts!=null?chartOpts.buttonstroke:void 0)!=null?ref7:"black";buttonround=(ref8=chartOpts!=null?chartOpts.buttonround:void 0)!=null?ref8:buttonsize*.2;buttondotcolor=(ref9=chartOpts!=null?chartOpts.buttondotcolor:void 0)!=null?ref9:"slateblue";buttondotsize=(ref10=chartOpts!=null?chartOpts.buttondotsize:void 0)!=null?ref10:buttonsize/4;tickheight=(ref11=chartOpts!=null?chartOpts.tickheight:void 0)!=null?ref11:10;tickgap=(ref12=chartOpts!=null?chartOpts.tickgap:void 0)!=null?ref12:tickheight/2;textsize=(ref13=chartOpts!=null?chartOpts.textsize:void 0)!=null?ref13:14;nticks=(ref14=chartOpts!=null?chartOpts.nticks:void 0)!=null?ref14:5;ticks=(ref15=chartOpts!=null?chartOpts.ticks:void 0)!=null?ref15:null;ticks_at_stops=(ref16=chartOpts!=null?chartOpts.ticks_at_stops:void 0)!=null?ref16:true;value=0;stopindex=0;slider_svg=null;_chart=function chart(selection,callback,range,stops,initial_value){var button,clamp_pixels,dragged,end_drag,xcscale,xscale;margin=d3panels.check_listarg_v_default(margin,{left:25,right:25,inner:0,top:40,bottom:40});margin.left+=margin.inner;margin.right+=margin.inner;if(range==null){range=[margin.left,width-margin.right]}if(margin.top!=null&&margin.top+margin.bottom>0){margin.top=height*margin.top/(margin.top+margin.bottom)}else{margin.top=height/2}if(initial_value!=null){value=initial_value;if(value<range[0]){value=range[0]}if(value>range[1]){value=range[1]}if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops)}if(stops!=null){value=stops[stopindex]}}else{if(stops!=null){stopindex=Math.floor(Math.random()*stops.length);value=stops[stopindex]}else{value=(range[1]-range[0])*Math.random()+range[0]}}slider_svg=selection.insert("svg").attr("height",height).attr("width",width);xcscale=d3.scaleLinear().range([margin.left,width-margin.right]).domain(range).clamp(true);xscale=function xscale(d){if(stops!=null){return xcscale(stops[d3panels.index_of_nearest(d,stops)])}return xcscale(d)};clamp_pixels=function clamp_pixels(pixels,interval){if(pixels<interval[0]){return interval[0]}if(pixels>interval[1]){return interval[1]}return pixels};slider_svg.insert("rect").attr("x",margin.left).attr("y",margin.top-rectheight/2).attr("rx",rectheight*.3).attr("ry",rectheight*.3).attr("width",width-margin.left-margin.right).attr("height",rectheight).attr("fill",rectcolor);if(ticks==null){ticks=xcscale.ticks(nticks)}slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top+rectheight/2+tickgap).attr("y2",margin.top+rectheight/2+tickgap+tickheight).attr("stroke","black").attr("shape-rendering","crispEdges");slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x",function(d){return xcscale(d)}).attr("y",margin.top+rectheight/2+tickgap*2+tickheight).text(function(d){return d}).style("font-size",textsize).style("dominant-baseline","hanging").style("text-anchor","middle").style("pointer-events","none").style("-webkit-user-select","none").style("-moz-user-select","none").style("-ms-user-select","none");if(stops!=null&&ticks_at_stops){slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top-rectheight/2-tickgap).attr("y2",margin.top-rectheight/2-tickgap-tickheight).attr("stroke","black").attr("shape-rendering","crispEdges")}button=slider_svg.insert("g").attr("id","button").attr("transform","translate("+xscale(value)+",0)");button.insert("rect").attr("x",-buttonsize/2).attr("y",margin.top-buttonsize/2).attr("height",buttonsize).attr("width",buttonsize).attr("rx",buttonround).attr("ry",buttonround).attr("stroke",buttonstroke).attr("stroke-width",2).attr("fill",buttoncolor);button.insert("circle").attr("cx",0).attr("cy",margin.top).attr("r",buttondotsize).attr("fill",buttondotcolor);dragged=function dragged(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value=xcscale.invert(clamped_pixels);d3.select(this).attr("transform","translate("+xcscale(value)+",0)");if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops);value=stops[stopindex]}if(callback!=null){return callback(_chart)}};end_drag=function end_drag(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value=xcscale.invert(clamped_pixels);if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops);value=stops[stopindex]}if(callback!=null){callback(_chart)}return d3.select(this).attr("transform","translate("+xcscale(value)+",0)")};button.call(d3.drag().on("drag",dragged).on("end",end_drag));if(callback!=null){return callback(_chart)}};_chart.value=function(){return value};_chart.stopindex=function(){return stopindex};_chart.remove=function(){return slider_svg.remove()};return _chart};"use strict";d3panels.double_slider=function(chartOpts){var buttoncolor,buttondotcolor,buttondotsize,buttonround,buttonsize,buttonstroke,_chart,height,margin,nticks,rectcolor,rectheight,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,slider_svg,stopindex,textsize,tickgap,tickheight,ticks,ticks_at_stops,value,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:80;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:25,right:25,inner:0,top:40,bottom:40};rectheight=(ref3=chartOpts!=null?chartOpts.rectheight:void 0)!=null?ref3:10;rectcolor=(ref4=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref4:"#ccc";buttonsize=(ref5=chartOpts!=null?chartOpts.buttonsize:void 0)!=null?ref5:rectheight*2;buttoncolor=(ref6=chartOpts!=null?chartOpts.buttoncolor:void 0)!=null?ref6:"#eee";buttonstroke=(ref7=chartOpts!=null?chartOpts.buttonstroke:void 0)!=null?ref7:"black";buttonround=(ref8=chartOpts!=null?chartOpts.buttonround:void 0)!=null?ref8:buttonsize*.2;buttondotcolor=(ref9=chartOpts!=null?chartOpts.buttondotcolor:void 0)!=null?ref9:["slateblue","orchid"];buttondotsize=(ref10=chartOpts!=null?chartOpts.buttondotsize:void 0)!=null?ref10:buttonsize/4;tickheight=(ref11=chartOpts!=null?chartOpts.tickheight:void 0)!=null?ref11:10;tickgap=(ref12=chartOpts!=null?chartOpts.tickgap:void 0)!=null?ref12:tickheight/2;textsize=(ref13=chartOpts!=null?chartOpts.textsize:void 0)!=null?ref13:14;nticks=(ref14=chartOpts!=null?chartOpts.nticks:void 0)!=null?ref14:5;ticks=(ref15=chartOpts!=null?chartOpts.ticks:void 0)!=null?ref15:null;ticks_at_stops=(ref16=chartOpts!=null?chartOpts.ticks_at_stops:void 0)!=null?ref16:true;value=[0,0];stopindex=[0,0];slider_svg=null;if(!Array.isArray(buttoncolor)){buttoncolor=[buttoncolor,buttoncolor]}if(!Array.isArray(buttonstroke)){buttonstroke=[buttonstroke,buttonstroke]}if(!Array.isArray(buttondotcolor)){buttondotcolor=[buttondotcolor,buttondotcolor]}_chart=function chart(selection,callback1,callback2,range,stops,initial_value){var buttons,callbacks,clamp_pixels,dragged,end_drag,start_drag,xcscale,xscale;margin=d3panels.check_listarg_v_default(margin,{left:25,right:25,inner:0,top:40,bottom:40});callbacks=[callback1,callback2];margin.left+=margin.inner;margin.right+=margin.inner;if(range==null){range=[margin.left,width-margin.right]}if(margin.top!=null&&margin.top+margin.bottom>0){margin.top=height*margin.top/(margin.top+margin.bottom)}else{margin.top=height/2}if(initial_value!=null){value=initial_value.map(function(d){if(d<range[0]){return range[0]}if(d>range[1]){return range[1]}return d});if(stops!=null){stopindex=value.map(function(d){return d3panels.index_of_nearest(d,stops)})}if(stops!=null){value=stopindex.map(function(i){return stops[i]})}}else{if(stops!=null){stopindex=[0,1].map(function(i){return Math.floor(Math.random()*stops.length)});value=stopindex.map(function(i){return stops[i]})}else{value=[0,1].map(function(i){return(range[1]-range[0])*Math.random()+range[0]})}}slider_svg=selection.insert("svg").attr("height",height).attr("width",width);xcscale=d3.scaleLinear().range([margin.left,width-margin.right]).domain(range).clamp(true);xscale=function xscale(d){if(stops!=null){return xcscale(stops[d3panels.index_of_nearest(d,stops)])}return xcscale(d)};clamp_pixels=function clamp_pixels(pixels,interval){if(pixels<interval[0]){return interval[0]}if(pixels>interval[1]){return interval[1]}return pixels};slider_svg.insert("rect").attr("x",margin.left).attr("y",margin.top-rectheight/2).attr("rx",rectheight*.3).attr("ry",rectheight*.3).attr("width",width-margin.left-margin.right).attr("height",rectheight).attr("fill",rectcolor);if(ticks==null){ticks=xcscale.ticks(nticks)}slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top+rectheight/2+tickgap).attr("y2",margin.top+rectheight/2+tickgap+tickheight).attr("stroke","black").attr("shape-rendering","crispEdges");slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x",function(d){return xcscale(d)}).attr("y",margin.top+rectheight/2+tickgap*2+tickheight).text(function(d){return d}).style("font-size",textsize).style("dominant-baseline","hanging").style("text-anchor","middle").style("pointer-events","none").style("-webkit-user-select","none").style("-moz-user-select","none").style("-ms-user-select","none");if(stops!=null&&ticks_at_stops){slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top-rectheight/2-tickgap).attr("y2",margin.top-rectheight/2-tickgap-tickheight).attr("stroke","black").attr("shape-rendering","crispEdges")}buttons=[0,1].map(function(i){return slider_svg.insert("g").attr("id","button"+(i+1)).attr("transform",function(d){return"translate("+xscale(value[i])+",0)"})});[0,1].map(function(i){buttons[i].insert("rect").attr("x",-buttonsize/2).attr("y",margin.top-buttonsize/2).attr("height",buttonsize).attr("width",buttonsize).attr("rx",buttonround).attr("ry",buttonround).attr("stroke",buttonstroke[i]).attr("stroke-width",2).attr("fill",buttoncolor[i]);return buttons[i].insert("circle").attr("cx",0).attr("cy",margin.top).attr("r",buttondotsize).attr("fill",buttondotcolor[i])});start_drag=function start_drag(i){return function(d){return buttons[i].raise()}};dragged=function dragged(i){return function(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value[i]=xcscale.invert(clamped_pixels);d3.select(this).attr("transform","translate("+xcscale(value[i])+",0)");if(stops!=null){stopindex[i]=d3panels.index_of_nearest(value[i],stops);value[i]=stops[stopindex[i]]}if(callbacks[i]!=null){return callbacks[i](_chart)}}};end_drag=function end_drag(i){return function(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value[i]=xcscale.invert(clamped_pixels);if(stops!=null){stopindex[i]=d3panels.index_of_nearest(value[i],stops);value[i]=stops[stopindex[i]]}if(callbacks[i]!=null){callbacks[i](_chart)}return d3.select(this).attr("transform","translate("+xcscale(value[i])+",0)")}};return[0,1].map(function(i){buttons[i].call(d3.drag().on("start",start_drag(i)).on("drag",dragged(i)).on("end",end_drag(i)));if(callbacks[i]!=null){return callbacks[i](_chart)}})};_chart.value=function(){return value};_chart.stopindex=function(){return stopindex};_chart.remove=function(){return slider_svg.remove()};return _chart};"use strict";d3panels.tooltip_create=function(selection,objects,options,tooltip_func){var direction,fill,fontcolor,fontsize,in_duration,out_duration,pad,ref,ref1,ref2,ref3,ref4,tipclass,tipdiv,tipgroup,triChar,tridiv;tipclass=(ref=options!=null?options.tipclass:void 0)!=null?ref:"d3panels-tooltip";direction=(ref1=options!=null?options.direction:void 0)!=null?ref1:"east";out_duration=(ref2=options!=null?options.out_duration:void 0)!=null?ref2:1e3;in_duration=(ref3=options!=null?options.in_duration:void 0)!=null?ref3:0;pad=(ref4=options!=null?options.pad:void 0)!=null?ref4:8;fill=options!=null?options.fill:void 0;fontcolor=options!=null?options.fontcolor:void 0;fontsize=options!=null?options.fontsize:void 0;tipgroup=selection.append("g").attr("class","d3panels-tooltip "+tipclass).style("opacity",0).datum({direction:direction,pad:pad});tipdiv=tipgroup.append("div").attr("class","d3panels-tooltip "+tipclass);if(direction==="east"){triChar="â—€"}else if(direction==="west"){triChar="â–¶"}else if(direction==="north"){triChar="â–¼"}else if(direction==="south"){triChar="â–²"}else{d3panels.displayError("tooltip_create: invalid direction ("+direction+")")}tridiv=tipgroup.append("div").attr("class","d3panels-tooltip-tri "+tipclass).html(triChar);if(fill!=null){tipdiv.style("background",fill)}if(fontcolor!=null){tipdiv.style("color",fontcolor)}if(fontsize!=null){tipdiv.style("font-size",fontsize+"px")}if(fill!=null){tridiv.style("color",fill)}if(fontsize!=null){tridiv.style("font-size",fontsize+"px")}objects.on("mouseover."+tipclass,function(d,i){var mouseX,mouseY;mouseX=d3.event.pageX*1;mouseY=d3.event.pageY*1;tipdiv.html(tooltip_func(d,i));d3panels.tooltip_move(tipgroup,mouseX,mouseY);return d3panels.tooltip_show(tipgroup,in_duration)});objects.on("mouseout."+tipclass,function(d){return d3panels.tooltip_hide(tipgroup,out_duration)});return tipgroup};d3panels.tooltip_move=function(tipgroup,x,y){var direction,divpad,fontsize,pad,posX,posY,shiftX,shiftY,tipbox_height,tipbox_width,tipdiv,triX,triY,tridiv;tipdiv=tipgroup.select("div.d3panels-tooltip");tridiv=tipgroup.select("div.d3panels-tooltip-tri");tipbox_height=tipdiv.node().getBoundingClientRect().height*1;tipbox_width=tipdiv.node().getBoundingClientRect().width*1;fontsize=tridiv.style("font-size").replace("px","")*1;pad=tipgroup.datum().pad*1+fontsize;direction=tipgroup.datum().direction;shiftX=shiftY=0;if(direction==="east"){posX=x+pad;posY=y-tipbox_height/2;divpad=tipdiv.style("padding-left").replace("px","")*1;shiftX=-fontsize-divpad;shiftY=tipbox_height/2-fontsize/2}else if(direction==="west"){posX=x-tipbox_width*1-pad;posY=y-tipbox_height/2;divpad=tipdiv.style("padding-right").replace("px","")*1;shiftX=tipbox_width-fontsize+divpad;shiftY=tipbox_height/2-fontsize/2}else if(direction==="north"){posX=x-tipbox_width/2;posY=y-tipbox_height-pad;divpad=tipdiv.style("padding-bottom").replace("px","")*1;shiftX=tipbox_width/2-fontsize;shiftY=tipbox_height+divpad/2-fontsize/2}else if(direction==="south"){posX=x-tipbox_width/2;posY=y+pad;divpad=tipdiv.style("padding-top").replace("px","")*1;shiftX=+tipbox_width/2-fontsize;shiftY=-fontsize}tipdiv.style("left",posX+"px").style("top",posY+"px");triX=posX+shiftX;triY=posY+shiftY;return tridiv.style("left",triX+"px").style("top",triY+"px").style("width",tipbox_width).style("height",tipbox_height)};d3panels.tooltip_text=function(tipgroup,text){return tipgroup.select("div.d3panels-tooltip").html(text)};d3panels.tooltip_show=function(tipgroup,duration){return tipgroup.transition().duration(duration).style("opacity",1)};d3panels.tooltip_hide=function(tipgroup,duration){return tipgroup.transition().duration(duration).style("opacity",0)};d3panels.tooltip_destroy=function(tipgroup){return tipgroup.remove()};if(typeof define==="function"&&define.amd)this.d3panels=d3panels,define(d3panels);else if(typeof module==="object"&&module.exports)module.exports=d3panels;else this.d3panels=d3panels}();
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/dataset_select_menu_orig.js b/gn2/wqflask/static/new/javascript/dataset_select_menu_orig.js new file mode 100644 index 00000000..25a703e6 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -0,0 +1,330 @@ +var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown; +process_json = function(data) { + window.jdata = data; + populate_species(); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return apply_default(); + } +}; + +range = function(size, startAt=0) { + return [...Array(size).keys()].map(idx => idx + startAt); +}; + +indicate_error = function (jqXHR, textStatus, errorThrown) { + errorElement = document.createElement("span"); + errorElement.setAttribute("class", "alert-danger"); + errorText = document.createTextNode( + "There was an error retrieving and setting the menu. Try again later."); + errorElement.appendChild(errorText); + if (document.getElementById("search")){ + form = document.getElementById("search").getElementsByTagName("form")[0]; + form.prepend(errorElement); + disable_element = function(select) { + select.setAttribute("disabled", "disabled"); + }; + Array.from(form.getElementsByTagName("select")).forEach(disable_element); + Array.from(form.getElementsByTagName("textarea")).forEach(disable_element); + } +}; + +defaultStatusCodeFunctions = range(200, 400).reduce( + function(acc, scode) { + acc[scode] = indicate_error; + return acc; + }, {}); + +if (typeof gn_server_url === 'undefined'){ + gn_server_url = $("#search form").attr("data-gn_server_url") +} + +$.ajax(gn_server_url +'/menu/generate/json', { + dataType: 'json', + success: process_json, + error: indicate_error, + statusCode: { + ...defaultStatusCodeFunctions, + } +}); + +populate_species = function() { + var species_list; + species_list = this.jdata.species; + redo_dropdown($('#species'), species_list); + return populate_group(); +}; +window.populate_species = populate_species; + +populate_group = function() { + var group_list, species; + species = $('#species').val(); + group_list = this.jdata.groups[species]; + for (_i = 0, _len = group_list.length; _i < (_len - 1); _i++) { + if (group_list[_i][0] == "BXD300"){ + group_list.splice(_i, 1) + } + } + redo_dropdown($('#group'), group_list); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } +}; +window.populate_group = populate_group; + +populate_type = function() { + var group, species, type_list; + species = $('#species').val(); + group = $('#group').val(); + type_list = this.jdata.types[species][group]; + redo_dropdown($('#type'), type_list); + return populate_dataset(); +}; +window.populate_type = populate_type; + +populate_dataset = function() { + var dataset_list, group, species, type; + species = $('#species').val(); + group = $('#group').val(); + type = $('#type').val(); + dataset_list = this.jdata.datasets[species][group][type]; + return redo_dropdown($('#dataset'), dataset_list); +}; +window.populate_dataset = populate_dataset; + +redo_dropdown = function(dropdown, items) { + var item, _i, _len, _results; + dropdown.empty(); + _results = []; + + if (dropdown.attr('id') == "species"){ + species_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + species_family = item[2].toString() + species_family_list.push([item[0], item[1], species_family]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = species_family_list.length; _i < _len; _i++) { + item = species_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == species_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == species_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && this_opt_group != null && item[2] == "None"){ + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else if (dropdown.attr('id') == "group"){ + group_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + group_family = item[2].toString().split(":")[1] + group_family_list.push([item[0], item[1], group_family]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = group_family_list.length; _i < _len; _i++) { + item = group_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == group_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == group_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && this_opt_group != null && item[2] == "None"){ + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else if (dropdown.attr('id') == "type"){ + type_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + type_family_list.push([item[0], item[1], item[2]]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = type_family_list.length; _i < _len; _i++) { + item = type_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else { + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else { + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + if (item.length > 2){ + _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } + + return _results; +}; + +$('#species').change((function(_this) { + return function() { + return populate_group(); + }; +})(this)); + +$('#group').change((function(_this) { + return function() { + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } + else { + return false + } + }; +})(this)); + +$('#type').change((function(_this) { + return function() { + return populate_dataset(); + }; +})(this)); + +open_window = function(url, name) { + var options; + options = "menubar=yes,toolbar=yes,titlebar=yes,location=yes,resizable=yes,status=yes,scrollbars=yes,directories=yes,width=900"; + return open(url, name, options).focus(); +}; + +group_info = function() { + var group, species, url; + species = $('#species').val(); + group = $('#group').val(); + url = "http://gn1.genenetwork.org/" + species + "Cross.html#" + group; + return open_window(url, "_blank"); +}; +$('#group_info').click(group_info); + +dataset_info = function() { + var dataset, url; + accession_id = $('#dataset option:selected').data("id"); + if (accession_id != "None") { + url = "https://info.genenetwork.org/infofile/source.php?GN_AccesionId=" + accession_id + } else { + species = $('#species').val(); + group = $('#group').val(); + url = "https://info.genenetwork.org/species/source.php?SpeciesName=" + species + "&InbredSetName=" + group + } + return open_window(url, "_blank"); +}; +$('#dataset_info').click(dataset_info); + +make_default = function() { + var holder, item, jholder, _i, _len, _ref; + alert("The current settings are now your default.") + holder = {}; + _ref = ['species', 'group', 'type', 'dataset']; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + holder[item] = $("#" + item).val(); + } + jholder = JSON.stringify(holder); + return $.cookie('search_defaults', jholder, { + expires: 365 + }); +}; + +apply_default = function() { + var defaults, item, populate_function, _i, _len, _ref, _results; + defaults = $.cookie('search_defaults'); + if (defaults) { + defaults = $.parseJSON(defaults); + } else { + defaults = { + species: "mouse", + group: "BXD", + type: "Hippocampus mRNA", + dataset: "HC_M2_0606_P" + }; + } + + _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]]; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + $("#" + item[0]).val(defaults[item[0]]); + if (item[1]) { + populate_function = "populate_" + item[1]; + _results.push(window[populate_function]()); + } else { + _results.push(void 0); + } + } + return _results; +}; + +check_search_term = function() { + var or_search_term, and_search_term; + or_search_term = $('#or_search').val(); + and_search_term = $('#and_search').val(); + if (or_search_term === "" && and_search_term === "") { + alert("Please enter one or more search terms or search equations."); + return false; + } +}; + +$("#make_default").click(make_default); diff --git a/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js b/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js new file mode 100644 index 00000000..f883c0d9 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js @@ -0,0 +1,913 @@ +var chart; +var srchart; + +x_val_range = js_data.x_range[1] - js_data.x_range[0] +y_val_range = js_data.y_range[1] - js_data.y_range[0] + +if (x_val_range >= 2 && x_val_range < 9){ + x_tick_digits = '.1f' +} else if (x_val_range >= 0.8 && x_val_range < 2) { + x_tick_digits = '.2f' +} else if (x_val_range < 0.8) { + x_tick_digits = '.3f' +} else { + x_tick_digits = 'f' +} + +if (y_val_range >= 2 && y_val_range < 8){ + y_tick_digits = '.1f' +} else if (y_val_range >= 0.8 && y_val_range < 2) { + y_tick_digits = '.2f' +} else if (y_val_range < 0.8) { + y_tick_digits = '.3f' +} else { + y_tick_digits = 'f' +} + +console.log("y_digits:", y_tick_digits) + +var layout = { + height: 700, + width: 800, + margin: { + l: 70, + r: 30, + t: 90, + b: 50 + }, + xaxis: { + range: [js_data.x_range[0], js_data.x_range[1]], + title: js_data.trait_1, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + ticklen: 4, + tickformat: x_tick_digits + }, + yaxis: { + range: [js_data.y_range[0], js_data.y_range[1]], + title: js_data.trait_2, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + ticklen: 4, + tickformat: y_tick_digits, + automargin: true + }, + hovermode: "closest", + showlegend: false, + annotations:[{ + xref: 'paper', + yref: 'paper', + x: 1, + xanchor: 'right', + y: 1.05, + yanchor: 'top', + text: '<i>r</i> = ' + js_data.r_value.toFixed(3) + ', <i>p</i> = ' + js_data.p_value.toExponential(3) + ', <i>n</i> = ' + js_data.num_overlap, + showarrow: false, + font: { + size: 14 + }, + } + ] +} + +var sr_layout = { + height: 700, + width: 800, + margin: { + l: 60, + r: 30, + t: 80, + b: 50 + }, + xaxis: { + range: [js_data.sr_range[0], js_data.sr_range[1]], + title: js_data.trait_1, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + yaxis: { + range: [js_data.sr_range[0], js_data.sr_range[1]], + title: js_data.trait_2, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + hovermode: "closest", + showlegend: false, + annotations:[{ + xref: 'paper', + yref: 'paper', + x: 1, + xanchor: 'right', + y: 1.05, + yanchor: 'top', + text: '<i>rho</i> = ' + js_data.srr_value.toFixed(3) + ', <i>P</i> = ' + js_data.srp_value.toExponential(3) + ', <i>n</i> = ' + js_data.num_overlap, + showarrow: false, + font: { + size: 14 + }, + } +] +} + +var modebar_options = { + modeBarButtonsToAdd:[{ + name: 'Export as SVG', + icon: Plotly.Icons.camera, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'svg'}) + } + }, + { + name: 'Export as JPEG', + icon: Plotly.Icons.disk, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'jpeg'}) + } + }], + showEditInChartStudio: true, + plotlyServerURL: "https://chart-studio.plotly.com", + modeBarButtonsToRemove:['toImage', 'sendDataToCloud', 'hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines'], + displaylogo: false +} + +cofactor1_dict = {} +ranked_cofactor1_dict = {} +//cofactor1_values = [] +//ranked_cofactor1_values = [] +cofactor2_dict = {} +ranked_cofactor2_dict = {} +//cofactor2_values = [] +//ranked_cofactor2_values = [] +cofactor3_dict = {} +ranked_cofactor3_dict = {} + +function drawg() { + x_values = [] + y_values = [] + sample_names = [] + for (j = 0; j < js_data.data[0].length; j++) { + x_values.push(js_data.data[0][j]) + y_values.push(js_data.data[1][j]) + sample_names.push(js_data.indIDs[j]) + } + + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: sample_names, + hoverinfo: "text+x+y" + } + + var trace2 = { + x: [js_data.intercept_coords[0][0], js_data.intercept_coords[1][0]], + y: [js_data.intercept_coords[0][1], js_data.intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + Plotly.newPlot('scatterplot2', [trace2, trace1], layout, modebar_options) + +} + +function srdrawg() { + x_values = [] + y_values = [] + sample_names = [] + for (j = 0; j < js_data.rdata[0].length; j++) { + x_values.push(js_data.rdata[0][j]) + y_values.push(js_data.rdata[1][j]) + sample_names.push(js_data.indIDs[j]) + } + + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: sample_names, + hoverinfo: "text+x+y" + } + + Plotly.newPlot('srscatterplot2', [trace1], sr_layout, modebar_options) +} + +function getdata() { + var data = []; + data.push({ + values: [], + slope: js_data.slope, + intercept: js_data.intercept + }); + + sizemin = 8; + sizemax = 30; + + samples1 = []; + samples2 = []; + samples3 = []; + + if ($('input[name=cofactor1_vals]').val()){ + vals1 = [] + val_sample_dict = {} + val_sample_pairs = $('input[name=cofactor1_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples1.push(val_sample_pairs[i].split(":")[0]) + vals1.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1]) + } + datamin1 = d3.min(vals1); + datamax1 = d3.max(vals1); + + cofactor1_dict = val_sample_dict + cofactor1_values = vals1 + } + + if ($('input[name=cofactor2_vals]').val()){ + vals2 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=cofactor2_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples2.push(val_sample_pairs[i].split(":")[0]) + vals2.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + datamin2 = d3.min(vals2); + datamax2 = d3.max(vals2); + + cofactor2_dict = val_sample_dict + cofactor2_values = vals2 + } + + if ($('input[name=cofactor3_vals]').val()){ + vals3 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=cofactor3_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples3.push(val_sample_pairs[i].split(":")[0]) + vals3.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + + datamin3 = d3.min(vals3); + datamax3 = d3.max(vals3); + + cofactor3_dict = val_sample_dict + cofactor3_values = vals3 + } + + x_values = [] + y_values = [] + sample_names = [] + sizes = [] + + size_cofactor_vals = [] + if ($('#cofactor1_type option:selected').val() == "size" && $('input[name=cofactor1_vals]').val()){ + size_cofactor_vals = cofactor1_values + cofactor_samples = samples1 + datamin = datamin1 + datamax = datamax1 + } else if ($('#cofactor2_type option:selected').val() == "size" && $('input[name=cofactor2_vals]').val()) { + size_cofactor_vals = cofactor2_values + cofactor_samples = samples2 + datamin = datamin2 + datamax = datamax2 + } else if ($('#cofactor3_type option:selected').val() == "size" && $('input[name=cofactor3_vals]').val()) { + size_cofactor_vals = cofactor3_values + cofactor_samples = samples3 + datamin = datamin3 + datamax = datamax3 + } + + unique_vals = [] + symbol_cofactor_vals = [] + if ($('#cofactor1_type option:selected').val() == "symbol" && $('input[name=cofactor1_vals]').val()){ + symbol_cofactor_vals = cofactor1_values + cofactor_samples = samples1 + } else if ($('#cofactor2_type option:selected').val() == "symbol" && $('input[name=cofactor2_vals]').val()) { + symbol_cofactor_vals = cofactor2_values + cofactor_samples = samples2 + } else if ($('#cofactor3_type option:selected').val() == "symbol" && $('input[name=cofactor3_vals]').val()) { + symbol_cofactor_vals = cofactor3_values + cofactor_samples = samples3 + } + + symbol_list = [] + if (symbol_cofactor_vals.length > 0) { + unique_vals = [...new Set(symbol_cofactor_vals)] + for (i=0; i<symbol_cofactor_vals.length; i++){ + val_pos = unique_vals.indexOf(symbol_cofactor_vals[i]) + if (val_pos != "-1") { + symbol_list.push(val_pos) + } else { + symbol_list.push(0) + } + } + } + + //This is needed to calculate samples shared by cofactors + cofactor_samples_array = [] + if (samples1.length > 0){ + cofactor_samples_array.push(samples1) + } + if (samples2.length > 0){ + cofactor_samples_array.push(samples2) + } + if (samples3.length > 0){ + cofactor_samples_array.push(samples3) + } + if (cofactor_samples_array.length > 0){ + shared_samples = _.intersection.apply(_, cofactor_samples_array) + } else { + shared_samples = js_data.indIDs + } + + for (j = 0; j < js_data.data[0].length; j++) { + + if (shared_samples.indexOf(js_data.indIDs[j]) == -1) { + continue + } + + sizev = 10; + datav = 0; + if (size_cofactor_vals.length > 0){ + if (cofactor_samples.indexOf(js_data.indIDs[j])) { + datav = size_cofactor_vals[j] + sizev = map1to2(datamin, datamax, sizemin, sizemax, datav); + } + } + + x_values.push(js_data.data[0][j]) + y_values.push(js_data.data[1][j]) + sample_names.push(js_data.indIDs[j]) + sizes.push(sizev) + + data[0].values.push({ + type: "normal", + x: js_data.data[0][j], + y: js_data.data[1][j], + name: js_data.indIDs[j], + size: sizev, + v3: datav + }); + } + + point_text = [] + for (j = 0; j < sample_names.length; j++) { + this_text = "" + this_text += sample_names[j] + if (sample_names[j] in cofactor1_dict){ + this_text += "<br>Cofactor 1: " + cofactor1_dict[sample_names[j]] + } + if (sample_names[j] in cofactor2_dict){ + this_text += "<br>Cofactor 2: " + cofactor2_dict[sample_names[j]] + } + if (sample_names[j] in cofactor3_dict){ + this_text += "<br>Cofactor 3: " + cofactor3_dict[sample_names[j]] + } + point_text.push(this_text) + } + + if (symbol_list.length > 0) { + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: point_text, + hoverinfo: "text+x+y", + marker: { + color: 'rgb(66, 66, 245)', + symbol: symbol_list, + size: sizes + } + } + } else { + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: point_text, + hoverinfo: "text+x+y", + marker: { + color: 'rgb(66, 66, 245)', + size: sizes + } + } + } + + var trace2 = { + x: [js_data.intercept_coords[0][0], js_data.intercept_coords[1][0]], + y: [js_data.intercept_coords[0][1], js_data.intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + return [trace2, trace1]; +} + +function map1to2 (min1, max1, min2, max2, v1) { + v2 = (v1 - min1) * (max2 - min2) / (max1 - min1) + min2; + return v2; +} + +function srgetdata() { + var data = []; + data.push({ + values: [], + slope: js_data.srslope, + intercept: js_data.srintercept + }); + + sizemin = 8; + sizemax = 30; + + ranked_cofactor_vals = "" + + samples1 = []; + samples2 = []; + samples3 = []; + + if ($('input[name=ranked_cofactor1_vals]').val()){ + vals1 = [] + val_sample_dict = {} + val_sample_pairs = $('input[name=ranked_cofactor1_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples1.push(val_sample_pairs[i].split(":")[0]) + vals1.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1]) + } + datamin1 = d3.min(vals1); + datamax1 = d3.max(vals1); + + ranked_cofactor1_dict = val_sample_dict + ranked_cofactor1_values = vals1 + } + + if ($('input[name=ranked_cofactor2_vals]').val()){ + vals2 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=ranked_cofactor2_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples2.push(val_sample_pairs[i].split(":")[0]) + vals2.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + datamin2 = d3.min(vals2); + datamax2 = d3.max(vals2); + + ranked_cofactor2_dict = val_sample_dict + ranked_cofactor2_values = vals2 + } + + if ($('input[name=ranked_cofactor3_vals]').val()){ + vals3 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=ranked_cofactor3_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples3.push(val_sample_pairs[i].split(":")[0]) + vals3.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + + datamin3 = d3.min(vals3); + datamax3 = d3.max(vals3); + + ranked_cofactor3_dict = val_sample_dict + ranked_cofactor3_values = vals3 + } + + x_values = [] + y_values = [] + sample_names = [] + sizes = [] + + if ($('#cofactor1_type option:selected').val() == "size" && $('input[name=ranked_cofactor1_vals]').val()){ + size_cofactor_vals = ranked_cofactor1_values + cofactor_samples = samples1 + datamin = datamin1 + datamax = datamax1 + } else if ($('#cofactor2_type option:selected').val() == "size" && $('input[name=ranked_cofactor2_vals]').val()) { + size_cofactor_vals = ranked_cofactor2_values + cofactor_samples = samples2 + datamin = datamin2 + datamax = datamax2 + } else if ($('#cofactor3_type option:selected').val() == "size" && $('input[name=ranked_cofactor3_vals]').val()) { + size_cofactor_vals = ranked_cofactor3_values + cofactor_samples = samples3 + datamin = datamin3 + datamax = datamax3 + } + + unique_vals = [] + symbol_cofactor_vals = [] + if ($('#cofactor1_type option:selected').val() == "symbol" && $('input[name=ranked_cofactor1_vals]').val()){ + symbol_cofactor_vals = cofactor1_values + cofactor_samples = samples1 + } else if ($('#cofactor2_type option:selected').val() == "symbol" && $('input[name=ranked_cofactor2_vals]').val()) { + symbol_cofactor_vals = cofactor2_values + cofactor_samples = samples2 + } else if ($('#cofactor3_type option:selected').val() == "symbol" && $('input[name=ranked_cofactor3_vals]').val()) { + symbol_cofactor_vals = cofactor3_values + cofactor_samples = samples3 + } + + symbol_list = [] + if (symbol_cofactor_vals.length > 0) { + unique_vals = [...new Set(symbol_cofactor_vals)] + for (i=0; i<symbol_cofactor_vals.length; i++){ + val_pos = unique_vals.indexOf(symbol_cofactor_vals[i]) + if (val_pos != "-1") { + symbol_list.push(val_pos) + } else { + symbol_list.push(0) + } + } + } + + //This is needed to calculate samples shared by cofactors + cofactor_samples_array = [] + if (samples1.length > 0){ + cofactor_samples_array.push(samples1) + } + if (samples2.length > 0){ + cofactor_samples_array.push(samples2) + } + if (samples3.length > 0){ + cofactor_samples_array.push(samples3) + } + if (cofactor_samples_array.length > 0){ + shared_samples = _.intersection.apply(_, cofactor_samples_array) + } else { + shared_samples = js_data.indIDs + } + + for (j = 0; j < js_data.rdata[0].length; j++) { + + if (shared_samples.indexOf(js_data.indIDs[j]) == -1) { + continue + } + + if (size_cofactor_vals.length > 0){ + if (cofactor_samples.indexOf(js_data.indIDs[j])) { + datav = size_cofactor_vals[j] + sizev = map1to2(datamin, datamax, sizemin, sizemax, datav); + } + } else { + sizev = 10; + } + + x_values.push(js_data.rdata[0][j]) + y_values.push(js_data.rdata[1][j]) + sample_names.push(js_data.indIDs[j]) + sizes.push(sizev) + + data[0].values.push({ + type: "ranked", + x: js_data.rdata[0][j], + y: js_data.rdata[1][j], + name: js_data.indIDs[j], + size: sizev, + }); + } + + point_text = [] + for (j = 0; j < sample_names.length; j++) { + this_text = "" + this_text += sample_names[j] + if (sample_names[j] in ranked_cofactor1_dict){ + this_text += "<br>Cofactor 1: " + ranked_cofactor1_dict[sample_names[j]] + } + if (sample_names[j] in ranked_cofactor2_dict){ + this_text += "<br>Cofactor 2: " + ranked_cofactor2_dict[sample_names[j]] + } + if (sample_names[j] in cofactor3_dict){ + this_text += "<br>Cofactor 3: " + ranked_cofactor3_dict[sample_names[j]] + } + point_text.push(this_text) + } + + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: point_text, + hoverinfo: "text+x+y", + marker: { + color: 'rgb(66, 66, 245)', + symbol: symbol_list, + size: sizes + } + } + + var trace2 = { + x: [js_data.sr_intercept_coords[0][0], js_data.sr_intercept_coords[1][0]], + y: [js_data.sr_intercept_coords[0][1], js_data.sr_intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + return [trace2, trace1]; +} + +function chartupdatewh() { + var width = $("#width").val(); + var height = $("#height").val(); + + width_height_update = { + height: height, + width: width + } + + Plotly.newPlot('scatterplot2', getdata(), layout, modebar_options) + Plotly.relayout('scatterplot2', width_height_update) + + Plotly.newPlot('srscatterplot2', srgetdata(), sr_layout, modebar_options) + Plotly.relayout('srscatterplot2', width_height_update) +} + +function colorer(d) { + if ($('#cofactor1_type option:selected').val() == "color"){ + datamin = d3.min(cofactor1_values); + datamax = d3.max(cofactor1_values); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + datamin = d3.min(cofactor2_values); + datamax = d3.max(cofactor2_values); + } else { + datamin = d3.min(cofactor3_values); + datamax = d3.max(cofactor3_values); + } + colormin = $("#cocolorfrom").val(); + colormax = $("#cocolorto").val(); + + compute = d3.interpolate("#"+colormin, "#"+colormax); + linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]); + + this_sample = d.tx.split("<br>")[0] + + if ($('#cofactor1_type option:selected').val() == "color"){ + c= compute(linear(cofactor1_dict[this_sample])); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + c= compute(linear(cofactor2_dict[this_sample])); + } else { + c= compute(linear(cofactor3_dict[this_sample])); + } + + return c; +} + +function ranked_colorer(d) { + if ($('#cofactor1_type option:selected').val() == "color"){ + datamin = d3.min(ranked_cofactor1_values); + datamax = d3.max(ranked_cofactor1_values); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + datamin = d3.min(ranked_cofactor2_values); + datamax = d3.max(ranked_cofactor2_values); + } else { + datamin = d3.min(ranked_cofactor3_values); + datamax = d3.max(ranked_cofactor3_values); + } + colormin = $("#cocolorfrom").val(); + colormax = $("#cocolorto").val(); + + compute = d3.interpolate("#"+colormin, "#"+colormax); + linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]); + + this_sample = d.tx.split("<br>")[0] + + if ($('#cofactor1_type option:selected').val() == "color"){ + c= compute(linear(ranked_cofactor1_dict[this_sample])); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + c= compute(linear(ranked_cofactor2_dict[this_sample])); + } else { + c= compute(linear(ranked_cofactor3_dict[this_sample])); + } + + return c; +} + +function chartupdatedata() { + var size = $("#marksize").val(); + var shape = $("#markshape").val(); + + var pearson_title_update = { + title: "Pearson Correlation Scatterplot" + } + var spearman_title_update = { + title: "Spearman Rank Correlation Scatterplot" + } + + Plotly.newPlot('scatterplot2', getdata(), layout, modebar_options) + Plotly.relayout('scatterplot2', pearson_title_update) + Plotly.newPlot('srscatterplot2', srgetdata(), sr_layout, modebar_options) + Plotly.relayout('srscatterplot2', spearman_title_update) + + if ($('#cofactor1_type option:selected').val() == "color"){ + $('#cofactor_color_selector').css("display", "inline") + if ($('input[name=cofactor1_vals]').val()){ + d3.select('#scatterplot2 svg').selectAll('.point') + .style({ + 'stroke': colorer, + 'fill': colorer + }); + d3.select('#srscatterplot2 svg').selectAll('.point') + .style({ + 'stroke': ranked_colorer, + 'fill': ranked_colorer + }); + } + } else if ($('#cofactor2_type option:selected').val() == "color"){ + $('#cofactor_color_selector').css("display", "inline") + if ($('input[name=cofactor2_vals]').val()){ + d3.select('#scatterplot2 svg').selectAll('.point') + .style({ + 'stroke': colorer, + 'fill': colorer + }); + d3.select('#srscatterplot2 svg').selectAll('.point') + .style({ + 'stroke': ranked_colorer, + 'fill': ranked_colorer + }); + } + } else { + $('#cofactor_color_selector').css("display", "inline") + if ($('input[name=cofactor3_vals]').val()){ + d3.select('#scatterplot2 svg').selectAll('.point') + .style({ + 'stroke': colorer, + 'fill': colorer + }); + d3.select('#srscatterplot2 svg').selectAll('.point') + .style({ + 'stroke': ranked_colorer, + 'fill': ranked_colorer + }); + } + } +} + +drawg(); +srdrawg(); + +$(".chartupdatewh").change(function () { + chartupdatewh(); +}); + +$(".chartupdatedata").change(function () { + chartupdatedata(); +}); + +$("#cofactor1_type").change(function () { + + the_types = ["color", "size", "symbol"] + + cofactor1_type = $(this).val() + cofactor2_type = $("#cofactor2_type option:selected").val() + cofactor3_type = $("#cofactor3_type option:selected").val() + + if (cofactor2_type == cofactor1_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor1_type && the_types[i] != cofactor3_type) { + $("#cofactor2_type").val(the_types[i]); + } + } + } + else if (cofactor3_type == cofactor1_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor1_type && the_types[i] != cofactor2_type) { + $("#cofactor3_type").val(the_types[i]); + } + } + } + + chartupdatedata(); +}); + +$("#cofactor2_type").change(function () { + + the_types = ["color", "size", "symbol"] + + cofactor2_type = $(this).val() + cofactor1_type = $("#cofactor1_type option:selected").val() + cofactor3_type = $("#cofactor3_type option:selected").val() + + if (cofactor1_type == cofactor2_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor3_type){ + $("#cofactor1_type").val(the_types[i]); + } + } + } + else if (cofactor3_type == cofactor2_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor1_type){ + $("#cofactor3_type").val(the_types[i]); + } + } + } + + chartupdatedata(); +}); + +$("#cofactor3_type").change(function () { + + the_types = ["color", "size", "symbol"] + + cofactor3_type = $(this).val() + cofactor1_type = $("#cofactor1_type option:selected").val() + cofactor2_type = $("#cofactor2_type option:selected").val() + + if (cofactor1_type == cofactor3_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor3_type){ + $("#cofactor1_type").val(the_types[i]); + } + } + } + else if (cofactor2_type == cofactor3_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor1_type){ + $("#cofactor3_type").val(the_types[i]); + } + } + } +}); + +open_covariate_selection = function() { + return $('#collections_holder').load('/collections/list #collections_list', (function(_this) { + return function() { + $.colorbox({ + inline: true, + href: "#collections_holder", + onComplete: function(){ + $.getScript("/static/new/javascript/get_traits_from_collection.js"); + } + }); + return $('a.collection_name').attr('onClick', 'return false'); + }; + })(this)); +}; + +remove_cofactors = function() { + $('input[name=cofactor1_vals]').val(""); + $('input[name=ranked_cofactor1_vals]').val(""); + $('input[name=cofactor2_vals]').val(""); + $('input[name=ranked_cofactor2_vals]').val(""); + $('input[name=cofactor3_vals]').val(""); + $('input[name=ranked_cofactor3_vals]').val(""); + + $('#select_cofactor1').text("Select Cofactor 1"); + $('#cofactor2_button').css("display", "none"); + $('#cofactor3_button').css("display", "none"); + + $('#cofactor_color_select').css("display", "none"); + + $('#cofactor1_info_container').css("display", "none"); + $('#cofactor2_info_container').css("display", "none"); + $('#cofactor3_info_container').css("display", "none"); + + chartupdatedata(); +}; + +$(document).ready(function(){ + chartupdatedata(); + + $('#select_cofactor1').click(function () { + $('input[name=selecting_which_cofactor]').val("1"); + open_covariate_selection(); + }); + + $('#select_cofactor2').click(function () { + $('input[name=selecting_which_cofactor]').val("2"); + open_covariate_selection(); + }); + + $('#select_cofactor3').click(function () { + $('input[name=selecting_which_cofactor]').val("3"); + open_covariate_selection(); + }); + + $('#remove_cofactors').click(function () { + remove_cofactors(); + }); + + $('#invert_axes').click(function () { + var [dataset_1, trait_1] = js_data.trait_2.split(": ") + var [dataset_2, trait_2] = js_data.trait_1.split(": ") + window.location.replace("/corr_scatter_plot?method=pearson&dataset_1=" + dataset_1 + "&dataset_2=" + dataset_2 + "&trait_1=" + trait_1 + "&trait_2=" + trait_2) + }); + +}); diff --git a/gn2/wqflask/static/new/javascript/draw_probability_plot.js b/gn2/wqflask/static/new/javascript/draw_probability_plot.js new file mode 100644 index 00000000..1b944d4f --- /dev/null +++ b/gn2/wqflask/static/new/javascript/draw_probability_plot.js @@ -0,0 +1,136 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var get_z_scores, redraw_prob_plot, root; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + get_z_scores = function(n) { + var i, j, osm_uniform, ref, x; + osm_uniform = new Array(n); + osm_uniform[n - 1] = Math.pow(0.5, 1.0 / n); + osm_uniform[0] = 1 - osm_uniform[n - 1]; + for (i = j = 1, ref = n - 2; 1 <= ref ? j <= ref : j >= ref; i = 1 <= ref ? ++j : --j) { + osm_uniform[i] = (i + 1 - 0.3175) / (n + 0.365); + } + return (function() { + var k, len, results; + results = []; + for (k = 0, len = osm_uniform.length; k < len; k++) { + x = osm_uniform[k]; + results.push(jStat.normal.inv(x, 0, 1)); + } + return results; + })(); + }; + + redraw_prob_plot = function(samples, sample_group) { + var container, h, margin, totalh, totalw, w; + h = 600; + w = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + totalh = h + margin.top + margin.bottom; + totalw = w + margin.left + margin.right; + container = $("#prob_plot_container"); + container.width(totalw); + container.height(totalh); + return nv.addGraph((function(_this) { + return function() { + var W, all_samples, chart, data, intercept, make_data, names, pvalue, pvalue_str, slope, sorted_names, sorted_values, sw_result, test_str, x, z_scores; + chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range()); + chart.pointRange([50, 50]); + chart.legend.updateState(false); + chart.xAxis.axisLabel("Expected Z score").axisLabelDistance(20).tickFormat(d3.format('.02f')); + chart.tooltipContent(function(obj) { + return '<b style="font-size: 20px">' + obj.point.name + '</b>'; + }); + all_samples = samples[sample_group]; + names = (function() { + var j, len, ref, results; + ref = _.keys(all_samples); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + if (all_samples[x] !== null) { + results.push(x); + } + } + return results; + })(); + sorted_names = names.sort(function(x, y) { + return all_samples[x].value - all_samples[y].value; + }); + max_decimals = 0 + sorted_values = (function() { + var j, len, results; + results = []; + for (j = 0, len = sorted_names.length; j < len; j++) { + x = sorted_names[j]; + results.push(all_samples[x].value); + if (all_samples[x].value.countDecimals() > max_decimals) { + max_decimals = all_samples[x].value.countDecimals()-1 + } + } + return results; + })(); + //ZS: 0.1 indicates buffer, increase to increase buffer + y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1] + chart.yDomain(y_domain) + chart.yAxis.axisLabel("Trait value").axisLabelDistance(10).tickFormat(d3.format('.0'+max_decimals.toString()+'f')); + sw_result = ShapiroWilkW(sorted_values); + W = sw_result.w.toFixed(3); + pvalue = sw_result.p.toFixed(3); + pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>"; + test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")"; + z_scores = get_z_scores(sorted_values.length); + //ZS: 0.1 indicates buffer, increase to increase buffer + x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1] + chart.xDomain(x_domain) + slope = jStat.stdev(sorted_values); + intercept = jStat.mean(sorted_values); + make_data = function(group_name) { + var sample, value, z_score; + return { + key: js_data.sample_group_types[group_name], + slope: slope, + intercept: intercept, + values: (function() { + var j, len, ref, ref1, results; + ref = _.zip(get_z_scores(sorted_values.length), sorted_values, sorted_names); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + ref1 = ref[j], z_score = ref1[0], value = ref1[1], sample = ref1[2]; + if (sample in samples[group_name]) { + results.push({ + x: z_score, + y: value, + name: sample + }); + } + } + return results; + })() + }; + }; + data = [make_data('samples_primary'), make_data('samples_other')]; + d3.select("#prob_plot_container svg").datum(data).call(chart); + if (js_data.trait_symbol != null) { + $("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>"); + } else { + $("#prob_plot_title").html("<h3>" + js_data.trait_id + "</h3>"); + } + $("#shapiro_wilk_text").html(test_str) + $("#prob_plot_container .nv-legendWrap").toggle(sample_group === "samples_all"); + return chart; + }; + })(this)); + }; + + root.redraw_prob_plot_impl = redraw_prob_plot; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/get_covariates_from_collection.js b/gn2/wqflask/static/new/javascript/get_covariates_from_collection.js new file mode 100644 index 00000000..ba8fa8b0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -0,0 +1,248 @@ +// Generated by CoffeeScript 1.8.0 +var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + +this_trait_data = null; + +selected_traits = {}; + +$('#collections_list').attr("style", "width: 100%;"); +$('#trait_table').dataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + }, + "columns": [ + { "type": "natural", "width": "3%" }, + { "type": "natural", "width": "8%" }, + { "type": "natural", "width": "20%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "15%" } + ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true +} ); + +if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { + $('#collection_table').dataTable( { + "createdRow": function ( row, data, index ) { + if ($('td', row).eq(2).text().length > 40) { + $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40)); + $('td', row).eq(2).text($('td', row).eq(2).text() + '...') + } + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + }, + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "ZRtr", + "iDisplayLength": -1, + "autoWidth": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); +} + +collection_click = function() { + var this_collection_url; + this_collection_url = $(this).find('.collection_name').prop("href"); + this_collection_url += "&json"; + collection_list = $("#collections_holder").html(); + return $.ajax({ + dataType: "json", + url: this_collection_url, + success: process_traits + }); +}; + +submit_click = function() { + var covariates_string = ""; + var covariates_as_set = new Set(); + $(".selected-covariates:first option").each(function() { + if ($(this).val() != ""){ + covariates_as_set.add($(this).val() + "," + $(this).text()); + } + }); + $('#collections_holder').find('input[type=checkbox]:checked').each(function() { + var this_dataset, this_trait; + this_trait = $(this).parents('tr').find('.trait').text(); + this_trait_display = $(this).parents('tr').find('.trait').data("display_name"); + this_description = $(this).parents('tr').find('.description').text(); + this_dataset = $(this).parents('tr').find('.dataset').data("dataset"); + this_covariate_display_string = this_trait_display + if (this_covariate_display_string.length > 50) { + this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..." + } + covariates_as_set.add(this_trait + ":" + this_dataset + "," + this_covariate_display_string) + }); + + covariates_as_list = Array.from(covariates_as_set) + + // Removed the starting "No covariates selected" option before adding options for each covariate + if (covariates_as_list.length > 0){ + $(".selected-covariates option[value='']").each(function() { + $(this).remove(); + }); + } + + $(".selected-covariates option").each(function() { + $(this).remove(); + }); + + covariate_list_for_form = [] + $.each(covariates_as_list, function (index, value) { + option_value = value.split(",")[0] + option_text = value.split(",")[1] + $(".selected-covariates").append($("<option/>", { + value: option_value, + text: option_text + })) + covariate_list_for_form.push(option_value) + }); + + $("input[name=covariates]").val(covariate_list_for_form.join(",")); + + cofactor_count = $(".selected-covariates:first option").length; + if (cofactor_count > 10){ + $(".selected-covariates").attr("size", 10); + } else { + $(".selected-covariates").attr("size", cofactor_count); + } + + return $.colorbox.close(); +}; + +trait_click = function() { + var dataset, this_trait_url, trait; + trait = $(this).parent().find('.trait').text(); + dataset = $(this).parent().find('.dataset').data("dataset"); + $("input[name=covariates]").val(trait + ":" + dataset) + $(".selected-covariates").text(trait) + return $.colorbox.close(); +}; + +add_trait_data = function(trait_data, textStatus, jqXHR) { + var trait_name, trait_sample_data; + trait_name = trait_data[0]; + trait_sample_data = trait_data[1]; + selected_traits[trait_name] = trait_sample_data; + return console.log("selected_traits:", selected_traits); +}; + +get_trait_data = function(trait_data, textStatus, jqXHR) { + var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len; + trait_sample_data = trait_data[1]; + samples = $('input[name=allsamples]').val().split(" "); + vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + if (__indexOf.call(Object.keys(trait_sample_data), sample) >= 0) { + vals.push(parseFloat(trait_sample_data[sample])); + } else { + vals.push(null); + } + } + if ($('input[name=samples]').length < 1) { + $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />'); + } + $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />'); + this_trait_vals = get_this_trait_vals(samples); + return color_by_trait(trait_sample_data); +}; + +get_this_trait_vals = function(samples) { + var sample, this_trait_vals, this_val, this_vals_json, _i, _len; + this_trait_vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + this_val = parseFloat($("input[name='value:" + sample + "']").val()); + if (!isNaN(this_val)) { + this_trait_vals.push(this_val); + } else { + this_trait_vals.push(null); + } + } + this_vals_json = '[' + this_trait_vals.toString() + ']'; + return this_trait_vals; +}; + +assemble_into_json = function(this_trait_vals) { + var json_data, json_ids, num_traits, samples; + num_traits = $('input[name=vals]').length; + samples = $('input[name=samples]').val(); + json_ids = samples; + json_data = '[' + this_trait_vals; + $('input[name=vals]').each((function(_this) { + return function(index, element) { + return json_data += ',' + $(element).val(); + }; + })(this)); + json_data += ']'; + return [json_ids, json_data]; +}; + +color_by_trait = function(trait_sample_data, textStatus, jqXHR) { + console.log('in color_by_trait:', trait_sample_data); + return root.bar_chart.color_by_trait(trait_sample_data); +}; + +process_traits = function(trait_data, textStatus, jqXHR) { + var the_html, trait, _i, _len; + the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; + the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; + the_html += " <button id='submit_cofactors' class='btn btn-primary btn-small submit'> Submit </button>"; + the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; + the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; + the_html += "<tbody>"; + for (_i = 0, _len = trait_data.length; _i < _len; _i++) { + trait = trait_data[_i]; + the_html += "<tr class='trait_line'>"; + the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>"; + if ("abbreviation" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>"; + } else if ("symbol" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>"; + } else { + the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>"; + } + the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>"; + the_html += "<td class='description'>" + trait.description + "</td>"; + } + the_html += "</tbody>"; + the_html += "</table>"; + the_html += "<script type='text/javascript' src='/static/new/javascript/get_covariates_from_collection.js'></script>" + $("#collections_holder").html(the_html); + return $('#collections_holder').colorbox.resize(); +}; + +back_to_collections = function() { + console.log("collection_list:", collection_list); + $("#collections_holder").html(collection_list); + $(document).on("click", ".collection_line", collection_click); + return $('#collections_holder').colorbox.resize(); +}; + +$(".collection_line").on("click", collection_click); +$(".submit").on("click", submit_click); +$(".trait").on("click", trait_click); +$("#back_to_collections").on("click", back_to_collections); diff --git a/gn2/wqflask/static/new/javascript/get_traits_from_collection.js b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js new file mode 100644 index 00000000..c115f3b0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js @@ -0,0 +1,414 @@ +// Generated by CoffeeScript 1.8.0 +var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + +this_trait_data = null; + +selected_traits = {}; + +$('#collections_list').attr("style", "width: 100%;"); +$('#trait_table').dataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + }, + "columns": [ + { "type": "natural", "width": "3%" }, + { "type": "natural", "width": "8%" }, + { "type": "natural", "width": "20%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "15%" } + ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true +} ); + +if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { + $('#collection_table').dataTable( { + "createdRow": function ( row, data, index ) { + if ($('td', row).eq(2).text().length > 40) { + $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40)); + $('td', row).eq(2).text($('td', row).eq(2).text() + '...') + } + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + }, + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "ZRtr", + "iDisplayLength": -1, + "autoWidth": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); +} + +collection_click = function() { + var this_collection_url; + + this_collection_url = $(this).find('.collection_name').prop("href"); + this_collection_url += "&json"; + collection_list = $("#collections_holder").html(); + return $.ajax({ + dataType: "json", + url: this_collection_url, + success: process_traits + }); +}; + +submit_click = function() { + var all_vals, sample, samples, scatter_matrix, this_trait_vals, trait, trait_names, trait_vals_csv, traits, _i, _j, _len, _len1, _ref; + selected_traits = {}; + traits = []; + $('#collections_holder').find('input[type=checkbox]:checked').each(function() { + var this_dataset, this_trait, this_trait_url; + this_trait = $(this).parents('tr').find('.trait').text(); + this_dataset = $(this).parents('tr').find('.dataset').text(); + this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset; + return $.ajax({ + dataType: "json", + url: this_trait_url, + async: false, + success: add_trait_data + }); + }); + trait_names = []; + samples = $('input[name=allsamples]').val().split(" "); + all_vals = []; + this_trait_vals = get_this_trait_vals(samples); + all_vals.push(this_trait_vals); + _ref = Object.keys(selected_traits); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + trait = _ref[_i]; + trait_names.push(trait); + this_trait_vals = []; + for (_j = 0, _len1 = samples.length; _j < _len1; _j++) { + sample = samples[_j]; + if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) { + this_trait_vals.push(parseFloat(selected_traits[trait][sample])); + } else { + this_trait_vals.push(null); + } + } + all_vals.push(this_trait_vals); + } + trait_vals_csv = create_trait_data_csv(selected_traits); + scatter_matrix = new ScatterMatrix(trait_vals_csv); + scatter_matrix.render(); + return $.colorbox.close(); +}; + +create_trait_data_csv = function(selected_traits) { + var all_vals, index, sample, sample_vals, samples, this_trait_vals, trait, trait_names, trait_vals_csv, _i, _j, _k, _l, _len, _len1, _len2, _len3, _ref; + trait_names = []; + trait_names.push($('input[name=trait_id]').val()); + samples = $('input[name=allsamples]').val().split(" "); + all_vals = []; + this_trait_vals = get_this_trait_vals(samples); + all_vals.push(this_trait_vals); + _ref = Object.keys(selected_traits); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + trait = _ref[_i]; + trait_names.push(trait); + this_trait_vals = []; + for (_j = 0, _len1 = samples.length; _j < _len1; _j++) { + sample = samples[_j]; + if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) { + this_trait_vals.push(parseFloat(selected_traits[trait][sample])); + } else { + this_trait_vals.push(null); + } + } + all_vals.push(this_trait_vals); + } + + trait_vals_csv = trait_names.join(","); + trait_vals_csv += "\n"; + for (index = _k = 0, _len2 = samples.length; _k < _len2; index = ++_k) { + sample = samples[index]; + if (all_vals[0][index] === null) { + continue; + } + sample_vals = []; + for (_l = 0, _len3 = all_vals.length; _l < _len3; _l++) { + trait = all_vals[_l]; + sample_vals.push(trait[index]); + } + trait_vals_csv += sample_vals.join(","); + trait_vals_csv += "\n"; + } + return trait_vals_csv; +}; + +trait_click = function() { + var dataset, this_trait_url, trait; + + trait = $(this).parent().find('.trait').text(); + dataset = $(this).parent().find('.dataset').text(); + this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset; + $.ajax({ + dataType: "json", + url: this_trait_url, + success: get_trait_data + }); + return $.colorbox.close(); +}; + +trait_row_click = function() { + var dataset, this_trait_url, trait; + trait = $(this).find('.trait').text(); + dataset = $(this).find('.dataset').data("dataset"); + this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset; + $.ajax({ + dataType: "json", + url: this_trait_url, + success: get_trait_data + }); + return $.colorbox.close(); +}; + +add_trait_data = function(trait_data, textStatus, jqXHR) { + var trait_name, trait_sample_data; + trait_name = trait_data[0]; + trait_sample_data = trait_data[1]; + selected_traits[trait_name] = trait_sample_data; + return console.log("selected_traits:", selected_traits); +}; + +populate_cofactor_info = function(trait_info) { + if ($('input[name=selecting_which_cofactor]').val() == "1"){ + $('#cofactor1_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor1').text("Change Cofactor 1"); + $('#cofactor1_info_container').css("display", "inline"); + $('#cofactor2_button').css("display", "inline-block"); + } else if ($('input[name=selecting_which_cofactor]').val() == "2"){ + $('#cofactor2_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor2').text("Change Cofactor 2"); + $('#cofactor2_info_container').css("display", "inline"); + $('#cofactor3_button').css("display", "inline-block"); + } else { + $('#cofactor3_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor3_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor3').text("Change Cofactor 3"); + $('#cofactor3_info_container').css("display", "inline"); + } +} + +get_trait_data = function(trait_data, textStatus, jqXHR) { + var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len; + trait_sample_data = trait_data[1]; + if ( $('input[name=allsamples]').length ) { + samples = $('input[name=allsamples]').val().split(" "); + } else { + samples = js_data.indIDs + } + sample_vals = []; + vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + if (sample in trait_sample_data) { + sample_vals.push(sample + ":" + parseFloat(trait_sample_data[sample])) + vals.push(parseFloat(trait_sample_data[sample])) + } else { + sample_vals.push(null) + vals.push(null) + } + } + if ( $('input[name=allsamples]').length ) { + if ($('input[name=samples]').length < 1) { + $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />'); + } + $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />'); + this_trait_vals = get_this_trait_vals(samples); + return color_by_trait(trait_sample_data); + } else{ + sorted = vals.slice().sort(function(a,b){return a-b}) + ranks = vals.slice().map(function(v){ return sorted.indexOf(v)+1 }); + sample_ranks = [] + for (_i = 0; _i < samples.length; _i++){ + if (samples[_i] in trait_sample_data){ + sample_ranks.push(samples[_i] + ":" + ranks[_i]) + } else { + sample_ranks.push(null) + } + } + + if ($('input[name=selecting_which_cofactor]').val() == "1"){ + if ($('#cofactor1_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor1_vals]').val(sample_vals) + $('input[name=ranked_cofactor1_vals]').val(sample_ranks) + } else if ($('input[name=selecting_which_cofactor]').val() == "2"){ + if ($('#cofactor2_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor2_vals]').val(sample_vals) + $('input[name=ranked_cofactor2_vals]').val(sample_ranks) + } else{ + if ($('#cofactor3_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor3_vals]').val(sample_vals) + $('input[name=ranked_cofactor3_vals]').val(sample_ranks) + } + populate_cofactor_info(trait_data[0]) + chartupdatedata(); + return false + } +}; + +get_this_trait_vals = function(samples) { + var sample, this_trait_vals, this_val, this_vals_json, _i, _len; + this_trait_vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + this_val = parseFloat($("input[name='value:" + sample + "']").val()); + if (!isNaN(this_val)) { + this_trait_vals.push(this_val); + } else { + this_trait_vals.push(null); + } + } + this_vals_json = '[' + this_trait_vals.toString() + ']'; + return this_trait_vals; +}; + +assemble_into_json = function(this_trait_vals) { + var json_data, json_ids, num_traits, samples; + num_traits = $('input[name=vals]').length; + samples = $('input[name=samples]').val(); + json_ids = samples; + json_data = '[' + this_trait_vals; + $('input[name=vals]').each((function(_this) { + return function(index, element) { + return json_data += ',' + $(element).val(); + }; + })(this)); + json_data += ']'; + return [json_ids, json_data]; +}; + +color_by_trait = function(trait_sample_data, textStatus, jqXHR) { + return root.bar_chart.color_by_trait(trait_sample_data); +}; + +process_traits = function(trait_data, textStatus, jqXHR) { + var the_html, trait, _i, _len; + the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; + the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; + the_html += " <button id='submit_cofactors' class='btn btn-primary btn-small submit'> Submit </button>"; + the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; + the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; + the_html += "<tbody>"; + for (_i = 0, _len = trait_data.length; _i < _len; _i++) { + trait = trait_data[_i]; + the_html += "<tr class='trait_line'>"; + the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>"; + if ("abbreviation" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>"; + } else if ("symbol" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>"; + } else { + the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>"; + } + the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>"; + the_html += "<td class='description'>" + trait.description + "</td>"; + } + the_html += "</tbody>"; + the_html += "</table>"; + the_html += "<script type='text/javascript' src='/static/new/javascript/get_traits_from_collection.js'></script>" + $("#collections_holder").html(the_html); + return $('#collections_holder').colorbox.resize(); +}; + +back_to_collections = function() { + $("#collections_holder").html(collection_list); + $(document).on("click", ".collection_line", collection_click); + return $('#collections_holder').colorbox.resize(); +}; + +$(".collection_line").on("click", collection_click); +$("#submit_cofactors").on("click", submit_click); +if ($('#scatterplot2').length){ + $(".trait_line").on("click", trait_row_click); +} else { + $(".trait").on("click", trait_click); +} +$("#back_to_collections").on("click", back_to_collections); diff --git a/gn2/wqflask/static/new/javascript/group_manager.js b/gn2/wqflask/static/new/javascript/group_manager.js new file mode 100644 index 00000000..cd56133a --- /dev/null +++ b/gn2/wqflask/static/new/javascript/group_manager.js @@ -0,0 +1,37 @@ +$('#add_to_admins').click(function() { + add_emails('admin') +}) + +$('#add_to_members').click(function() { + add_emails('member') +}) + +$('#clear_admins').click(function(){ + clear_emails('admin') +}) + +$('#clear_members').click(function(){ + clear_emails('member') +}) + + +function add_emails(user_type){ + let email_address = $('input[name=user_email]').val(); + let email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim() + if (email_list_string == ""){ + let email_set = new Set(); + } else { + let email_set = new Set(email_list_string.split(",")) + } + email_set.add(email_address) + + $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(',')) + + let emails_display_string = Array.from(email_set).join('\n') + $('.added_' + user_type + 's').val(emails_display_string) +} + +function clear_emails(user_type){ + $('input[name=' + user_type + '_emails_to_add]').val("") + $('.added_' + user_type + 's').val("") +} diff --git a/gn2/wqflask/static/new/javascript/histogram.js b/gn2/wqflask/static/new/javascript/histogram.js new file mode 100644 index 00000000..f71080e8 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/histogram.js @@ -0,0 +1,134 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var Histogram, root; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + Histogram = (function() { + function Histogram(sample_list1, sample_group) { + this.sample_list = sample_list1; + this.sample_group = sample_group; + this.sort_by = "name"; + this.format_count = d3.format(",.0f"); + this.margin = { + top: 10, + right: 30, + bottom: 30, + left: 30 + }; + this.plot_width = 960 - this.margin.left - this.margin.right; + this.plot_height = 500 - this.margin.top - this.margin.bottom; + this.x_buffer = this.plot_width / 20; + this.y_buffer = this.plot_height / 20; + this.plot_height -= this.y_buffer; + this.get_sample_vals(this.sample_list); + this.redraw(this.sample_vals); + } + + Histogram.prototype.redraw = function(sample_vals) { + this.sample_vals = sample_vals; + this.y_min = d3.min(this.sample_vals); + this.y_max = d3.max(this.sample_vals) * 1.1; + this.create_x_scale(); + this.get_histogram_data(); + this.create_y_scale(); + $("#histogram").empty(); + this.svg = this.create_svg(); + return this.create_graph(); + }; + + Histogram.prototype.get_sample_vals = function(sample_list) { + var sample; + return this.sample_vals = (function() { + var i, len, results; + results = []; + for (i = 0, len = sample_list.length; i < len; i++) { + sample = sample_list[i]; + if (sample.value !== null) { + results.push(sample.value); + } + } + return results; + })(); + }; + + Histogram.prototype.create_svg = function() { + var svg; + svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")"); + return svg; + }; + + Histogram.prototype.create_x_scale = function() { + var x0; + console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals)); + x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals)); + return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice(); + }; + + Histogram.prototype.get_histogram_data = function() { + var n_bins; + console.log("sample_vals:", this.sample_vals); + n_bins = 2*Math.sqrt(this.sample_vals.length); //Was originally just the square root, but increased to 2*; ideally would be a GUI for changing this + this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(n_bins))(this.sample_vals); + return console.log("histogram_data:", this.histogram_data[0]); + }; + + Histogram.prototype.create_y_scale = function() { + return this.y_scale = d3.scale.linear().domain([ + 0, d3.max(this.histogram_data, (function(_this) { + return function(d) { + return d.y; + }; + })(this)) + ]).range([this.plot_height, 0]); + }; + + Histogram.prototype.create_graph = function() { + this.add_x_axis(); + this.add_y_axis(); + return this.add_bars(); + }; + + Histogram.prototype.add_x_axis = function() { + var x_axis; + x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom"); + return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis); + }; + + Histogram.prototype.add_y_axis = function() { + var yAxis; + yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end"); + }; + + Histogram.prototype.add_bars = function() { + var bar, rect_width; + bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) { + return function(d) { + return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")"; + }; + })(this)); + rect_width = this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - this.x_scale(this.histogram_data[0].x); + bar.append("rect").attr("x", 1).attr("width", rect_width - 1).attr("height", (function(_this) { + return function(d) { + return _this.plot_height - _this.y_scale(d.y); + }; + })(this)); + return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", rect_width / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) { + return function(d) { + var bar_height; + bar_height = _this.plot_height - _this.y_scale(d.y); + if (bar_height > 20) { + return _this.format_count(d.y); + } + }; + })(this)); + }; + + return Histogram; + + })(); + + root.Histogram = Histogram; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/init_genome_browser.js b/gn2/wqflask/static/new/javascript/init_genome_browser.js new file mode 100644 index 00000000..508f5bf2 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/init_genome_browser.js @@ -0,0 +1,82 @@ +snps_filename = "/browser_input?filename=" + js_data.browser_files[0] +annot_filename = "/browser_input?filename=" + js_data.browser_files[1] + +localUrls = +{ + snps: snps_filename, + annotations: annot_filename +}; + +var coordinateSystem = js_data.chr_lengths + +var vscaleWidth = 90.0; +var legendWidth = 150.0; + +if ('significant' in js_data) { + var significant_score = parseFloat(js_data.significant) +} else { + var significant_score = js_data.max_score * 0.75 +} +var score = { min: 0.0, max: js_data.max_score, sig: significant_score }; +var gwasPadding = { top: 35.0, + bottom: 35.0, + left: vscaleWidth, + right: legendWidth }; +var gwasHeight = 500.0; +var config = +{ score: score, + urls: localUrls, + tracks: { + gwas: { + trackHeight: gwasHeight, + padding: gwasPadding, + snps: { + radius: 3.75, + lineWidth: 1.0, + color: { outline: "#FFFFFF", + fill: "#00008B" }, + pixelOffset: {x: 0.0, y: 0.0} + }, + annotations: { + urls: { + url: "GeneNetwork" + }, + radius: 5.5, + outline: "#000000", + snpColor: "#0074D9", + geneColor: "#FF4136" + }, + score: score, + legend: { + fontSize: 14, + hPad: 0.1, + vPad: 0.2 + }, + vscale: { + color: "#000000", + hPad: 0.125, + numSteps: 3, + fonts: { labelSize: 18, scaleSize: 16 } + }, + }, + }, + chrs: { + chrBG1: "#FFFFFF", + chrBG2: "#EEEEEE", + chrLabels: { fontSize: 16 }, + }, + // initialChrs: { left: "1", right: "5" } + coordinateSystem: coordinateSystem, +}; + +if (js_data.selected_chr != -1) { + config['initialChrs'] = {left: js_data.selected_chr, right: js_data.selected_chr} +} + +$('#browser_tab').click(function() { + if ($('#gwas').length == 0){ + GenomeBrowser.main(config)(); + } +}); + +document.getElementById("controls").style.visibility = "visible";
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js new file mode 100644 index 00000000..44076c17 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -0,0 +1,246 @@ +// This file initializes the tables for the show_trait page + +// This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable +var attributeStartPos = 3; +if (js_data.se_exists) { + attributeStartPos += 2; +} +if (js_data.has_num_cases === true) { + attributeStartPos += 1; +} + +buildColumns = function() { + let columnList = [ + { + 'data': null, + 'orderDataType': "dom-checkbox", + 'searchable' : false, + 'targets': 0, + 'width': "25px", + 'render': function() { + return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">' + } + }, + { + 'title': "ID", + 'type': "natural", + 'searchable' : false, + 'targets': 1, + 'width': "35px", + 'data': "this_id" + }, + { + 'title': "Sample", + 'type': "natural", + 'data': null, + 'targets': 2, + 'width': "60px", + 'render': function(data) { + return '<span class="edit_sample_sample_name">' + data.name + '</span>' + } + }, + { + 'title': "<div style='text-align: right;'>Value</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 3, + 'width': "60px", + 'render': function(data) { + if (data.value == null) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=' + js_data.max_digits[0] + '>' + } else { + if (js_data.no_decimal_place == false) { + return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=' + js_data.max_digits[0] + '>' + } else { + return '<input type="text" data-value="' + data.value + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value + '" size=' + js_data.max_digits[0] + '>' + } + } + } + } + ]; + + attrStart = 4 + if (js_data.se_exists) { + attrStart += 2 + columnList.push( + { + 'bSortable': false, + 'type': "natural", + 'data': null, + 'targets': 4, + 'searchable' : false, + 'width': "25px", + 'render': function() { + return '±' + } + }, + { + 'title': "<div style='text-align: right;'>SE</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 5, + 'width': "60px", + 'render': function(data) { + if (data.variance == null) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="x" size=6>' + } else { + return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6>' + } + } + } + ); + + if (js_data.has_num_cases === true) { + attrStart += 1 + columnList.push( + { + 'title': "<div style='text-align: right;'>N</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 6, + 'width': "60px", + 'render': function(data) { + if (data.num_cases == null || data.num_cases == undefined) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' + } else { + return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' + } + } + } + ); + } + } + else { + if (js_data.has_num_cases === true) { + attrStart += 1 + columnList.push( + { + 'title': "<div style='text-align: right;'>N</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 4, + 'width': "60px", + 'render': function(data) { + if (data.num_cases == null || data.num_cases == undefined) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' + } else { + return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' + } + } + } + ); + } + } + + attrKeys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].id > js_data.attributes[b].id) ? 1 : -1) + for (i = 0; i < attrKeys.length; i++){ + columnList.push( + { + 'title': "<div title='" + js_data.attributes[attrKeys[i]].description + "' style='text-align: " + js_data.attributes[attrKeys[i]].alignment + "'>" + js_data.attributes[attrKeys[i]].name + "</div>", + 'type': "natural", + 'data': null, + 'targets': attrStart + i, + 'render': function(data, type, row, meta) { + attr_name = Object.keys(data.extra_attributes).sort((a, b) => (parseInt(a) > parseInt(b)) ? 1 : -1)[meta.col - data.first_attr_col] + + if (attr_name != null && attr_name != undefined){ + if (Array.isArray(data.extra_attributes[attr_name])){ + return '<a href="' + data.extra_attributes[attr_name][1] + '">' + data.extra_attributes[attr_name][0] + '</a>' + } else { + return data.extra_attributes[attr_name] + } + } else { + return "" + } + } + } + ) + } + return columnList +} + +columnDefs = buildColumns(); + +tableIds = ["samples_primary"] +if (js_data.sample_lists.length > 1) { + tableIds.push("samples_other") +} + +for (var i = 0; i < tableIds.length; i++) { + tableId = tableIds[i] + + if (tableId == "samples_primary"){ + tableType = "Primary" + } else { + tableType = "Other" + } + + tableSettings = { + "drawCallback": function( settings ) { + $('#' + tableId + ' tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected") && event.target.tagName.toLowerCase() !== 'a'){ + $(this).removeClass("selected") + } else if (event.target.tagName.toLowerCase() !== 'a') { + $(this).addClass("selected") + } + }); + }, + 'createdRow': function ( row, data, index ) { + $(row).attr('id', tableType + "_" + data.this_id) + $(row).addClass("value_se"); + if (data.outlier) { + $(row).addClass("outlier"); + $(row).attr("style", "background-color: orange;"); + } + $('td', row).eq(1).addClass("column_name-Index") + $('td', row).eq(2).addClass("column_name-Sample") + $('td', row).eq(3).addClass("column_name-Value") + if (js_data.se_exists) { + $('td', row).eq(5).addClass("column_name-SE") + if (js_data.has_num_cases === true) { + $('td', row).eq(6).addClass("column_name-num_cases") + } else { + if (js_data.has_num_cases === true) { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + } else { + if (js_data.has_num_cases === true) { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + + for (j=0; j < attrKeys.length; j++) { + $('td', row).eq(attributeStartPos + j + 1).addClass("column_name-" + js_data.attributes[attrKeys[j]].name) + $('td', row).eq(attributeStartPos + j + 1).attr("style", "text-align: " + js_data.attributes[attrKeys[j]].alignment + "; padding-top: 2px; padding-bottom: 0px;") + } + } + } + + create_table(tableId, js_data['sample_lists'][i], columnDefs, tableSettings); + + // Enable mapping compute buttons and replace their text only after table has loaded + // This is because submitting the form prior to the table loading causes an error + $('button.submit_special').html('<span class="glyphicon glyphicon-play-circle"></span> Compute'); + $('button.submit_special').prop('disabled', false); +} + +primary_table = $('#samples_primary').DataTable(); +$('#primary_searchbox').on( 'keyup', function () { + primary_table.search($(this).val()).draw(); +} ); + +if ($('#samples_other').length) { + other_table = $('#samples_other').DataTable(); + $('#other_searchbox').on( 'keyup', function () { + other_table.search($(this).val()).draw(); + } ); +} diff --git a/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js b/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js new file mode 100644 index 00000000..5ecf46e1 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js @@ -0,0 +1,114 @@ +// Generated by CoffeeScript 1.8.0 +var iplotMScanone_noeff, lod_data; + +iplotMScanone_noeff = function(lod_data, times, chartOpts) { + var axispos, chartdivid, chrGap, colors, darkrect, extra_digits, g_heatmap, g_lodchart, hbot, htop, i, lightrect, linecolor, linewidth, lod4curves, lod_labels, lod_ylab, lodchart_curves, lodcolumn, lodcurve, margin, mylodchart, mylodheatmap, nullcolor, nxticks, plotLodCurve, pos, svg, titlepos, totalh, totalw, wleft, wright, x, xticks, y, zlim, zthresh, _ref, _ref1, _ref10, _ref11, _ref12, _ref13, _ref14, _ref15, _ref16, _ref17, _ref18, _ref19, _ref2, _ref20, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9; + wleft = (_ref = chartOpts != null ? chartOpts.wleft : void 0) != null ? _ref : 1000; + wright = (_ref1 = chartOpts != null ? chartOpts.wright : void 0) != null ? _ref1 : 500; + htop = (_ref2 = chartOpts != null ? chartOpts.htop : void 0) != null ? _ref2 : 350; + hbot = (_ref3 = chartOpts != null ? chartOpts.hbot : void 0) != null ? _ref3 : 350; + margin = (_ref4 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref4 : { + left: 100, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = (_ref5 = chartOpts != null ? chartOpts.axispos : void 0) != null ? _ref5 : { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = (_ref6 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? _ref6 : 20; + chrGap = (_ref7 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? _ref7 : 8; + darkrect = (_ref8 = chartOpts != null ? chartOpts.darkrect : void 0) != null ? _ref8 : "#C8C8C8"; + lightrect = (_ref9 = chartOpts != null ? chartOpts.lightrect : void 0) != null ? _ref9 : "#E6E6E6"; + nullcolor = (_ref10 = chartOpts != null ? chartOpts.nullcolor : void 0) != null ? _ref10 : "#E6E6E6"; + colors = (_ref11 = chartOpts != null ? chartOpts.colors : void 0) != null ? _ref11 : ["slateblue", "white", "crimson"]; + zlim = (_ref12 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref12 : null; + zthresh = (_ref13 = chartOpts != null ? chartOpts.zthresh : void 0) != null ? _ref13 : null; + lod_ylab = (_ref14 = chartOpts != null ? chartOpts.lod_ylab : void 0) != null ? _ref14 : ""; + linecolor = (_ref15 = chartOpts != null ? chartOpts.linecolor : void 0) != null ? _ref15 : "darkslateblue"; + linewidth = (_ref16 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? _ref16 : 2; + nxticks = (_ref17 = chartOpts != null ? chartOpts.nxticks : void 0) != null ? _ref17 : 5; + xticks = (_ref18 = chartOpts != null ? chartOpts.xticks : void 0) != null ? _ref18 : null; + lod_labels = (_ref19 = chartOpts != null ? chartOpts.lod_labels : void 0) != null ? _ref19 : null; + chartdivid = (_ref20 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref20 : 'chart'; + totalh = htop + hbot + 2 * (margin.top + margin.bottom); + totalw = wleft + wright + 2 * (margin.left + margin.right); + if (lod_labels == null) { + lod_labels = times != null ? (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = times.length; _i < _len; _i++) { + x = times[_i]; + _results.push(formatAxis(times, extra_digits = 1)(x)); + } + return _results; + })() : lod_data.lodnames; + } + mylodheatmap = lodheatmap().height(htop).width(wleft).margin(margin).axispos(axispos); + svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw); + g_heatmap = svg.append("g").attr("id", "heatmap").datum(lod_data).call(mylodheatmap); + mylodchart = lodchart().height(hbot).width(wleft).margin(margin).axispos(axispos).titlepos(titlepos).chrGap(chrGap).linecolor("none").pad4heatmap(true).darkrect(darkrect).lightrect(lightrect).ylim([0, d3.max(mylodheatmap.zlim())]).pointsAtMarkers(false); + g_lodchart = svg.append("g").attr("transform", "translate(0," + (htop + margin.top + margin.bottom) + ")").attr("id", "lodchart").datum(lod_data).call(mylodchart); + lodcurve = function(chr, lodcolumn) { + return d3.svg.line().x(function(d) { + return mylodchart.xscale()[chr](d); + }).y(function(d, i) { + return mylodchart.yscale()(Math.abs(lod_data.lodByChr[chr][i][lodcolumn])); + }); + }; + lodchart_curves = null; + plotLodCurve = function(lodcolumn) { + var chr, _i, _len, _ref21, _results; + g_lodchart.selectAll("g#curves").remove(); + lodchart_curves = g_lodchart.append("g").attr("id", "lodcurves"); + _ref21 = lod_data.chrnames; + _results = []; + for (_i = 0, _len = _ref21.length; _i < _len; _i++) { + chr = _ref21[_i]; + _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none")); + } + return _results; + }; + lod4curves = { + data: [] + }; + for (pos in lod_data.pos) { + y = (function() { + var _i, _len, _ref21, _results; + _ref21 = lod_data.lodnames; + _results = []; + for (_i = 0, _len = _ref21.length; _i < _len; _i++) { + lodcolumn = _ref21[_i]; + _results.push(Math.abs(lod_data[lodcolumn][pos])); + } + return _results; + })(); + x = (function() { + var _results; + _results = []; + for (i in lod_data.lodnames) { + _results.push(+i); + } + return _results; + })(); + lod4curves.data.push({ + x: x, + y: y + }); + } + return mylodheatmap.cellSelect().on("mouseover", function(d) { + var p; + plotLodCurve(d.lodindex); + g_lodchart.select("g.title text").text("" + lod_labels[d.lodindex]); + return p = d3.format(".1f")(d.pos); + }).on("mouseout", function(d) { + lodchart_curves.remove(); + return g_lodchart.select("g.title text").text(""); + }); +}; + +iplotMScanone_noeff(lod_data = js_data.json_data); diff --git a/gn2/wqflask/static/new/javascript/loadings_plot.js b/gn2/wqflask/static/new/javascript/loadings_plot.js new file mode 100644 index 00000000..c44288c0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/loadings_plot.js @@ -0,0 +1,109 @@ +var margin = {top: 20, right: 70, bottom: 60, left: 60} + , width = 960 - margin.left - margin.right + , height = 500 - margin.top - margin.bottom; + +var x = d3.scale.linear() + .domain([d3.min(loadings, function(d) { return d[0]; }) + 0.1*d3.min(loadings, function(d) { return d[0]; }), d3.max(loadings, function(d) { return d[0]; })]) + .range([ 0, width ]); + +var y = d3.scale.linear() + .domain([d3.min(loadings, function(d) { return d[1]; }) + 0.1*d3.min(loadings, function(d) { return d[1]; }), d3.max(loadings, function(d) { return d[1]; })]) + .range([ height, 0 ]); + +var chart = d3.select('#loadings_plot') + .append('svg:svg') + .attr('width', width + margin.right + margin.left) + .attr('height', height + margin.top + margin.bottom) + .attr('class', 'chart') + +var main = chart.append('g') + .attr('transform', 'translate(' + margin.left + ',' + margin.top + ')') + .attr('width', width) + .attr('height', height) + .attr('class', 'main') + +// draw the x axis +var xAxis = d3.svg.axis() + .scale(x) + .orient('bottom'); + +main.append('g') + .attr('transform', 'translate(0,' + height + ')') + .attr('class', 'x axis') + .call(xAxis); + +chart.append("text") + .attr("class", "x label") + .attr("text-anchor", "end") + .attr("x", 550) + .attr("y", 480) + .style("font-size", 14) + .style("fill", "blue") + .text("Factor (1)"); + +chart.append("text") + .attr("class", "y label") + .attr("text-anchor", "end") + .attr("x", -200) + .attr("y", 5) + .attr("dy", ".75em") + .attr("transform", "rotate(-90)") + .style("font-size", 14) + .style("fill", "blue") + .text("Factor (2)"); + +// draw the y axis +var yAxis = d3.svg.axis() + .scale(y) + .orient('left'); + +main.append('g') + .attr('transform', 'translate(0,0)') + .attr('class', 'y axis') + .call(yAxis); + +chart.select('.x.axis') + .selectAll("text") + .style("font-size","14px"); + +chart.select('.y.axis') + .selectAll("text") + .style("font-size","14px"); + +var g = main.append("svg:g"); + +g.selectAll("scatter-dots") + .data(loadings) + .enter().append("svg:circle") + .attr("cx", function (d,i) { return x(d[0]); } ) + .attr("cy", function (d) { return y(d[1]); } ) + .attr("r", 4) + .style("fill", "blue"); + +traits_and_loadings = [] +for (i = 0; i < js_data.traits.length; i++) { + this_trait_loadings = [] + this_trait_loadings[0] = js_data.traits[i] + this_trait_loadings[1] = [loadings[i][0], loadings[i][1]] + traits_and_loadings[i] = this_trait_loadings +} + +g.selectAll("scatter-dots") + .data(traits_and_loadings) + .enter().append("text") + .attr("x", function(d, i) { return x(d[1][0]); }) + .attr("y", function(d) { return y(d[1][1]); }) + .text(function(d) { return d[0]; }) + .style("font-size", 12) + .style("fill", "blue"); + +g.selectAll("scatter-lines") + .data(loadings) + .enter().append("svg:line") + .attr("x1", x(0)) + .attr("y1", y(0)) + .attr("x2", function (d,i) {return x(d[0]); } ) + .attr("y2", function (d) { return y(d[1]); } ) + .attr("stroke-width", 1) + .attr("stroke", "red"); +
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/lod_chart.js b/gn2/wqflask/static/new/javascript/lod_chart.js new file mode 100644 index 00000000..014bf59b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/lod_chart.js @@ -0,0 +1,473 @@ +// Generated by CoffeeScript 1.9.2 +var lodchart; + +lodchart = function() { + var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; + width = 800; + height = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + manhattanPlot = false; + ylim = null; + additive_ylim = null; + nyticks = 5; + yticks = null; + additive_yticks = null; + chrGap = 8; + darkrect = "#F1F1F9"; + lightrect = "#FBFBFF"; + lodlinecolor = "darkslateblue"; + additivelinecolor_plus = "red"; + additivelinecolor_negative = "green"; + linewidth = 2; + suggestivecolor = "gainsboro"; + significantcolor = "#EBC7C7"; + pointcolor = "#E9CFEC"; + pointsize = 0; + pointstroke = "black"; + title = ""; + xlab = "Chromosome"; + ylab = "LRS score"; + additive_ylab = "Additive Effect"; + rotate_ylab = null; + yscale = d3.scale.linear(); + additive_yscale = d3.scale.linear(); + xscale = null; + pad4heatmap = false; + lodcurve = null; + lodvarname = null; + markerSelect = null; + chrSelect = null; + pointsAtMarkers = true; + chart = function(selection) { + return selection.each(function(data) { + var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, j, k, len, len1, lodvarnum, markerpoints, markertip, redraw_plot, ref, ref1, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis; + if (manhattanPlot === true) { + pointcolor = "darkslateblue"; + pointsize = 2; + } + lodvarname = lodvarname != null ? lodvarname : data.lodnames[0]; + data[lodvarname] = (function() { + var j, len, ref, results; + ref = data[lodvarname]; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + results.push(Math.abs(x)); + } + return results; + })(); + ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])]; + + if ('additive' in data) { + data['additive'] = (function() { + var j, len, ref, results; + ref = data['additive']; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + results.push(x); + } + return results; + })(); + additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])]; + } + lodvarnum = data.lodnames.indexOf(lodvarname); + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none"); + yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]); + yticks = yticks != null ? yticks : yscale.ticks(nyticks); + if ('additive' in data) { + additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]); + additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks); + } + reorgLodData(data, lodvarname); + data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale); + xscale = data.xscale; + chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { + return "chrrect" + d[0]; + }).attr("x", function(d, i) { + if (i === 0 && pad4heatmap) { + return data.chrStart[i]; + } + return data.chrStart[i] - chrGap / 2; + }).attr("width", function(d, i) { + if ((i === 0 || i + 1 === data.chrnames.length) && pad4heatmap) { + return data.chrEnd[i] - data.chrStart[i] + chrGap / 2; + } + return data.chrEnd[i] - data.chrStart[i] + chrGap; + }).attr("y", margin.top).attr("height", height).attr("fill", function(d, i) { + if (i % 2) { + return darkrect; + } + return lightrect; + }).attr("stroke", "none").on("click", function(d) { + console.log("d is:", d); + return redraw_plot(d); + }); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) { + return d[0]; + }).attr("x", function(d, i) { + return (data.chrStart[i] + data.chrEnd[i]) / 2; + }).attr("y", margin.top + height + axispos.xlabel).attr("dominant-baseline", "hanging").attr("text-anchor", "middle").attr("cursor", "pointer").on("click", function(d) { + return redraw_plot(d); + }); + xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).attr("fill", "slateblue").text(xlab); + redraw_plot = function(chr_ob) { + var chr_plot; + $('#topchart').remove(); + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale); + }; + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue"); + if ('additive' in data) { + rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1; + additive_yaxis = g.append("g").attr("class", "y axis"); + additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) { + return additive_yscale(d); + }).attr("y2", function(d) { + return additive_yscale(d); + }).attr("x1", margin.left + width).attr("x2", margin.left + width - 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("text").attr("y", function(d) { + return additive_yscale(d); + }).attr("x", function(d) { + return margin.left + width + axispos.ylabel + 20; + }).attr("fill", "green").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) { + return formatAxis(additive_yticks)(d); + }); + additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "").attr("text-anchor", "middle").attr("fill", "green"); + } + if ('suggestive' in data) { + suggestive_bar = g.append("g").attr("class", "suggestive"); + suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none"); + suggestive_bar = g.append("g").attr("class", "significant"); + suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none"); + } + if (manhattanPlot === false) { + lodcurve = function(chr, lodcolumn) { + return d3.svg.line().x(function(d) { + return xscale[chr](d); + }).y(function(d, i) { + return yscale(data.lodByChr[chr][i][lodcolumn]); + }); + }; + if ('additive' in data) { + additivecurve = function(chr, lodcolumn) { + if (data.additiveByChr[chr][0] < 0) { + pos_neg = "negative" + } + else { + pos_neg = "positive" + } + return [pos_neg, d3.svg.line().x(function(d) { + return xscale[chr](d); + }).y(function(d, i) { + return additive_yscale(Math.abs(data.additiveByChr[chr][i])); + })]; + }; + } + curves = g.append("g").attr("id", "curves"); + ref = data.chrnames; + for (j = 0, len = ref.length; j < len; j++) { + chr = ref[j]; + if (chr.indexOf(data['chr'])) { + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"); + } + } + if ('additive' in data) { + ref1 = data.chrnames; + for (k = 0, len1 = ref1.length; k < len1; k++) { + chr = ref1[k]; + if (chr.indexOf(data['chr'])) { + if (additivecurve(chr[0], lodvarnum)[0] == "negative") { + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); + } + else { + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); + } + } + } + } + } + console.log("before pointsize"); + if (pointsize > 0) { + console.log("pointsize > 0 !!!"); + } + markerpoints = g.append("g").attr("id", "markerpoints_visible"); + markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) { + return xscale[d.chr](d.pos); + }).attr("cy", function(d) { + return yscale(d.lod); + }).attr("r", pointsize).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden"); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", function() { + if (pad4heatmap) { + return data.chrEnd.slice(-1)[0] - margin.left; + } + return data.chrEnd.slice(-1)[0] - margin.left + chrGap / 2; + }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + if (pointsAtMarkers) { + hiddenpoints = g.append("g").attr("id", "markerpoints_hidden"); + markertip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return [d.name, " LRS = " + (d3.format('.2f')(d.lod))]; + }).direction("e").offset([0, 10]); + svg.call(markertip); + return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) { + return xscale[d.chr](d.pos); + }).attr("cy", function(d) { + return yscale(d.lod); + }).attr("id", function(d) { + return d.name; + }).attr("r", d3.max([pointsize * 2, 3])).attr("opacity", 0).attr("fill", pointcolor).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover.paneltip", function(d) { + d3.select(this).attr("opacity", 1); + return markertip.show(d); + }).on("mouseout.paneltip", function() { + return d3.select(this).attr("opacity", 0).call(markertip.hide); + }); + } + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.manhattanPlot = function(value) { + if (!arguments.length) { + return manhattanPlot; + } + manhattanPlot = value; + return chart; + }; + chart.mappingScale = function(value) { + if (!arguments.length) { + return mappingScale; + } + mappingScale = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.additive_ylim = function(value) { + if (!arguments.length) { + return additive_ylim; + } + additive_ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.chrGap = function(value) { + if (!arguments.length) { + return chrGap; + } + chrGap = value; + return chart; + }; + chart.darkrect = function(value) { + if (!arguments.length) { + return darkrect; + } + darkrect = value; + return chart; + }; + chart.lightrect = function(value) { + if (!arguments.length) { + return lightrect; + } + lightrect = value; + return chart; + }; + chart.linecolor = function(value) { + var linecolor; + if (!arguments.length) { + return linecolor; + } + linecolor = value; + return chart; + }; + chart.linewidth = function(value) { + if (!arguments.length) { + return linewidth; + } + linewidth = value; + return chart; + }; + chart.pointcolor = function(value) { + if (!arguments.length) { + return pointcolor; + } + pointcolor = value; + return chart; + }; + chart.pointsize = function(value) { + if (!arguments.length) { + return pointsize; + } + pointsize = value; + return chart; + }; + chart.pointstroke = function(value) { + if (!arguments.length) { + return pointstroke; + } + pointstroke = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.lodvarname = function(value) { + if (!arguments.length) { + return lodvarname; + } + lodvarname = value; + return chart; + }; + chart.pad4heatmap = function(value) { + if (!arguments.length) { + return pad4heatmap; + } + pad4heatmap = value; + return chart; + }; + chart.pointsAtMarkers = function(value) { + if (!arguments.length) { + return pointsAtMarkers; + } + pointsAtMarkers = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.additive_yscale = function() { + return additive_yscale; + }; + chart.xscale = function() { + return xscale; + }; + if (manhattanPlot === false) { + chart.lodcurve = function() { + return lodcurve; + }; + } + chart.additivecurve = function() { + return additivecurve; + }; + chart.markerSelect = function() { + return markerSelect; + }; + chart.chrSelect = function() { + return chrSelect; + }; + return chart; +};
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/lodheatmap.js b/gn2/wqflask/static/new/javascript/lodheatmap.js new file mode 100644 index 00000000..b82c95ad --- /dev/null +++ b/gn2/wqflask/static/new/javascript/lodheatmap.js @@ -0,0 +1,277 @@ +// Generated by CoffeeScript 1.8.0 +var lodheatmap; + +lodheatmap = function() { + var axispos, cellSelect, chart, chrGap, colors, height, margin, rectcolor, rotate_ylab, title, titlepos, width, xlab, xscale, ylab, yscale, zlim, zscale, zthresh; + width = 1200; + height = 600; + margin = { + left: 100, + top: 40, + right: 40, + bottom: 40 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + chrGap = 8; + titlepos = 20; + rectcolor = d3.rgb(230, 230, 230); + colors = ["slateblue", "white", "red"]; + title = ""; + xlab = "Chromosome"; + ylab = ""; + rotate_ylab = null; + zlim = null; + zthresh = null; + xscale = d3.scale.linear(); + yscale = d3.scale.linear(); + zscale = d3.scale.linear(); + cellSelect = null; + chart = function(selection) { + return selection.each(function(data) { + var cells, celltip, chr, chr_ob, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4; + data = reorgLodData(data); + data = chrscales(data, width, chrGap, margin.left, true); + xscale = data.xscale; + nlod = data.lodnames.length; + yscale.domain([-0.5, nlod - 0.5]).range([margin.top + height, margin.top]); + rectHeight = yscale(0) - yscale(1); + xLR = {}; + _ref = data.chrnames; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + chr = _ref[_i]; + if (data.posByChr[chr[0]].length > 0){ + xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); + } + } + zmin = 0; + zmax = 0; + _ref1 = data.lodnames; + for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { + lodcol = _ref1[_j]; + extent = d3.extent(data[lodcol]); + if (extent[0] < zmin) { + zmin = extent[0]; + } + if (extent[1] > zmax) { + zmax = extent[1]; + } + } + if (-zmin > zmax) { + zmax = -zmin; + } + zlim = zlim != null ? zlim : [-zmax, 0, zmax]; + if (zlim.length !== colors.length) { + console.log("zlim.length (" + zlim.length + ") != colors.length (" + colors.length + ")"); + } + zscale.domain(zlim).range(colors); + zthresh = zthresh != null ? zthresh : zmin - 1; + data.cells = []; + _ref2 = data.chrnames; + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + chr_ob = _ref2[_k]; + chr = chr_ob[0]; + _ref3 = data.posByChr[chr]; + for (i = _l = 0, _len3 = _ref3.length; _l < _len3; i = ++_l) { + pos = _ref3[i]; + _ref4 = data.lodByChr[chr][i]; + for (j = _m = 0, _len4 = _ref4.length; _m < _len4; j = ++_m) { + lod = _ref4[j]; + if (lod >= zthresh || lod <= -zthresh) { + data.cells.push({ + z: lod, + left: (xscale[chr](pos) + xscale[chr](xLR[chr][pos].left)) / 2, + right: (xscale[chr](pos) + xscale[chr](xLR[chr][pos].right)) / 2, + lodindex: j, + chr: chr, + pos: pos + }); + } + } + } + } + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { + return "box" + d[0]; + }).attr("x", function(d, i) { + return data.chrStart[i]; + }).attr("y", function(d) { + return margin.top; + }).attr("height", height).attr("width", function(d, i) { + return data.chrEnd[i] - data.chrStart[i]; + }).attr("fill", rectcolor).attr("stroke", "none"); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("x", function(d, i) { + return (data.chrStart[i] + data.chrEnd[i]) / 2; + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return d[0]; + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab); + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + yaxis.selectAll("empty").data(data.lodnames).enter().append("text").attr("id", function(d, i) { + return "yaxis" + i; + }).attr("y", function(d, i) { + return yscale(i); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return d; + }).attr("opacity", 0); + celltip = d3.tip().attr('class', 'd3-tip').html(function(d) { + var p, z; + z = d3.format(".2f")(Math.abs(d.z)); + p = d3.format(".1f")(d.pos); + return "" + d.chr + "@" + p + " → " + z; + }).direction('e').offset([0, 10]); + svg.call(celltip); + cells = g.append("g").attr("id", "cells"); + cellSelect = cells.selectAll("empty").data(data.cells).enter().append("rect").attr("x", function(d) { + return d.left; + }).attr("y", function(d) { + return yscale(d.lodindex) - rectHeight / 2; + }).attr("width", function(d) { + return d.right - d.left; + }).attr("height", rectHeight).attr("class", function(d, i) { + return "cell" + i; + }).attr("fill", function(d) { + return zscale(d.z); + }).attr("stroke", "none").attr("stroke-width", "1").on("mouseover.paneltip", function(d) { + yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 1); + d3.select(this).attr("stroke", "black"); + return celltip.show(d, this); + }).on("mouseout.paneltip", function(d) { + yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 0); + d3.select(this).attr("stroke", "none"); + return celltip.hide(); + }); + return g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { + return "box" + d; + }).attr("x", function(d, i) { + return data.chrStart[i]; + }).attr("y", function(d) { + return margin.top; + }).attr("height", height).attr("width", function(d, i) { + return data.chrEnd[i] - data.chrStart[i]; + }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.colors = function(value) { + if (!arguments.length) { + return colors; + } + colors = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.zthresh = function(value) { + if (!arguments.length) { + return zthresh; + } + zthresh = value; + return chart; + }; + chart.zlim = function(value) { + if (!arguments.length) { + return zlim; + } + zlim = value; + return chart; + }; + chart.chrGap = function(value) { + if (!arguments.length) { + return chrGap; + } + chrGap = value; + return chart; + }; + chart.xscale = function() { + return xscale; + }; + chart.yscale = function() { + return yscale; + }; + chart.zscale = function() { + return zscale; + }; + chart.cellSelect = function() { + return cellSelect; + }; + return chart; +}; diff --git a/gn2/wqflask/static/new/javascript/login.js b/gn2/wqflask/static/new/javascript/login.js new file mode 100644 index 00000000..2fe9ba3c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/login.js @@ -0,0 +1,41 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + var form_success, modalize, submit_form; + modalize = function(event) { + event.preventDefault(); + console.log("in modal_replace:", $(this).attr("href")); + return $.colorbox({ + open: true, + href: this.href, + onComplete: function() { + return $(".focused").focus(); + } + }); + }; + $(document).one("click", ".modalize", modalize); + console.log("Modalized click!!!"); + form_success = function(data) { + return $.colorbox({ + open: true, + html: data, + onComplete: function() { + return $("form").on("submit", submit_form); + } + }); + }; + submit_form = function(event) { + var data, submit_to; + event.preventDefault(); + submit_to = $(this).attr('action'); + data = $(this).serialize(); + console.log("submit_to is:", submit_to); + return $.ajax({ + type: "POST", + url: submit_to, + data: data, + dataType: "html", + success: form_success + }); + }; + return $("#colorbox form").on("submit", submit_form); +}); diff --git a/gn2/wqflask/static/new/javascript/network_graph.js b/gn2/wqflask/static/new/javascript/network_graph.js new file mode 100644 index 00000000..480443ee --- /dev/null +++ b/gn2/wqflask/static/new/javascript/network_graph.js @@ -0,0 +1,259 @@ +var default_style = [ // the stylesheet for the graph + { + selector: 'node', + style: { + 'background-color': '#666', + 'label': 'data(label)', + 'font-size': 10 + } + }, + + { + selector: 'edge', + style: { + 'width': 'data(width)', + 'line-color': 'data(color)', + 'target-arrow-color': '#ccc', + 'target-arrow-shape': 'triangle', + 'font-size': 8 + } + } + ] + +var default_layout = { name: 'circle', + fit: true, // whether to fit the viewport to the graph + padding: 30 // the padding on fit + //idealEdgeLength: function( edge ){ return edge.data['correlation']*10; }, + } + +window.onload=function() { + // id of Cytoscape Web container div + //var div_id = "cytoscapeweb"; + + var cy = cytoscape({ + container: $('#cytoscapeweb'), // container to render in + + elements: elements_list, + + style: default_style, + + zoom: 12, + layout: default_layout, + + zoomingEnabled: true, + userZoomingEnabled: true, + panningEnabled: true, + userPanningEnabled: true, + boxSelectionEnabled: false, + selectionType: 'single', + + // rendering options: + styleEnabled: true + }); + + var eles = cy.$() // var containing all elements, so elements can be restored after being removed + + var defaults = { + zoomFactor: 0.05, // zoom factor per zoom tick + zoomDelay: 45, // how many ms between zoom ticks + minZoom: 0.1, // min zoom level + maxZoom: 10, // max zoom level + fitPadding: 30, // padding when fitting + panSpeed: 10, // how many ms in between pan ticks + panDistance: 10, // max pan distance per tick + panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction) + panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed) + panInactiveArea: 8, // radius of inactive area in pan drag box + panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0 + zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution) + fitSelector: undefined, // selector of elements to fit + animateOnFit: function(){ // whether to animate on fit + return false; + }, + fitAnimationDuration: 1000, // duration of animation on fit + + // icon class names + sliderHandleIcon: 'fa fa-minus', + zoomInIcon: 'fa fa-plus', + zoomOutIcon: 'fa fa-minus', + resetIcon: 'fa fa-expand' + }; + + cy.panzoom( defaults ); + + function create_qtips(cy){ + cy.nodes().qtip({ + content: function(){ + qtip_content = '' + gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().id.split(":")[0] + '&dataset=' + this.data().id.split(":")[1] + '" >'+this.data().id +'</a>'+'</b><br>' + qtip_content += gn_link + if (typeof(this.data().geneid) !== 'undefined'){ + ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>' + qtip_content += ncbi_link + } + if (typeof(this.data().omim) !== 'undefined'){ + omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>' + qtip_content += omim_link + } + return qtip_content + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + + cy.edges().qtip({ + content: function(){ + correlation_line = '<b>Sample r: ' + this.data().correlation + '</b><br>' + p_value_line = 'Sample p(r): ' + this.data().p_value + '<br>' + overlap_line = 'Overlap: ' + this.data().overlap + '<br>' + scatter_plot = '<a href="' + gn2_url + '/corr_scatter_plot?method=pearson&dataset_1=' + this.data().source.split(":")[1] + '&dataset_2=' + this.data().target.split(":")[1] + '&trait_1=' + this.data().source.split(":")[0] + '&trait_2=' + this.data().target.split(":")[0] + '" >View Scatterplot</a>' + return correlation_line + p_value_line + overlap_line + scatter_plot + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + } + + create_qtips(cy) + + $('#neg_slide').change(function() { + eles.restore() + + pos_slide_val = $('#pos_slide').val(); + cy.$("node[max_corr > " + $(this).val() + "][max_corr < " + pos_slide_val + "]").remove(); + cy.$("edge[correlation > " + $(this).val() + "][correlation < " + pos_slide_val + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + + }); + $('#pos_slide').change(function() { + eles.restore() + + neg_slide_val = $('#neg_slide').val(); + cy.$("node[max_corr > " + neg_slide_val +"][max_corr < " + $(this).val() + "]").remove(); + cy.$("edge[correlation > " + neg_slide_val +"][correlation < " + $(this).val() + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + + }); + + $('#reset_graph').click(function() { + eles.restore() + $('#pos_slide').val(0) + $('#neg_slide').val(0) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=focus_select]').change(function() { + focus_trait = $(this).val() + + eles.restore() + cy.$('edge[source != "' + focus_trait + '"][target != "' + focus_trait + '"]').remove() + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=layout_select]').change(function() { + layout_type = $(this).val() + cy.layout({ name: layout_type, + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=font_size]').change(function() { + font_size = $(this).val() + + new_style = default_style + new_style[0]['style']['font-size'] = parseInt(font_size) + cy.style().fromJson(new_style).update() + }); + $('select[name=edge_width]').change(function() { + //eles.restore() + + //ZS: This is needed, or else it alters the original object + orig_elements = JSON.parse(JSON.stringify(elements_list)); + + width_multiplier = $(this).val() + updated_elements = [] + for (i=0; i < orig_elements.length; i++){ + this_element = orig_elements[i] + if ('source' in this_element['data']) { + orig_width = this_element['data']['width'] + this_element['data']['width'] = orig_width * width_multiplier + } + updated_elements.push(this_element) + } + cy.remove(eles) + cy.add(updated_elements) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=edge_width]').change(function() { + //eles.restore() + + //ZS: This is needed, or else it alters the original object + orig_elements = JSON.parse(JSON.stringify(elements_list)); + + width_multiplier = $(this).val() + updated_elements = [] + for (i=0; i < orig_elements.length; i++){ + this_element = orig_elements[i] + if ('source' in this_element['data']) { + orig_width = this_element['data']['width'] + this_element['data']['width'] = orig_width * width_multiplier + } + updated_elements.push(this_element) + } + cy.remove(eles) + cy.add(updated_elements) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $("a#image_link").click(function(e) { + var pngData = cy.png(); + + $(this).attr('href', pngData); + $(this).attr('download', 'network_graph.png'); + }); + + +}; + + diff --git a/gn2/wqflask/static/new/javascript/panelutil.js b/gn2/wqflask/static/new/javascript/panelutil.js new file mode 100644 index 00000000..ea55a7cf --- /dev/null +++ b/gn2/wqflask/static/new/javascript/panelutil.js @@ -0,0 +1,462 @@ +// Generated by CoffeeScript 1.8.0 +var abs, calc_crosstab, chrscales, colSums, displayError, expand2vector, forceAsArray, formatAxis, getLeftRight, log10, log2, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, missing2null, pullVarAsArray, reorgLodData, rowSums, selectGroupColors, sumArray, transpose, unique; + +formatAxis = function(d, extra_digits) { + var ndig; + if (extra_digits == null) { + extra_digits = 0; + } + d = d[1] - d[0]; + ndig = Math.floor(Math.log(d % 10) / Math.log(10)); + if (ndig > 0) { + ndig = 0; + } + ndig = Math.abs(ndig) + extra_digits; + return d3.format("." + ndig + "f"); +}; + +unique = function(x) { + var output, v, _i, _len, _results; + output = {}; + for (_i = 0, _len = x.length; _i < _len; _i++) { + v = x[_i]; + if (v) { + output[v] = v; + } + } + _results = []; + for (v in output) { + _results.push(output[v]); + } + return _results; +}; + +pullVarAsArray = function(data, variable) { + var i, v; + v = []; + for (i in data) { + v = v.concat(data[i][variable]); + } + return v; +}; + +reorgLodData = function(data, lodvarname) { + var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2; + if (lodvarname == null) { + lodvarname = null; + } + data.posByChr = {}; + data.lodByChr = {}; + if ('additive' in data){ + data.additiveByChr = {}; + } + _ref = data.chrnames; + for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) { + chr = _ref[i]; + data.posByChr[chr[0]] = []; + data.lodByChr[chr[0]] = []; + if ('additive' in data){ + data.additiveByChr[chr[0]] = []; + } + _ref1 = data.pos; + + for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) { + pos = _ref1[j]; + if (data.chr[j].toString() === chr[0]) { + data.posByChr[chr[0]].push(pos); + if (!Array.isArray(data.lodnames)) { + data.lodnames = [data.lodnames]; + } + lodval = (function() { + var _k, _len2, _ref2, _results; + _ref2 = data.lodnames; + _results = []; + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + lodcolumn = _ref2[_k]; + _results.push(data[lodcolumn][j]); + } + return _results; + })(); + data.lodByChr[chr[0]].push(lodval); + + if ('additive' in data){ + addval = data['additive'][j] + data.additiveByChr[chr[0]].push(addval); + } + + } + } + } + if (lodvarname != null) { + data.markers = []; + _ref2 = data.markernames; + for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) { + marker = _ref2[i]; + if (marker !== "") { + data.markers.push({ + name: marker, + chr: data.chr[i], + pos: data.pos[i], + lod: data[lodvarname][i] + }); + } + } + } + return data; +}; + +chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) { + var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1; + chrStart = []; + chrEnd = []; + chrLength = []; + totalChrLength = 0; + maxd = 0; + _ref = data.chrnames; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + chr = _ref[_i]; + d = maxdiff(data.posByChr[chr[0]]); + if (d > maxd) { + maxd = d; + } + //rng = d3.extent(data.posByChr[chr[0]]); + //chrStart.push(rng[0]); + //chrEnd.push(rng[1]); + //L = rng[1] - rng[0]; + chrStart.push(0); + chrEnd.push(chr[1]); + L = chr[1] + chrLength.push(L); + totalChrLength += L; + } + if (pad4heatmap) { + data.recwidth = maxd; + chrStart = chrStart.map(function(x) { + return x - maxd / 2; + }); + chrEnd = chrEnd.map(function(x) { + return x + maxd / 2; + }); + chrLength = chrLength.map(function(x) { + return x + maxd; + }); + totalChrLength += chrLength.length * maxd; + } + data.chrStart = []; + data.chrEnd = []; + cur = leftMargin; + if (!pad4heatmap) { + cur += chrGap / 2; + } + data.xscale = {}; + _ref1 = data.chrnames; + for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) { + chr = _ref1[i]; + data.chrStart.push(cur); + w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]); + data.chrEnd.push(cur + w); + cur = data.chrEnd[i] + chrGap; + + if (mappingScale == "morgan") { + max_pos = d3.max(data.posByChr[chr[0]]) + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]); + } + else { + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); + } + } + return data; +}; + +selectGroupColors = function(ngroup, palette) { + if (ngroup === 0) { + return []; + } + if (palette === "dark") { + if (ngroup === 1) { + return ["slateblue"]; + } + if (ngroup === 2) { + return ["MediumVioletRed", "slateblue"]; + } + if (ngroup <= 9) { + return colorbrewer.Set1[ngroup]; + } + return d3.scale.category20().range().slice(0, ngroup); + } else { + if (ngroup === 1) { + return ["#bebebe"]; + } + if (ngroup === 2) { + return ["lightpink", "lightblue"]; + } + if (ngroup <= 9) { + return colorbrewer.Pastel1[ngroup]; + } + return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup); + } +}; + +expand2vector = function(input, n) { + var i; + if (input == null) { + return input; + } + if (Array.isArray(input) && input.length >= n) { + return input; + } + if (!Array.isArray(input)) { + input = [input]; + } + if (input.length === 1 && n > 1) { + input = (function() { + var _results; + _results = []; + for (i in d3.range(n)) { + _results.push(input[0]); + } + return _results; + })(); + } + return input; +}; + +median = function(x) { + var n; + if (x == null) { + return null; + } + n = x.length; + x.sort(function(a, b) { + return a - b; + }); + if (n % 2 === 1) { + return x[(n - 1) / 2]; + } + return (x[n / 2] + x[(n / 2) - 1]) / 2; +}; + +getLeftRight = function(x) { + var i, n, result, v, xdif, _i, _j, _k, _len, _ref; + n = x.length; + x.sort(function(a, b) { + return a - b; + }); + xdif = []; + result = {}; + for (_i = 0, _len = x.length; _i < _len; _i++) { + v = x[_i]; + result[v] = {}; + } + for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) { + xdif.push(x[i] - x[i - 1]); + result[x[i]].left = x[i - 1]; + } + for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) { + result[x[i]].right = x[i + 1]; + } + xdif = median(xdif); + result.mediandiff = xdif; + result[x[0]].left = x[0] - xdif; + result[x[n - 1]].right = x[n - 1] + xdif; + result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2]; + return result; +}; + +maxdiff = function(x) { + var d, i, result, _i, _ref; + if (x.length < 2) { + return null; + } + result = x[1] - x[0]; + if (x.length < 3) { + return result; + } + for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) { + d = x[i] - x[i - 1]; + if (d > result) { + result = d; + } + } + return result; +}; + +matrixMin = function(mat) { + var i, j, result; + result = mat[0][0]; + for (i in mat) { + for (j in mat[i]) { + if (result > mat[i][j]) { + result = mat[i][j]; + } + } + } + return result; +}; + +matrixMax = function(mat) { + var i, j, result; + result = mat[0][0]; + for (i in mat) { + for (j in mat[i]) { + if (result < mat[i][j]) { + result = mat[i][j]; + } + } + } + return result; +}; + +matrixMaxAbs = function(mat) { + var i, j, result; + result = Math.abs(mat[0][0]); + for (i in mat) { + for (j in mat[i]) { + if (result < mat[i][j]) { + result = Math.abs(mat[i][j]); + } + } + } + return result; +}; + +matrixExtent = function(mat) { + return [matrixMin(mat), matrixMax(mat)]; +}; + +d3.selection.prototype.moveToFront = function() { + return this.each(function() { + return this.parentNode.appendChild(this); + }); +}; + +d3.selection.prototype.moveToBack = function() { + return this.each(function() { + var firstChild; + firstChild = this.parentNode.firstchild; + if (firstChild) { + return this.parentNode.insertBefore(this, firstChild); + } + }); +}; + +forceAsArray = function(x) { + if (x == null) { + return x; + } + if (Array.isArray(x)) { + return x; + } + return [x]; +}; + +missing2null = function(vec, missingvalues) { + if (missingvalues == null) { + missingvalues = ['NA', '']; + } + return vec.map(function(value) { + if (missingvalues.indexOf(value) > -1) { + return null; + } else { + return value; + } + }); +}; + +displayError = function(message) { + if (d3.select("div.error").empty()) { + d3.select("body").insert("div", ":first-child").attr("class", "error"); + } + return d3.select("div.error").append("p").text(message); +}; + +sumArray = function(vec) { + return vec.reduce(function(a, b) { + return a + b; + }); +}; + +calc_crosstab = function(data) { + var col, cs, i, ncol, nrow, result, row, rs, _i, _j; + nrow = data.ycat.length; + ncol = data.xcat.length; + result = (function() { + var _i, _results; + _results = []; + for (row = _i = 0; 0 <= nrow ? _i <= nrow : _i >= nrow; row = 0 <= nrow ? ++_i : --_i) { + _results.push((function() { + var _j, _results1; + _results1 = []; + for (col = _j = 0; 0 <= ncol ? _j <= ncol : _j >= ncol; col = 0 <= ncol ? ++_j : --_j) { + _results1.push(0); + } + return _results1; + })()); + } + return _results; + })(); + for (i in data.x) { + result[data.y[i]][data.x[i]] += 1; + } + rs = rowSums(result); + cs = colSums(result); + for (i = _i = 0; 0 <= ncol ? _i < ncol : _i > ncol; i = 0 <= ncol ? ++_i : --_i) { + result[nrow][i] = cs[i]; + } + for (i = _j = 0; 0 <= nrow ? _j < nrow : _j > nrow; i = 0 <= nrow ? ++_j : --_j) { + result[i][ncol] = rs[i]; + } + result[nrow][ncol] = sumArray(rs); + return result; +}; + +rowSums = function(mat) { + var x, _i, _len, _results; + _results = []; + for (_i = 0, _len = mat.length; _i < _len; _i++) { + x = mat[_i]; + _results.push(sumArray(x)); + } + return _results; +}; + +transpose = function(mat) { + var i, j, _i, _ref, _results; + _results = []; + for (j = _i = 0, _ref = mat[0].length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) { + _results.push((function() { + var _j, _ref1, _results1; + _results1 = []; + for (i = _j = 0, _ref1 = mat.length; 0 <= _ref1 ? _j < _ref1 : _j > _ref1; i = 0 <= _ref1 ? ++_j : --_j) { + _results1.push(mat[i][j]); + } + return _results1; + })()); + } + return _results; +}; + +colSums = function(mat) { + return rowSums(transpose(mat)); +}; + +log2 = function(x) { + if (x == null) { + return x; + } + return Math.log(x) / Math.log(2.0); +}; + +log10 = function(x) { + if (x == null) { + return x; + } + return Math.log(x) / Math.log(10.0); +}; + +abs = function(x) { + if (x == null) { + return x; + } + return Math.abs(x); +};
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/partial_correlations.js b/gn2/wqflask/static/new/javascript/partial_correlations.js new file mode 100644 index 00000000..5de1204c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/partial_correlations.js @@ -0,0 +1,26 @@ +function selected_traits() { + traits = $("#trait_table input:checked").map(function() { + return $(this).attr("data-trait-info"); + }).get(); + if (traits.length == 0){ + num_traits = $("#trait_table input").length + if (num_traits <= 100){ + traits = $("#trait_table input").map(function() { + return $(this).attr("data-trait-info"); + }).get(); + } + } + return traits +} + +$("#partial-correlations").on("click", function() { + // Submit the form to the `partial_correlations` endpoint + url = $(this).data("url") + traits = selected_traits(); + $("#trait_list").val(traits.reduce(function(acc, str) { + return acc.concat(";;;".concat(str)); + })); + $("input[name=tool_used]").val("Partial Correlation") + $("input[name=form_url]").val(url) + return submit_special(url) +}) diff --git a/gn2/wqflask/static/new/javascript/password_strength.js b/gn2/wqflask/static/new/javascript/password_strength.js new file mode 100644 index 00000000..a8a45f7d --- /dev/null +++ b/gn2/wqflask/static/new/javascript/password_strength.js @@ -0,0 +1,57 @@ +// Generated by CoffeeScript 1.8.0 + +$(function() { + var word_score; + $("#password").keyup(function() { + var crack_time, display, passtext, result, word; + passtext = $(this).val(); + result = zxcvbn(passtext); + if (passtext.length < 6) { + let error_message = `<strong style="color:red;">the password must have a length greater than six characters</strong>` + $("#password_strength").html(error_message); + return $("#password_alert").fadeIn(); + } else { + word = word_score(result.score); + crack_time = result.crack_times_display.online_throttling_100_per_hour; + if (crack_time === "instant") { + crack_time = "a second"; + } + display = `This is ${word} password.` + $("#password_strength").html(display); + return $("#password_alert").fadeIn(); + } + }); + return word_score = function(num_score) { + num_score = parseInt(num_score); + console.log("num_score is:", num_score); + + let passwordFeedback = { + 0:{ + color:"#cc1818", + feedback:"a weak" + }, + + 1:{ + color:"#cc1818", + feedback:"a bad" + }, + + 2:{ + color:"#f59105", + feedback:"a mediocre" + }, + + 3:{ + color:"#44ba34", + feedback:"a strong" + }, + 4:{ + color:"green", + feedback:"a stronger" + } + } + + let mappingResult = `<strong style="color:${passwordFeedback[num_score].color};">${passwordFeedback[num_score].feedback}</strong>` + return mappingResult; + }; +}); diff --git a/gn2/wqflask/static/new/javascript/plotly_probability_plot.js b/gn2/wqflask/static/new/javascript/plotly_probability_plot.js new file mode 100644 index 00000000..bc1e021b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/plotly_probability_plot.js @@ -0,0 +1,308 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var get_z_scores, redraw_prob_plot, root; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + get_z_scores = function(n) { + var i, j, osm_uniform, ref, x; + osm_uniform = new Array(n); + osm_uniform[n - 1] = Math.pow(0.5, 1.0 / n); + osm_uniform[0] = 1 - osm_uniform[n - 1]; + for (i = j = 1, ref = n - 2; 1 <= ref ? j <= ref : j >= ref; i = 1 <= ref ? ++j : --j) { + osm_uniform[i] = (i + 1 - 0.3175) / (n + 0.365); + } + return (function() { + var k, len, results; + results = []; + for (k = 0, len = osm_uniform.length; k < len; k++) { + x = osm_uniform[k]; + results.push(jStat.normal.inv(x, 0, 1)); + } + return results; + })(); + }; + + redraw_prob_plot = function(samples, sample_group) { + var container, h, margin, totalh, totalw, w; + h = 550; + w = 600; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + totalh = h + margin.top + margin.bottom; + totalw = w + margin.left + margin.right; + container = $("#prob_plot_container"); + container.width(totalw); + container.height(totalh); + var W, all_samples, chart, data, intercept, make_data, names, pvalue, pvalue_str, slope, sorted_names, sorted_values, sw_result, test_str, x, z_scores; + all_samples = samples[sample_group]; + names = (function() { + var j, len, ref, results; + ref = _.keys(all_samples); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + if (all_samples[x] !== null) { + results.push(x); + } + } + return results; + })(); + sorted_names = names.sort(function(x, y) { + return all_samples[x].value - all_samples[y].value; + }); + max_decimals = 0 + sorted_values = (function() { + var j, len, results; + results = []; + for (j = 0, len = sorted_names.length; j < len; j++) { + x = sorted_names[j]; + results.push(all_samples[x].value); + if (all_samples[x].value.countDecimals() > max_decimals) { + max_decimals = all_samples[x].value.countDecimals()-1 + } + } + return results; + })(); + //ZS: 0.1 indicates buffer, increase to increase buffer + y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1] + //sw_result = ShapiroWilkW(sorted_values); + //W = sw_result.w.toFixed(3); + //pvalue = sw_result.p.toFixed(3); + //pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>"; + //test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")"; + z_scores = get_z_scores(sorted_values.length); + //ZS: 0.1 indicates buffer, increase to increase buffer + x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1] + slope = jStat.stdev(sorted_values); + intercept = jStat.mean(sorted_values); + make_data = function(group_name) { + var sample, value, z_score; + return { + key: js_data.sample_group_types[group_name], + slope: slope, + intercept: intercept, + values: (function() { + var j, len, ref, ref1, results; + ref = _.zip(get_z_scores(sorted_values.length), sorted_values, sorted_names); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + ref1 = ref[j], z_score = ref1[0], value = ref1[1], sample = ref1[2]; + if (sample in samples[group_name]) { + results.push({ + x: z_score, + y: value, + name: sample + }); + } + } + return results; + })() + }; + }; + data = [make_data('samples_primary'), make_data('samples_other'), make_data('samples_all')]; + x_values = {} + y_values = {} + point_names = {} + for (i = 0; i < 3; i++){ + these_x_values = [] + these_y_values = [] + these_names = [] + for (j = 0; j < data[i].values.length; j++){ + these_x_values.push(data[i].values[j].x) + these_y_values.push(data[i].values[j].y) + these_names.push(data[i].values[j].name) + } + if (i == 0){ + x_values['samples_primary'] = these_x_values + y_values['samples_primary'] = these_y_values + point_names['samples_primary'] = these_names + } else if (i == 1) { + x_values['samples_other'] = these_x_values + y_values['samples_other'] = these_y_values + point_names['samples_other'] = these_names + } else { + x_values['samples_all'] = these_x_values + y_values['samples_all'] = these_y_values + point_names['samples_all'] = these_names + } + } + + intercept_line = {} + + if (sample_group == "samples_primary"){ + first_x = Math.floor(x_values['samples_primary'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_primary'][x_values['samples_primary'].length - 1]) + last_x = last_x + last_x*0.1 + first_value = data[0].intercept + data[0].slope * first_x + last_value = data[0].intercept + data[0].slope * last_x + intercept_line['samples_primary'] = [[first_x, last_x], [first_value, last_value]] + } else if (sample_group == "samples_other") { + first_x = Math.floor(x_values['samples_other'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_other'][x_values['samples_other'].length - 1]) + last_x = last_x + last_x*0.1 + first_value = data[1].intercept + data[1].slope * first_x + last_value = data[1].intercept + data[1].slope * last_x + intercept_line['samples_other'] = [[first_x, last_x], [first_value, last_value]] + } else { + first_x = Math.floor(x_values['samples_all'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_all'][x_values['samples_all'].length - 1]) + first_value = data[2].intercept + data[2].slope * first_x + last_x = last_x + last_x*0.1 + last_value = data[2].intercept + data[2].slope * last_x + intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]] + } + + val_range = Math.max(...y_values['samples_all']) - Math.min(...y_values['samples_all']) + if (val_range < 4){ + tick_digits = '.1f' + } else if (val_range < 0.4) { + tick_digits = '.2f' + } else { + tick_digits = 'f' + } + + var layout = { + title: { + x: 0, + y: 10, + xanchor: 'left', + text: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", + }, + margin: { + l: 100, + r: 30, + t: 100, + b: 60 + }, + legend: { + x: 0.05, + y: 0.9, + xanchor: 'left' + }, + xaxis: { + title: "<b>normal quantiles</b>", + range: [first_x, last_x], + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + titlefont: { + family: "arial", + size: 16 + }, + ticklen: 4, + tickfont: { + size: 16 + } + }, + yaxis: { + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + title: "<b>" + js_data.unit_type + "</b>", + titlefont: { + family: "arial", + size: 16 + }, + ticklen: 4, + tickfont: { + size: 16 + }, + tickformat: tick_digits, + automargin: true + }, + width: 600, + height: 600, + hovermode: "closest", + dragmode: false + } + + var primary_trace = { + x: x_values['samples_primary'], + y: y_values['samples_primary'], + mode: 'markers', + type: 'scatter', + name: 'Samples', + text: point_names['samples_primary'], + marker: { + color: 'blue', + width: 6 + } + } + if ("samples_other" in js_data.sample_group_types) { + var other_trace = { + x: x_values['samples_other'], + y: y_values['samples_other'], + mode: 'markers', + type: 'scatter', + name: js_data.sample_group_types['samples_other'], + text: point_names['samples_other'], + marker: { + color: 'blue', + width: 6 + } + } + } + + if (sample_group == "samples_primary"){ + var primary_intercept_trace = { + x: intercept_line['samples_primary'][0], + y: intercept_line['samples_primary'][1], + mode: 'lines', + type: 'scatter', + name: 'Normal Function', + line: { + color: 'black', + width: 1 + } + } + } else if (sample_group == "samples_other"){ + var other_intercept_trace = { + x: intercept_line['samples_other'][0], + y: intercept_line['samples_other'][1], + mode: 'lines', + type: 'scatter', + name: 'Normal Function', + line: { + color: 'black', + width: 1 + } + } + } else { + var all_intercept_trace = { + x: intercept_line['samples_all'][0], + y: intercept_line['samples_all'][1], + mode: 'lines', + type: 'scatter', + name: 'Normal Function', + line: { + color: 'black', + width: 1 + } + } + } + + if (sample_group == "samples_primary"){ + var data = [primary_intercept_trace, primary_trace] + } else if (sample_group == "samples_other"){ + var data = [other_intercept_trace, other_trace] + } else { + var data = [all_intercept_trace, primary_trace, other_trace] + } + + Plotly.newPlot('prob_plot_div', data, layout, root.modebar_options) + }; + + root.redraw_prob_plot_impl = redraw_prob_plot; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/scatter-matrix.js b/gn2/wqflask/static/new/javascript/scatter-matrix.js new file mode 100644 index 00000000..31cb384b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/scatter-matrix.js @@ -0,0 +1,551 @@ +// Heavily influenced by Mike Bostock's Scatter Matrix example +// http://mbostock.github.io/d3/talk/20111116/iris-splom.html +// + +/* +ScatterMatrix = function(url) { + this.__url = url; + this.__data = undefined; + this.__cell_size = 140; +}; +*/ + +ScatterMatrix = function(csv_string) { + this.__csv_string = csv_string; + this.__data = undefined; + this.__cell_size = 140; +}; + +ScatterMatrix.prototype.cellSize = function(n) { + this.__cell_size = n; + return this; +}; + +/* +ScatterMatrix.prototype.onData = function(cb) { + if (this.__data) { cb(); return; } + var self = this; + d3.csv(self.__url, function(data) { + self.__data = data; + cb(); + }); +}; +*/ + +ScatterMatrix.prototype.onData = function(cb) { + if (this.__data) { cb(); return; } + var self = this; + console.log("self.csv_string:", self.__csv_string) + + data = d3.csv.parse(self.__csv_string); + self.__data = data; + cb(); + +/* + d3.csv.parseRows(self.__csv_string, function(data) { + self.__data = data; + cb(); + }); +*/ + +}; + +ScatterMatrix.prototype.render = function () { + var self = this; + + var container = d3.select('#scatterplot_container').append('div') + .attr('class', 'scatter-matrix-container'); + var control = container.append('div') + .attr('class', 'scatter-matrix-control') + .style({'float':'left', 'margin-right':'50px'}) + var svg = container.append('div') + .attr('class', 'scatter-matrix-svg') + .style({'float':'left'}) + .html('<em>Loading data...</em>'); + + this.onData(function() { + var data = self.__data; + + // Fetch data and get all string variables + var string_variables = [undefined]; + var numeric_variables = []; + var numeric_variable_values = {}; + + for (k in data[0]) { + if (isNaN(+data[0][k])) { string_variables.push(k); } + else { numeric_variables.push(k); numeric_variable_values[k] = []; } + } + + console.log("data:", data) + + data.forEach(function(d) { + for (var j in numeric_variables) { + var k = numeric_variables[j]; + var value = d[k]; + if (numeric_variable_values[k].indexOf(value) < 0) { + numeric_variable_values[k].push(value); + } + } + }); + + var size_control = control.append('div').attr('class', 'scatter-matrix-size-control'); + var color_control = control.append('div').attr('class', 'scatter-matrix-color-control'); + var filter_control = control.append('div').attr('class', 'scatter-matrix-filter-control'); + var variable_control = control.append('div').attr('class', 'scatter-matrix-variable-control'); + var drill_control = control.append('div').attr('class', 'scatter-matrix-drill-control'); + + // shared control states + var to_include = []; + var color_variable = undefined; + var selected_colors = undefined; + for (var j in numeric_variables) { + var v = numeric_variables[j]; + to_include.push(v); + } + var drill_variables = []; + + function set_filter(variable) { + filter_control.selectAll('*').remove(); + if (variable) { + // Get unique values for this variable + var values = []; + data.forEach(function(d) { + var v = d[variable]; + if (values.indexOf(v) < 0) { values.push(v); } + }); + + selected_colors = []; + for (var j in values) { + var v = values[j]; + selected_colors.push(v); + } + + var filter_li = + filter_control + .append('p').text('Filter by '+variable+': ') + .append('ul') + .selectAll('li') + .data(values) + .enter().append('li'); + + filter_li.append('input') + .attr('type', 'checkbox') + .attr('checked', 'checked') + .on('click', function(d, i) { + var new_selected_colors = []; + for (var j in selected_colors) { + var v = selected_colors[j]; + if (v !== d || this.checked) { new_selected_colors.push(v); } + } + if (this.checked) { new_selected_colors.push(d); } + selected_colors = new_selected_colors; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + filter_li.append('label') + .html(function(d) { return d; }); + } + } + + size_a = size_control.append('p').text('Change cell size: '); + size_a.append('a') + .attr('href', '#') + .html('-') + .on('click', function() { + self.__cell_size *= 0.75; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + size_a.append('span').html(' '); + size_a.append('a') + .attr('href', '#') + .html('+') + .on('click', function() { + self.__cell_size *= 1.25; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + + color_control.append('p').text('Select a variable to color:') + color_control + .append('ul') + .selectAll('li') + .data(string_variables) + .enter().append('li') + .append('a') + .attr('href', '#') + .text(function(d) { return d ? d : 'None'; }) + .on('click', function(d, i) { + color_variable = d; + selected_colors = undefined; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + set_filter(d); + }); + + var variable_li = + variable_control + .append('p').text('Include variables: ') + .append('ul') + .selectAll('li') + .data(numeric_variables) + .enter().append('li'); + + variable_li.append('input') + .attr('type', 'checkbox') + .attr('checked', 'checked') + .on('click', function(d, i) { + var new_to_include = []; + for (var j in to_include) { + var v = to_include[j]; + if (v !== d || this.checked) { new_to_include.push(v); } + } + if (this.checked) { new_to_include.push(d); } + to_include = new_to_include; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + variable_li.append('label') + .html(function(d) { return d; }); + + drill_li = + drill_control + .append('p').text('Drill and Expand: ') + .append('ul') + .selectAll('li') + .data(numeric_variables) + .enter().append('li'); + + drill_li.append('input') + .attr('type', 'checkbox') + .on('click', function(d, i) { + var new_drill_variables = []; + for (var j in drill_variables) { + var v = drill_variables[j]; + if (v !== d || this.checked) { new_drill_variables.push(v); } + } + if (this.checked) { new_drill_variables.push(d); } + drill_variables = new_drill_variables; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + drill_li.append('label') + .html(function(d) { return d+' ('+numeric_variable_values[d].length+')'; }); + + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); +}; + +ScatterMatrix.prototype.__draw = + function(cell_size, container_el, color_variable, selected_colors, to_include, drill_variables) { + var self = this; + this.onData(function() { + var data = self.__data; + + if (color_variable && selected_colors) { + data = []; + self.__data.forEach(function(d) { + if (selected_colors.indexOf(d[color_variable]) >= 0) { data.push(d); } + }); + } + + container_el.selectAll('*').remove(); + + // If no data, don't do anything + if (data.length == 0) { return; } + + // Parse headers from first row of data + var numeric_variables = []; + for (k in data[0]) { + if (!isNaN(+data[0][k]) && to_include.indexOf(k) >= 0) { numeric_variables.push(k); } + } + numeric_variables.sort(); + + // Get values of the string variable + var colors = []; + if (color_variable) { + // Using self.__data, instead of data, so our css classes are consistent when + // we filter by value. + self.__data.forEach(function(d) { + var s = d[color_variable]; + if (colors.indexOf(s) < 0) { colors.push(s); } + }); + } + + function color_class(d) { + var c = d; + if (color_variable && d[color_variable]) { c = d[color_variable]; } + return colors.length > 0 ? 'color-'+colors.indexOf(c) : 'color-2'; + } + + // Size parameters + var size = cell_size, padding = 10, + axis_width = 20, axis_height = 15, legend_width = 200, label_height = 15; + + // Get x and y scales for each numeric variable + var x = {}, y = {}; + numeric_variables.forEach(function(trait) { + // Coerce values to numbers. + data.forEach(function(d) { d[trait] = +d[trait]; }); + + var value = function(d) { return d[trait]; }, + domain = [d3.min(data, value), d3.max(data, value)], + range_x = [padding / 2, size - padding / 2], + range_y = [padding / 2, size - padding / 2]; + + x[trait] = d3.scale.linear().domain(domain).range(range_x); + y[trait] = d3.scale.linear().domain(domain).range(range_y.reverse()); + }); + + // When drilling, user select one or more variables. The first drilled + // variable becomes the x-axis variable for all columns, and each column + // contains only data points that match specific values for each of the + // drilled variables other than the first. + + var drill_values = []; + var drill_degrees = [] + drill_variables.forEach(function(variable) { + // Skip first one, since that's just the x axis + if (drill_values.length == 0) { + drill_values.push([]); + drill_degrees.push(1); + } + else { + var values = []; + data.forEach(function(d) { + var v = d[variable]; + if (v !== undefined && values.indexOf(v) < 0) { values.push(v); } + }); + values.sort(); + drill_values.push(values); + drill_degrees.push(values.length); + } + }); + var total_columns = 1; + drill_degrees.forEach(function(d) { total_columns *= d; }); + + // Pick out stuff to draw on horizontal and vertical dimensions + + if (drill_variables.length > 0) { + // First drill is now the x-axis variable for all columns + x_variables = []; + for (var i=0; i<total_columns; i++) { + x_variables.push(drill_variables[0]); + } + } + else { + x_variables = numeric_variables.slice(0); + } + + if (drill_variables.length > 0) { + // Don't draw any of the "drilled" variables in vertical dimension + y_variables = []; + numeric_variables.forEach(function(variable) { + if (drill_variables.indexOf(variable) < 0) { y_variables.push(variable); } + }); + } + else { + y_variables = numeric_variables.slice(0); + } + + var filter_descriptions = 0; + if (drill_variables.length > 1) { + filter_descriptions = drill_variables.length-1; + } + + // Axes + var x_axis = d3.svg.axis(); + var y_axis = d3.svg.axis(); + var intf = d3.format('d'); + var fltf = d3.format('.f'); + var scif = d3.format('e'); + + x_axis.ticks(5) + .tickSize(size * y_variables.length) + .tickFormat(function(d) { + if (Math.abs(+d) > 10000 || (Math.abs(d) < 0.001 && Math.abs(d) != 0)) { return scif(d); } + if (parseInt(d) == +d) { return intf(d); } + return fltf(d); + }); + + y_axis.ticks(5) + .tickSize(size * x_variables.length) + .tickFormat(function(d) { + if (Math.abs(+d) > 10000 || (Math.abs(d) < 0.001 && Math.abs(d) != 0)) { return scif(d); } + if (parseInt(d) == +d) { return intf(d); } + return fltf(d); + }); + + // Brush - for highlighting regions of data + var brush = d3.svg.brush() + .on("brushstart", brushstart) + .on("brush", brush) + .on("brushend", brushend); + + // Root panel + var svg = container_el.append("svg:svg") + .attr("width", label_height + size * x_variables.length + axis_width + padding + legend_width) + .attr("height", size * y_variables.length + axis_height + label_height + label_height*filter_descriptions) + .append("svg:g") + .attr("transform", "translate("+label_height+",0)"); + + // Push legend to the side + var legend = svg.selectAll("g.legend") + .data(colors) + .enter().append("svg:g") + .attr("class", "legend") + .attr("transform", function(d, i) { + return "translate(" + (label_height + size * x_variables.length + padding) + "," + (i*20+10) + ")"; + }); + + legend.append("svg:circle") + .attr("class", function(d, i) { return color_class(d); }) + .attr("r", 3); + + legend.append("svg:text") + .attr("x", 12) + .attr("dy", ".31em") + .text(function(d) { return d; }); + + // Draw X-axis + svg.selectAll("g.x.axis") + .data(x_variables) + .enter().append("svg:g") + .attr("class", "x axis") + .attr("transform", function(d, i) { return "translate(" + i * size + ",0)"; }) + .each(function(d) { d3.select(this).call(x_axis.scale(x[d]).orient("bottom")); }); + + // Draw Y-axis + svg.selectAll("g.y.axis") + .data(y_variables) + .enter().append("svg:g") + .attr("class", "y axis") + .attr("transform", function(d, i) { return "translate(0," + i * size + ")"; }) + .each(function(d) { d3.select(this).call(y_axis.scale(y[d]).orient("right")); }); + + // Draw scatter plot + var cell = svg.selectAll("g.cell") + .data(cross(x_variables, y_variables)) + .enter().append("svg:g") + .attr("class", "cell") + .attr("transform", function(d) { return "translate(" + d.i * size + "," + d.j * size + ")"; }) + .each(plot); + + // Add titles for y variables + cell.filter(function(d) { return d.i == 0; }).append("svg:text") + .attr("x", padding-size) + .attr("y", -label_height) + .attr("dy", ".71em") + .attr("transform", function(d) { return "rotate(-90)"; }) + .text(function(d) { return d.y; }); + + function plot(p) { + // console.log(p); + + var data_to_draw = data; + + // If drilling, compute what values of the drill variables correspond to + // this column. + // + var filter = {}; + if (drill_variables.length > 1) { + var column = p.i; + + var cap = 1; + for (var i=drill_variables.length-1; i > 0; i--) { + var var_name = drill_variables[i]; + var var_value = undefined; + + if (i == drill_variables.length-1) { + // for the last drill variable, we index by % + var_value = drill_values[i][column % drill_degrees[i]]; + } + else { + // otherwise divide by capacity of subsequent variables to get value array index + var_value = drill_values[i][parseInt(column/cap)]; + } + + filter[var_name] = var_value; + cap *= drill_degrees[i]; + } + + data_to_draw = []; + data.forEach(function(d) { + var pass = true; + for (k in filter) { if (d[k] != filter[k]) { pass = false; break; } } + if (pass === true) { data_to_draw.push(d); } + }); + } + + var cell = d3.select(this); + + // Frame + cell.append("svg:rect") + .attr("class", "frame") + .attr("x", padding / 2) + .attr("y", padding / 2) + .attr("width", size - padding) + .attr("height", size - padding); + + // Scatter plot dots + cell.selectAll("circle") + .data(data_to_draw) + .enter().append("svg:circle") + .attr("class", function(d) { return color_class(d); }) + .attr("cx", function(d) { return x[p.x](d[p.x]); }) + .attr("cy", function(d) { return y[p.y](d[p.y]); }) + .attr("r", 5); + + // Add titles for x variables and drill variable values + if (p.j == y_variables.length-1) { + cell.append("svg:text") + .attr("x", padding) + .attr("y", size+axis_height) + .attr("dy", ".71em") + .text(function(d) { return d.x; }); + + if (drill_variables.length > 1) { + var i = 0; + for (k in filter) { + i += 1; + cell.append("svg:text") + .attr("x", padding) + .attr("y", size+axis_height+label_height*i) + .attr("dy", ".71em") + .text(function(d) { return filter[k]+': '+k; }); + } + } + } + + // Brush + cell.call(brush.x(x[p.x]).y(y[p.y])); + } + + // Clear the previously-active brush, if any + function brushstart(p) { + if (brush.data !== p) { + cell.call(brush.clear()); + brush.x(x[p.x]).y(y[p.y]).data = p; + } + } + + // Highlight selected circles + function brush(p) { + var e = brush.extent(); + svg.selectAll(".cell circle").attr("class", function(d) { + return e[0][0] <= d[p.x] && d[p.x] <= e[1][0] + && e[0][1] <= d[p.y] && d[p.y] <= e[1][1] + ? color_class(d) : null; + }); + } + + // If brush is empty, select all circles + function brushend() { + if (brush.empty()) svg.selectAll(".cell circle").attr("class", function(d) { + return color_class(d); + }); + } + + function cross(a, b) { + var c = [], n = a.length, m = b.length, i, j; + for (i = -1; ++i < n;) for (j = -1; ++j < m;) c.push({x: a[i], i: i, y: b[j], j: j}); + return c; + } + }); + +}; + diff --git a/gn2/wqflask/static/new/javascript/scatterplot.js b/gn2/wqflask/static/new/javascript/scatterplot.js new file mode 100644 index 00000000..3fea0503 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/scatterplot.js @@ -0,0 +1,414 @@ +// Generated by CoffeeScript 1.8.0 +var root, scatterplot; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +scatterplot = function() { + var axispos, chart, dataByInd, height, margin, nxticks, nyticks, pointcolor, pointsSelect, pointsize, pointstroke, rectcolor, rotate_ylab, title, titlepos, width, xNA, xlab, xlim, xscale, xticks, xvar, yNA, ylab, ylim, yscale, yticks, yvar; + width = 800; + height = 600; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 45, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + xNA = { + handle: true, + force: false, + width: 15, + gap: 10 + }; + yNA = { + handle: true, + force: false, + width: 15, + gap: 10 + }; + xlim = null; + ylim = null; + nxticks = 5; + xticks = null; + nyticks = 5; + yticks = null; + rectcolor = d3.rgb(230, 230, 230); + pointcolor = null; + pointstroke = "black"; + pointsize = 3; + title = "Correlation Scatterplot"; + xlab = "X"; + ylab = "Y"; + rotate_ylab = null; + yscale = d3.scale.linear(); + xscale = d3.scale.linear(); + xvar = 0; + yvar = 1; + pointsSelect = null; + dataByInd = false; + chart = function(selection) { + return selection.each(function(data) { + var g, gEnter, group, i, indID, indtip, maxx, minx, na_value, ngroup, panelheight, paneloffset, panelwidth, points, svg, titlegrp, x, xaxis, xrange, xs, y, yaxis, yrange, ys, _i, _ref, _ref1, _ref2, _results; + if (dataByInd) { + x = data.data.map(function(d) { + return d[xvar]; + }); + y = data.data.map(function(d) { + return d[yvar]; + }); + } else { + x = data.data[xvar]; + y = data.data[yvar]; + } + + indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null; + indID = indID != null ? indID : (function() { + _results = []; + for (var _i = 1, _ref1 = x.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); } + return _results; + }).apply(this); + + group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = x.length; _j < _len; _j++) { + i = x[_j]; + _results1.push(1); + } + return _results1; + })(); + ngroup = d3.max(group); + group = (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = group.length; _j < _len; _j++) { + g = group[_j]; + _results1.push(g - 1); + } + return _results1; + })(); + pointcolor = pointcolor != null ? pointcolor : selectGroupColors(ngroup, "dark"); + pointcolor = expand2vector(pointcolor, ngroup); + if (x.every(function(v) { + return (v != null) && !xNA.force; + })) { + xNA.handle = false; + } + if (y.every(function(v) { + return (v != null) && !yNA.force; + })) { + yNA.handle = false; + } + if (xNA.handle) { + paneloffset = xNA.width + xNA.gap; + panelwidth = width - paneloffset; + } else { + paneloffset = 0; + panelwidth = width; + } + if (yNA.handle) { + panelheight = height - (yNA.width + yNA.gap); + } else { + panelheight = height; + } + xlim = xlim != null ? xlim : d3.extent(x); + ylim = ylim != null ? ylim : d3.extent(y); + na_value = d3.min(x.concat(y)) - 100; + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", paneloffset + margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none"); + if (xNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none"); + } + if (xNA.handle && yNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none"); + } + if (yNA.handle) { + g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none"); + } + xrange = [margin.left + paneloffset + margin.inner, margin.left + paneloffset + panelwidth - margin.inner]; + yrange = [margin.top + panelheight - margin.inner, margin.top + margin.inner]; + xscale.domain(xlim).range(xrange); + yscale.domain(ylim).range(yrange); + xs = d3.scale.linear().domain(xlim).range(xrange); + ys = d3.scale.linear().domain(ylim).range(yrange); + if (xNA.handle) { + xscale.domain([na_value].concat(xlim)).range([margin.left + xNA.width / 2].concat(xrange)); + x = x.map(function(e) { + if (e != null) { + return e; + } else { + return na_value; + } + }); + } + if (yNA.handle) { + yscale.domain([na_value].concat(ylim)).range([height + margin.top - yNA.width / 2].concat(yrange)); + y = y.map(function(e) { + if (e != null) { + return e; + } else { + return na_value; + } + }); + } + minx = xlim[0]; + maxx = xlim[1]; + yticks = yticks != null ? yticks : ys.ticks(nyticks); + xticks = xticks != null ? xticks : xs.ticks(nxticks); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).style("fill", "black").style("font-size", "24px").text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) { + return xscale(d); + }).attr("x2", function(d) { + return xscale(d); + }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) { + return xscale(d); + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return formatAxis(xticks)(d); + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).style("fill", "black").text(xlab); + if (xNA.handle) { + xaxis.append("text").attr("x", margin.left + xNA.width / 2).attr("y", margin.top + height + axispos.xlabel).text("N/A"); + } + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).style("fill", "black").text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + if (yNA.handle) { + yaxis.append("text").attr("x", margin.left - axispos.ylabel).attr("y", margin.top + height - yNA.width / 2).text("N/A"); + } + indtip = d3.tip().attr('class', 'd3-tip').html(function(d, i) { + return indID[i]; + }).direction('e').offset([0, 10]); + svg.call(indtip); + if (js_data.slope && js_data.intercept) { + g.append("line").attr("x1", xscale(minx) - margin.inner).attr('y1', yscale(js_data.slope * minx + js_data.intercept)).attr("x2", xscale(maxx * 1) + margin.inner).attr("y2", yscale(slope * maxx * 1 + intercept)).style("stroke", "black").style("stroke-width", 2); + } + points = g.append("g").attr("id", "points"); + pointsSelect = points.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx", function(d, i) { + return xscale(x[i]); + }).attr("cy", function(d, i) { + return yscale(y[i]); + }).attr("class", function(d, i) { + return "pt" + i; + }).attr("r", pointsize).attr("fill", function(d, i) { + return pointcolor[group[i]]; + }).attr("stroke", pointstroke).attr("stroke-width", "1").attr("opacity", function(d, i) { + if (((x[i] != null) || xNA.handle) && ((y[i] != null) || yNA.handle)) { + return 1; + } + return 0; + }).on("mouseover.paneltip", indtip.show).on("mouseout.paneltip", indtip.hide); + g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + if (xNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + } + if (xNA.handle && yNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + } + if (yNA.handle) { + return g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + } + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.xlim = function(value) { + if (!arguments.length) { + return xlim; + } + xlim = value; + return chart; + }; + chart.nxticks = function(value) { + if (!arguments.length) { + return nxticks; + } + nxticks = value; + return chart; + }; + chart.xticks = function(value) { + if (!arguments.length) { + return xticks; + } + xticks = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.pointcolor = function(value) { + if (!arguments.length) { + return pointcolor; + } + pointcolor = value; + return chart; + }; + chart.pointsize = function(value) { + if (!arguments.length) { + return pointsize; + } + pointsize = value; + return chart; + }; + chart.pointstroke = function(value) { + if (!arguments.length) { + return pointstroke; + } + pointstroke = value; + return chart; + }; + chart.dataByInd = function(value) { + if (!arguments.length) { + return dataByInd; + } + dataByInd = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.xvar = function(value) { + if (!arguments.length) { + return xvar; + } + xvar = value; + return chart; + }; + chart.yvar = function(value) { + if (!arguments.length) { + return yvar; + } + yvar = value; + return chart; + }; + chart.xNA = function(value) { + if (!arguments.length) { + return xNA; + } + xNA = value; + return chart; + }; + chart.yNA = function(value) { + if (!arguments.length) { + return yNA; + } + yNA = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.xscale = function() { + return xscale; + }; + chart.pointsSelect = function() { + return pointsSelect; + }; + return chart; +}; + +root.scatterplot = scatterplot; diff --git a/gn2/wqflask/static/new/javascript/search_autocomplete.js b/gn2/wqflask/static/new/javascript/search_autocomplete.js new file mode 100644 index 00000000..10c22c95 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/search_autocomplete.js @@ -0,0 +1,173 @@ + //replace with gn search hints + + + + + + function autocomplete(inp, arr) { + /*the autocomplete function takes two arguments, + the text field element and an array of possible autocompleted values:*/ + var currentFocus; + /*execute a function when someone writes in the text field:*/ + + inp.addEventListener("focus", function(e) { + + + var a, b, i, val = this.value; + closeAllLists(); + currentFocus = -1; + a = document.createElement("DIV"); + a.setAttribute("id", this.id + "autocomplete-list"); + a.setAttribute("class", "autocomplete-items"); + this.parentNode.appendChild(a); + let historySearch = retrieveSearchHistory().splice(0, 5) + let text_title = document.createElement("DIV") + text_title.innerHTML = "<strong>RECENT SEARCH</strong><input id='clear_all' type='button' value='clear_all'>"; + text_title.setAttribute("class", "recent-search-title") + text_title.setAttribute('disabled', true); + + a.appendChild(text_title); + for (i = 0; i < historySearch.length; i++) { + b = document.createElement("DIV"); + b.innerHTML = "<span>" + historySearch[i].substr(0, val.length) + "</span>"; + b.style.color = "blue"; + b.innerHTML += historySearch[i].substr(val.length); + b.innerHTML += "<input type='hidden' value='" + historySearch[i] + "'>"; + b.addEventListener("click", function(e) { + inp.value = this.getElementsByTagName("input")[0].value; + closeAllLists(); + }); + a.appendChild(b); + + } + document.getElementById("clear_all").addEventListener("click",(event)=>{ + + + deleteSearchHistory() + }) + + }); + + + + inp.addEventListener("input", function(e) { + var a, b, i, val = this.value; + /*close any already open lists of autocompleted values*/ + closeAllLists(); + if (!val) { return false; } + currentFocus = -1; + /*create a DIV element that will contain the items (values):*/ + a = document.createElement("DIV"); + a.setAttribute("id", this.id + "autocomplete-list"); + a.setAttribute("class", "autocomplete-items"); + /*append the DIV element as a child of the autocomplete container:*/ + this.parentNode.appendChild(a); + /*for each item in the array...*/ + for (i = 0; i < arr.length; i++) { + /*check if the item starts with the same letters as the text field value:*/ + if (arr[i].substr(0, val.length).toUpperCase() == val.toUpperCase()) { + /*create a DIV element for each matching element:*/ + b = document.createElement("DIV"); + /*make the matching letters bold:*/ + b.innerHTML = "<strong>" + arr[i].substr(0, val.length) + "</strong>"; + b.innerHTML += arr[i].substr(val.length); + /*insert a input field that will hold the current array item's value:*/ + b.innerHTML += "<input type='hidden' value='" + arr[i] + "'>"; + /*execute a function when someone clicks on the item value (DIV element):*/ + b.addEventListener("click", function(e) { + /*insert the value for the autocomplete text field:*/ + inp.value = this.getElementsByTagName("input")[0].value; + /*close the list of autocompleted values, + (or any other open lists of autocompleted values:*/ + closeAllLists(); + }); + a.appendChild(b); + } + } + }); + /*execute a function presses a key on the keyboard:*/ + inp.addEventListener("keydown", function(e) { + var x = document.getElementById(this.id + "autocomplete-list"); + if (x) x = x.getElementsByTagName("div"); + if (e.keyCode == 40) { + /*If the arrow DOWN key is pressed, + increase the currentFocus variable:*/ + currentFocus++; + /*and and make the current item more visible:*/ + addActive(x); + } else if (e.keyCode == 38) { //up + /*If the arrow UP key is pressed, + decrease the currentFocus variable:*/ + currentFocus--; + /*and and make the current item more visible:*/ + addActive(x); + } else if (e.keyCode == 13) { + /*If the ENTER key is pressed, prevent the form from being submitted,*/ + e.preventDefault(); + if (currentFocus > -1) { + /*and simulate a click on the "active" item:*/ + if (x) x[currentFocus].click(); + } + } + }); + + function addActive(x) { + /*a function to classify an item as "active":*/ + if (!x) return false; + /*start by removing the "active" class on all items:*/ + removeActive(x); + if (currentFocus >= x.length) currentFocus = 0; + if (currentFocus < 0) currentFocus = (x.length - 1); + /*add class "autocomplete-active":*/ + x[currentFocus].classList.add("autocomplete-active"); + } + + function removeActive(x) { + /*a function to remove the "active" class from all autocomplete items:*/ + for (var i = 0; i < x.length; i++) { + x[i].classList.remove("autocomplete-active"); + } + } + + function closeAllLists(elmnt) { + /*close all autocomplete lists in the document, + except the one passed as an argument:*/ + var x = document.getElementsByClassName("autocomplete-items"); + for (var i = 0; i < x.length; i++) { + if (elmnt != x[i] && elmnt != inp) { + x[i].parentNode.removeChild(x[i]); + } + } + } + + + + /*execute a function when someone clicks in the document:*/ + document.addEventListener("click", function(e) { + closeAllLists(e.target); + }) + + } + + function retrieveSearchHistory() { + let results = localStorage.getItem("gn_search_history") + + return results ? JSON.parse(results) : [] + } + + + + + + function saveBeforeSubmit(new_search) { + + let search = retrieveSearchHistory() + search.unshift(new_search) + + localStorage.setItem("gn_search_history", JSON.stringify([...new Set(search)].splice(0,8))) + + } + + function deleteSearchHistory(){ + localStorage.setItem("gn_search_history", []) + }
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/search_results.js b/gn2/wqflask/static/new/javascript/search_results.js new file mode 100644 index 00000000..c263ef49 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/search_results.js @@ -0,0 +1,386 @@ +change_buttons = function(check_node = 0) { + var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2; + buttons = ["#add", "#remove"]; + + num_checked = 0 + table_api = $('#trait_table').DataTable(); + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + if (check_cells[i].childNodes[check_node].checked){ + num_checked += 1 + } + } + + if (num_checked === 0) { + for (_i = 0, _len = buttons.length; _i < _len; _i++) { + button = buttons[_i]; + $(button).prop("disabled", true); + } + } else { + for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { + button = buttons[_j]; + $(button).prop("disabled", false); + } + } +}; + +$(function() { + let selectAll, deselectAll, invert; + + selectAll = function() { + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + check_cells[i].childNodes[0].checked = true; + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + check_rows[i].classList.add("selected"); + } + + change_buttons(); + }; + + deselectAll = function() { + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + check_cells[i].childNodes[0].checked = false; + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + check_rows[i].classList.remove("selected") + } + + change_buttons(); + }; + + invert = function() { + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + if (check_cells[i].childNodes[0].checked){ + check_cells[i].childNodes[0].checked = false; + } else { + check_cells[i].childNodes[0].checked = true; + } + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + if (check_rows[i].classList.contains("selected")){ + check_rows[i].classList.remove("selected") + } else { + check_rows[i].classList.add("selected") + } + } + + change_buttons(); + }; + + $('#searchbox').keyup(function(){ + if ($(this).val() != ""){ + $('#filter_term').val($(this).val()); + } else { + $('#filter_term').val("None"); + } + $('#trait_table').DataTable().search($(this).val()).draw(); + }); + + /** + * parseIndexString takes a string consisting of integers, + * hyphens, and/or commas to indicate range(s) of indices + * to select a rows and returns the corresponding set of indices + * For example - "1, 5-10, 15" would return a set of 8 rows + * @return {Set} The list of indices as a Set + */ + parseIndexString = function(idx_string) { + index_list = []; + + _ref = idx_string.split(","); + for (_i = 0; _i < _ref.length; _i++) { + index_set = _ref[_i]; + if (!/^ *([0-9]+$) *| *([0-9]+ *- *[0-9]+$) *|(^$)$/.test(index_set)) { + $('#select_samples_invalid').show(); + break + } else { + $('#select_samples_invalid').hide(); + } + if (index_set.indexOf('-') !== -1) { + start_index = parseInt(index_set.split("-")[0]); + end_index = parseInt(index_set.split("-")[1]); + + // If start index is higher than end index (for example is the string "10-5" exists) swap values so it'll be interpreted as "5-10" instead + if (start_index > end_index) { + [start_index, end_index] = [end_index, start_index] + } + + for (index = start_index; index <= end_index; index++) { + index_list.push(index); + } + } else { + index = parseInt(index_set); + index_list.push(index); + } + } + return new Set(index_list) + } + + filterByIndex = function() { + indexString = $('#select_top').val() + indexSet = parseIndexString(indexString) + + tableApi = $('#trait_table').DataTable(); + checkNodes = tableApi.column(0).nodes().to$(); + checkNodes.each(function(index) { + if (indexSet.has(index + 1)){ + $(this)[0].childNodes[0].checked = true + } + }) + + checkRows = tableApi.rows().nodes().to$(); + checkRows.each(function(index) { + if (indexSet.has(index + 1)){ + $(this)[0].classList.add("selected"); + } + }) + } + + $(window).keydown(function(event){ + if((event.keyCode == 13)) { + event.preventDefault(); + return false; + } + }); + + $('#select_top').keyup(function(event){ + if (event.keyCode === 13) { + filterByIndex() + } + }); + + $('#select_top').blur(function() { + filterByIndex() + }); + + addToCollection = function() { + var traits; + table_api = $('#trait_table').DataTable(); + check_nodes = table_api.column(0).nodes().to$(); + traits = Array.from(check_nodes.map(function() { + if ($(this)[0].childNodes[0].checked){ + return $(this)[0].childNodes[0].value + } + })) + + var traits_hash = md5(traits.toString()); + + $.ajax({ + type: "POST", + url: "/collections/store_trait_list", + data: { + hash: traits_hash, + traits: traits.toString() + } + }); + + return $.colorbox({ + href: "/collections/add", + data: { + "traits": traits.toString(), + "hash": traits_hash + } + }); + + }; + + submitBnw = function() { + trait_data = submitTraits("trait_table", "submit_bnw") + } + + exportTraits = function() { + trait_data = submitTraits("trait_table", "export_traits_csv") + }; + + exportCollection = function() { + trait_data = submitTraits("trait_table", "export_collection") + } + + fetchTraits = function(table_name){ + trait_table = $('#'+table_name); + table_dict = {}; + + headers = []; + trait_table.find('th').each(function () { + if ($(this).data('export')){ + headers.push($(this).data('export')) + } + }); + table_dict['headers'] = headers; + + selected_rows = []; + all_rows = []; // If no rows are checked, export all + table_api = $('#' + table_name).DataTable(); + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + this_node = check_cells[i].childNodes[0]; + all_rows.push(this_node.value) + if (this_node.checked){ + selected_rows.push(this_node.value) + } + } + + if (selected_rows.length > 0){ + table_dict['rows'] = selected_rows; + } else { + table_dict['rows'] = all_rows; + } + + json_table_dict = JSON.stringify(table_dict); + $('input[name=export_data]').val(json_table_dict); + } + + submitTraits = function(table_name, destination) { + fetchTraits(table_name); + $('#export_form').attr('action', '/' + destination); + $('#export_form').submit(); + }; + + getTraitsFromTable = function(){ + traits = $("#trait_table input:checked").map(function() { + return $(this).val(); + }).get(); + if (traits.length == 0){ + num_traits = $("#trait_table input").length + if (num_traits <= 100){ + traits = $("#trait_table input").map(function() { + return $(this).val(); + }).get(); + } + } + return traits + } + + $("#corr_matrix").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Correlation Matrix") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#network_graph").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Network Graph") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#wgcna_setup").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("WGCNA Setup") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#ctl_setup").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("CTL Setup") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#heatmap").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Heatmap") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#comp_bar_chart").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Comparison Bar Chart") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + + $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + url = $(this).data("url") + return submit_special(url) + }); + + + $("#select_all").click(selectAll); + $("#deselect_all").click(deselectAll); + $("#invert").click(invert); + $("#add").click(addToCollection); + $("#submit_bnw").click(submitBnw); + $("#export_traits").click(exportTraits); + $("#export_collection").click(exportCollection); + + let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] + let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] + + let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A + + function extractInnerText(the_string){ + var span = document.createElement('span'); + span.innerHTML = the_string; + return span.textContent || span.innerText; + } + + function sortNAs(a, b, sort_function){ + if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { + return 0; + } + if (na_equivalent_vals.includes(a)){ + return 1 + } + if (na_equivalent_vals.includes(b)) { + return -1; + } + return sort_function(a, b) + } + + $.extend( $.fn.dataTableExt.oSort, { + "natural-minus-na-asc": function (a, b) { + return sortNAs(extractInnerText(a), extractInnerText(b), naturalAsc) + }, + "natural-minus-na-desc": function (a, b) { + return sortNAs(extractInnerText(a), extractInnerText(b), naturalDesc) + } + }); + + $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $('input', td).prop('checked') ? '1' : '0'; + } ); + }; + + $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $(td).text(); + } ); + } + + applyDefault = function() { + let default_collection_id = $.cookie('default_collection'); + if (default_collection_id) { + let the_option = $('[name=existing_collection] option').filter(function() { + return ($(this).text().split(":")[0] == default_collection_id); + }) + the_option.prop('selected', true); + } + } + applyDefault(); + +}); diff --git a/gn2/wqflask/static/new/javascript/show_trait.js b/gn2/wqflask/static/new/javascript/show_trait.js new file mode 100644 index 00000000..c5214947 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/show_trait.js @@ -0,0 +1,1677 @@ +var statTableRows, isNumber, + __hasProp = {}.hasOwnProperty, + __slice = [].slice; + +isNumber = function(o) { + return !isNaN((o - 0) && o !== null); +}; + +statTableRows = [ + { + vn: "n_of_samples", + pretty: "N of Samples", + digits: 0 + }, { + vn: "mean", + pretty: "Mean", + digits: 3 + }, { + vn: "median", + pretty: "Median", + digits: 3 + }, { + vn: "std_error", + pretty: "Standard Error (SE)", + digits: 3 + }, { + vn: "std_dev", + pretty: "Standard Deviation (SD)", + digits: 3 + }, { + vn: "min", + pretty: "Minimum", + digits: 3 + }, { + vn: "max", + pretty: "Maximum", + digits: 3 + } +] + +if (js_data.dataset_type == "ProbeSet"){ + if (js_data.data_scale == "linear_positive" || js_data.data_scale == "log2") { + statTableRows.push({ + vn: "range", + pretty: "Range (log2)", + digits: 3 + }) + } else { + statTableRows.push({ + vn: "range", + pretty: "Range", + digits: 3 + }) + } +} else { + statTableRows.push({ + vn: "range", + pretty: "Range", + digits: 3 + }) +} + +statTableRows.push( + { + vn: "range_fold", + pretty: "Range (fold)", + digits: 3 + }, { + vn: "interquartile", + pretty: "<font color='black'>Interquartile Range</font>", + url: "http://www.genenetwork.org/glossary.html#Interquartile", + digits: 3 + }, { + vn: "skewness", + pretty: "Skewness", + url: "https://en.wikipedia.org/wiki/Skewness", + digits: 3 + }, { + vn: "kurtosis", + pretty: "Excess Kurtosis", + url: "https://en.wikipedia.org/wiki/Kurtosis", + digits: 3 + } +); + +toggleDescription = function() { + if ($('.truncDesc').is(':visible')) { + $('.truncDesc').hide(); + $('.fullDesc').show(); + } else { + $('.truncDesc').show(); + $('.fullDesc').hide(); + } +} + +add = function() { + var trait; + trait = $("input[name=trait_hmac]").val(); + return $.colorbox({ + href: "/collections/add", + data: { + "traits": trait + } + }); +}; +$('#add_to_collection').click(add); + +sampleLists = js_data.sample_lists; +sampleGroupTypes = js_data.sample_group_types; + +$(".select_covariates").click(function () { + openCovariateSelection(); +}); + +$(".remove_covariates").click(function () { + $(".selected-covariates option:selected").each(function() { + this_val = $(this).val(); + $(".selected-covariates option").each(function(){ + if ($(this).val() == this_val){ + $(this).remove(); + } + }) + cofactor_count = $(".selected-covariates:first option").length + if (cofactor_count > 2 && cofactor_count < 11){ + $(".selected-covariates").each(function() { + $(this).attr("size", $(".selected-covariates:first option").length) + }); + } else if (cofactor_count > 10) { + $(".selected-covariates").each(function() { + $(this).attr("size", 10) + }); + } else { + $(".selected-covariates").each(function() { + $(this).attr("size", 2) + }); + } + if (cofactor_count == 0){ + $(".selected-covariates").each(function() { + $(this).append($("<option/>", { + value: "", + text: "No covariates selected" + })) + }) + } + }); + + covariates_list = []; + $(".selected-covariates:first option").each(function() { + covariates_list.push($(this).val()); + }) + $("input[name=covariates]").val(covariates_list.join(",")) +}); + +$(".remove_all_covariates").click(function() { + $(".selected-covariates option").each(function() { + $(this).remove(); + }); + $(".selected-covariates").attr("size", 2) + $("input[name=covariates]").val(""); +}) + +openTraitSelection = function() { + return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { + return function() { + $.colorbox({ + inline: true, + href: "#collections_holder", + onComplete: function(){ + $.getScript("/static/new/javascript/get_traits_from_collection.js"); + } + }); + return $('a.collection_name').attr('onClick', 'return false'); + }; + })(this)); +}; +openCovariateSelection = function() { + return $('#collections_holder').load('/collections/list #collections_list', (function(_this) { + return function() { + $.colorbox({ + inline: true, + href: "#collections_holder", + width: "1000px", + height: "700px", + onComplete: function(){ + $.getScript("/static/new/javascript/get_covariates_from_collection.js"); + } + }); + return $('a.collection_name').attr('onClick', 'return false'); + }; + })(this)); +}; +hideTabs = function(start) { + var x, _i, _results; + _results = []; + for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) { + _results.push($("#stats_tabs" + x).hide()); + } + return _results; +}; +statsMdpChange = function() { + var selected; + selected = $(this).val(); + hideTabs(0); + return $("#stats_tabs" + selected).show(); +}; +changeStatsValue = function(sample_sets, category, value_type, decimal_places, effects) { + var current_value, id, in_box, the_value, title_value; + id = "#" + processId(category, value_type); + in_box = $(id).html; + current_value = parseFloat($(in_box)).toFixed(decimal_places); + the_value = sample_sets[category][value_type](); + if (decimal_places > 0) { + title_value = the_value.toFixed(decimal_places * 2); + the_value = the_value.toFixed(decimal_places); + } else { + title_value = null; + } + if (the_value !== current_value) { + if (effects) { + $(id).html(the_value).effect("highlight"); + } else { + $(id).html(the_value); + } + } + if (title_value) { + return $(id).attr('title', title_value); + } +}; +updateStatValues = function(sample_sets) { + var category, row, show_effects, _i, _len, _ref, _results; + show_effects = $(".tab-pane.active").attr("id") === "stats_tab"; + _ref = ['samples_primary', 'samples_other', 'samples_all']; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + category = _ref[_i]; + _results.push((function() { + var _j, _len1, _results1; + _results1 = []; + for (_j = 0, _len1 = statTableRows.length; _j < _len1; _j++) { + row = statTableRows[_j]; + _results1.push(changeStatsValue(sample_sets, category, row.vn, row.digits, show_effects)); + } + return _results1; + })()); + } + return _results; +}; + +updateHistogram_width = function() { + num_bins = $('#histogram').find('g.trace.bars').find('g.point').length + + if (num_bins < 10) { + width_update = { + width: 400 + } + + Plotly.relayout('histogram', width_update) + } +} + +updateHistogram = function() { + var x; + var _i, _len, _ref, data; + _ref = _.values(root.selected_samples[root.stats_group]); + var trait_vals = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + x = _ref[_i]; + trait_vals.push(x.value); + } + root.histogram_data[0]['x'] = trait_vals + + if ($('input[name="transform"]').val() != ""){ + root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>" + } else { + root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + "</b>" + } + + Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options); + updateHistogram_width() +}; + +updateBarChart = function() { + var x; + var _i, _len, _ref, data; + _ref = _.values(root.selected_samples[root.stats_group]); + names_and_values = [] + for (i = 0; i < _ref.length; i++){ + _ref[i]["name"] = Object.keys(root.selected_samples[root.stats_group])[i] + } + trait_vals = []; + trait_vars = []; + trait_samples = []; + + function sortFunction(a, b) { + if (a.value === b.value) { + return 0; + } + else { + return (a.value < b.value) ? -1 : 1; + } + } + + if (root.bar_sort == "value") { + _ref.sort(sortFunction) + } + + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + x = _ref[_i]; + trait_samples.push(x.name) + trait_vals.push(x.value); + if (x["variance"] != undefined) { + trait_vars.push(x.variance); + } else{ + trait_vars.push(null) + } + } + + new_chart_range = getBarRange(trait_vals, trait_vars) + + root.bar_layout['yaxis']['range'] = new_chart_range + + if ($('input[name="transform"]').val() != ""){ + root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>" + } else { + root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>" + } + + root.bar_data[0]['y'] = trait_vals + root.bar_data[0]['error_y'] = { + type: 'data', + array: trait_vars, + visible: root.errors_exist + } + root.bar_data[0]['x'] = trait_samples + + if (trait_vals.length < 256) { + Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options); + } +}; + +updateViolinPlot = function() { + var y_value_list = [] + if (sampleLists.length > 1) { + i = 0; + for (var sample_group in root.selected_samples){ + var trait_sample_data = _.values(root.selected_samples[sample_group]) + var trait_vals = []; + for (j = 0, len = trait_sample_data.length; j < len; j++) { + this_sample_data = trait_sample_data[j]; + trait_vals.push(this_sample_data.value); + } + root.violin_data[i]['y'] = trait_vals + i++; + } + } else { + var trait_sample_data = _.values(root.selected_samples['samples_all']) + var trait_vals = []; + for (j = 0, len = trait_sample_data.length; j < len; j++) { + this_sample_data = trait_sample_data[j]; + trait_vals.push(this_sample_data.value); + } + root.violin_data[0]['y'] = trait_vals + } + + if ($('input[name="transform"]').val() != ""){ + root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>" + } else { + root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>" + } + + Plotly.newPlot('violin_plot', root.violin_data, root.violin_layout, root.modebar_options) +} + + +updateProbPlot = function() { + return root.redraw_prob_plot_impl(root.selected_samples, root.prob_plot_group); +}; + +makeTable = function() { + var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1; + if (js_data.trait_symbol != null) { + header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; + } else if (js_data.dataset_type == "Geno"){ + header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Marker " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; + } else { + header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + ": " + js_data.short_description + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; + } + _ref = js_data.sample_group_types; + for (key in _ref) { + if (!__hasProp.call(_ref, key)) continue; + value = _ref[key]; + the_id = processId("column", key); + if (Object.keys(_ref).length > 1) { + header += "<th id=\"" + the_id + "\" style=\"text-align: right; padding-left: 5px;\">" + value + "</th>"; + } else { + header += "<th id=\"" + the_id + "\" style=\"text-align: right; padding-left: 5px;\">Value</th>"; + } + } + + header += "</thead>"; + the_rows = "<tbody>"; + for (_i = 0, _len = statTableRows.length; _i < _len; _i++) { + row = statTableRows[_i]; + if ((row.vn == "range_fold") && js_data.dataset_type == "Publish"){ + continue; + } + row_line = "<tr>"; + if (row.url != null) { + row_line += "<td id=\"" + row.vn + "\" align=\"right\"><a href=\"" + row.url + "\" style=\"color: #0000EE;\">" + row.pretty + "</a></td>"; + } else { + row_line += "<td id=\"" + row.vn + "\" align=\"right\">" + row.pretty + "</td>"; + } + _ref1 = js_data.sample_group_types; + for (key in _ref1) { + if (!__hasProp.call(_ref1, key)) continue; + value = _ref1[key]; + the_id = processId(key, row.vn); + row_line += "<td id=\"" + the_id + "\" align=\"right\">N/A</td>"; + } + row_line += "</tr>"; + the_rows += row_line; + } + the_rows += "</tbody>"; + table = header + the_rows; + return $("#stats_table").append(table); +}; +processId = function() { + var processed, value, values, _i, _len; + values = 1 <= arguments.length ? __slice.call(arguments, 0) : []; + + /* Make an id or a class valid javascript by, for example, eliminating spaces */ + processed = ""; + for (_i = 0, _len = values.length; _i < _len; _i++) { + value = values[_i]; + value = value.replace(" ", "_"); + if (processed.length) { + processed += "-"; + } + processed += value; + } + return processed; +}; + +fetchSampleValues = function() { + // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster) + sample_val_dict = {}; + + table = 'samples_primary'; + if ($('#' + table).length){ + tableApi = $('#' + table).DataTable(); + val_nodes = tableApi.column(3).nodes().to$(); + for (_j = 0; _j < val_nodes.length; _j++){ + sample_name = val_nodes[_j].childNodes[0].name.split(":")[1] + sample_val = val_nodes[_j].childNodes[0].value + sample_val_dict[sample_name] = sample_val + } + } + + return sample_val_dict; +} + +editDataChange = function() { + var already_seen, sample_sets, table, tables, _i, _j, _len; + already_seen = {}; + sample_sets = { + samples_primary: new Stats([]), + samples_other: new Stats([]), + samples_all: new Stats([]) + }; + root.selected_samples = { + samples_primary: {}, + samples_other: {}, + samples_all: {} + }; + + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length){ + tableApi = $('#' + table).DataTable(); + sample_vals = []; + name_nodes = tableApi.column(2).nodes().to$(); + val_nodes = tableApi.column(3).nodes().to$(); + var_nodes = tableApi.column(5).nodes().to$(); + for (_j = 0; _j < val_nodes.length; _j++){ + sample_val = val_nodes[_j].childNodes[0].value + sample_name = $.trim(name_nodes[_j].childNodes[0].textContent) + if (isNumber(sample_val) && sample_val !== "") { + sample_val = parseFloat(sample_val); + sample_sets[table].add_value(sample_val); + try { + sample_var = var_nodes[_j].childNodes[0].value + if (isNumber(sample_var)) { + sample_var = parseFloat(sample_var) + } else { + sample_var = null; + } + } catch { + sample_var = null; + } + sample_dict = { + value: sample_val, + variance: sample_var + } + root.selected_samples[table][sample_name] = sample_dict; + if (!(sample_name in already_seen)) { + sample_sets['samples_all'].add_value(sample_val); + root.selected_samples['samples_all'][sample_name] = sample_dict; + already_seen[sample_name] = true; + } + } + } + } + + } + + updateStatValues(sample_sets); + + if ($('#histogram').hasClass('js-plotly-plot')){ + updateHistogram(); + } + if ($('#bar_chart').hasClass('js-plotly-plot')){ + updateBarChart(); + } + if ($('#violin_plot').hasClass('js-plotly-plot')){ + updateViolinPlot(); + } + if ($('#prob_plot_div').hasClass('js-plotly-plot')){ + return updateProbPlot(); + } +}; + +showHideOutliers = function() { + var label; + label = $('#showHideOutliers').val(); + if (label === "Hide Outliers") { + return $('#showHideOutliers').val("Show Outliers"); + } else if (label === "Show Outliers") { + $('#showHideOutliers').val("Hide Outliers"); + return console.log("Should be now Hide Outliers"); + } +}; + +onCorrMethodChange = function() { + var corr_method; + corr_method = $('select[name=corr_type]').val(); + $('.correlation_desc').hide(); + $('#' + corr_method + "_r_desc").show().effect("highlight"); + if (corr_method === "lit") { + return $("#corr_sample_method").hide(); + } else { + return $("#corr_sample_method").show(); + } +}; +$('select[name=corr_type]').change(onCorrMethodChange); + +on_dataset_change = function() { + let dataset_type = $('select[name=corr_dataset] option:selected').data('type'); + let location_type = $('select[name=location_type] option:selected').val(); + + if (dataset_type == "mrna_assay"){ + $('#min_expr_filter').show(); + $('select[name=location_type] option:disabled').prop('disabled', false) + } + else if (dataset_type == "pheno"){ + $('#min_expr_filter').show(); + $('select[name=location_type]>option:eq(0)').prop('disabled', true).attr('selected', false); + $('select[name=location_type]>option:eq(1)').prop('disabled', false).attr('selected', true); + } + else { + $('#min_expr_filter').hide(); + $('select[name=location_type]>option:eq(0)').prop('disabled', false).attr('selected', true); + $('select[name=location_type]>option:eq(1)').prop('disabled', true).attr('selected', false); + } +} + +$('select[name=corr_dataset]').change(on_dataset_change); +$('select[name=location_type]').change(on_dataset_change); + +submit_special = function(url) { + $("input[name=sample_vals]").val(JSON.stringify(fetchSampleValues())) + $("#trait_data_form").attr("action", url); + + $("#trait_data_form").submit(); +}; + +var corrInputList = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr', + 'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper',"use_cache"] + +$(".test_corr_compute").on("click", (function(_this) { + return function() { + $('input[name=tool_used]').val("Correlation"); + $('input[name=form_url]').val("/test_corr_compute"); + $('input[name=wanted_inputs]').val(corrInputList.join(",")); + + + url = "/loading"; + return submit_special(url); + }; +})(this)); + +$(".corr_compute").on("click", (function(_this) { + + return function() { + + + $('input[name=tool_used]').val("Correlation"); + $('input[name=form_url]').val("/corr_compute"); + $('input[name=wanted_inputs]').val(corrInputList.join(",")); + + + $('input[name=use_cache]').val($('#use_cache').is(":checked") ? "true": "false"); + + url = "/loading"; + return submit_special(url); + }; +})(this)); + +createValueDropdown = function(value) { + return "<option val=" + value + ">" + value + "</option>"; +}; + +populateSampleAttributesValuesDropdown = function() { + var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; + $('#attribute_values').empty(); + sample_attributes = []; + + var attributesAsList = Object.keys(js_data.attributes).map(function(key) { + return [key, js_data.attributes[key].id]; + }); + + attributesAsList.sort(function(first, second) { + if (second[1] > first[1]){ + return -1 + } + if (first[1] > second[1]){ + return 1 + } + return 0 + }); + + for (i=0; i < attributesAsList.length; i++) { + attribute_info = js_data.attributes[attributesAsList[i][1]] + sample_attributes.push(attribute_info.distinct_values); + } + + selected_attribute = $('#exclude_column').val() + _ref1 = sample_attributes[selected_attribute - 1]; + _results = []; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + value = _ref1[_i]; + if (value != ""){ + _results.push($(createValueDropdown(value)).appendTo($('#attribute_values'))); + } + } + return _results; +}; + +if (js_data.categorical_attr_exists == "true"){ + populateSampleAttributesValuesDropdown(); +} + +$('#exclude_column').change(populateSampleAttributesValuesDropdown); +blockByAttributeValue = function() { + var attribute_name, cell_class, exclude_by_value; + + let exclude_group = $('#exclude_by_attr_group').val(); + let exclude_column = $('#exclude_column').val(); + + if (exclude_group === "other") { + var tableApi = $('#samples_other').DataTable(); + } else { + var tableApi = $('#samples_primary').DataTable(); + } + + exclude_by_value = $('#attribute_values').val(); + + let val_nodes = tableApi.column(3).nodes().to$(); + let exclude_val_nodes = tableApi.column(attributeStartPos + parseInt(exclude_column)).nodes().to$(); + + for (i = 0; i < exclude_val_nodes.length; i++) { + if (exclude_val_nodes[i].hasChildNodes()) { + let this_col_value = exclude_val_nodes[i].childNodes[0].data; + let this_val_node = val_nodes[i].childNodes[0]; + + if (this_col_value == exclude_by_value){ + this_val_node.value = "x"; + } + } + } + + editDataChange(); +}; +$('#exclude_by_attr').click(blockByAttributeValue); + +blockByIndex = function() { + var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref; + index_string = $('#remove_samples_field').val(); + index_list = []; + _ref = index_string.split(","); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + index_set = _ref[_i]; + if (index_set.indexOf('-') !== -1) { + try { + start_index = parseInt(index_set.split("-")[0]); + end_index = parseInt(index_set.split("-")[1]); + for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) { + index_list.push(index); + } + } catch (_error) { + error = _error; + alert("Syntax error"); + } + } else { + index = parseInt(index_set); + index_list.push(index); + } + } + + let block_group = $('#block_group').val(); + if (block_group === "other") { + tableApi = $('#samples_other').DataTable(); + } else { + tableApi = $('#samples_primary').DataTable(); + } + val_nodes = tableApi.column(3).nodes().to$(); + for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { + index = index_list[_k]; + val_nodes[index - 1].childNodes[0].value = "x"; + } +}; + +filter_by_study = function() { + let this_study = $('#filter_study').val(); + + let study_sample_data = JSON.parse($('input[name=study_samplelists]').val()) + let filter_samples = study_sample_data[parseInt(this_study)]['samples'] + + if ($('#filter_study_group').length){ + let block_group = $('#filter_study_group').val(); + if (block_group === "other") { + tableApi = $('#samples_other').DataTable(); + } else { + tableApi = $('#samples_primary').DataTable(); + } + } + + let sample_nodes = tableApi.column(2).nodes().to$(); + let val_nodes = tableApi.column(3).nodes().to$(); + for (i = 0; i < sample_nodes.length; i++) { + this_sample = sample_nodes[i].childNodes[0].innerText; + if (!filter_samples.includes(this_sample)){ + val_nodes[i].childNodes[0].value = "x"; + } + } +} + +filter_by_value = function() { + let filter_logic = $('#filter_logic').val(); + let filter_column = $('#filter_column').val(); + let filter_value = $('#filter_value').val(); + let block_group = $('#filter_group').val(); + + if (block_group === "other") { + var tableApi = $('#samples_other').DataTable(); + } else { + var tableApi = $('#samples_primary').DataTable(); + } + + let val_nodes = tableApi.column(3).nodes().to$(); + if (filter_column == "value"){ + var filter_val_nodes = tableApi.column(3).nodes().to$(); + } + else if (filter_column == "stderr"){ + var filter_val_nodes = tableApi.column(5).nodes().to$(); + } + else if (!isNaN(filter_column)){ + var filter_val_nodes = tableApi.column(attributeStartPos + parseInt(filter_column)).nodes().to$(); + } + else { + return false + } + + for (i = 0; i < filter_val_nodes.length; i++) { + if (filter_column == "value" || filter_column == "stderr"){ + var this_col_value = filter_val_nodes[i].childNodes[0].value; + } else { + if (filter_val_nodes[i].childNodes[0] !== undefined){ + var this_col_value = filter_val_nodes[i].innerText; + } else { + continue + } + } + let this_val_node = val_nodes[i].childNodes[0]; + + if(!isNaN(this_col_value) && !isNaN(filter_value)) { + if (filter_logic == "greater_than"){ + if (parseFloat(this_col_value) <= parseFloat(filter_value)){ + this_val_node.value = "x"; + } + } + else if (filter_logic == "less_than"){ + if (parseFloat(this_col_value) >= parseFloat(filter_value)){ + this_val_node.value = "x"; + } + } + else if (filter_logic == "greater_or_equal"){ + if (parseFloat(this_col_value) < parseFloat(filter_value)){ + this_val_node.value = "x"; + } + } + else if (filter_logic == "less_or_equal"){ + if (parseFloat(this_col_value) > parseFloat(filter_value)){ + this_val_node.value = "x"; + } + } + } + } +}; + +hideNoValue_filter = function( settings, data, dataIndex ) { + this_value = tableApi.column(3).nodes().to$()[dataIndex].childNodes[0].value; + if (this_value == "x"){ + return false + } else { + return true + } +} + +hideNoValue = function() { + tables = ['samples_primary', 'samples_other']; + filter_active = $(this).data("active"); + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + tableApi = $('#' + table).DataTable(); + if (filter_active == "true"){ + $(this).val("Hide No Value") + tableApi.draw(); + $(this).data("active", "false"); + } else { + $(this).val("Show No Value") + $.fn.dataTable.ext.search.push(hideNoValue_filter); + tableApi.search(); + tableApi.draw(); + $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hideNoValue_filter, 1)); + $(this).data("active", "true"); + } + } + } +}; +$('#hideNoValue').click(hideNoValue); + +blockOutliers = function() { + return $('.outlier').each((function(_this) { + return function(_index, element) { + return $(element).find('.trait-value-input').val('x'); + }; + })(this)); +}; +$('#blockOutliers').click(blockOutliers); + +resetSamplesTable = function() { + $('input[name="transform"]').val(""); + $('span[name="transform_text"]').text("") + $('#hideNoValue').val("Hide No Value") + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + tableApi = $('#' + table).DataTable(); + val_nodes = tableApi.column(3).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0]; + this_node.value = this_node.attributes["data-value"].value; + } + if (js_data.se_exists){ + se_nodes = tableApi.column(5).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0]; + this_node.value = this_node.attributes["data-value"].value; + } + } + tableApi.draw(); + } + } +}; +$('.reset').click(function() { + $('.selected').each(function() { + $(this).removeClass('selected'); + $(this).find('.edit_sample_checkbox').prop("checked", false); + }) + resetSamplesTable(); + $('input[name="transform"]').val(""); + editDataChange(); +}); + +checkForZeroToOneVals = function() { + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + tableApi = $('#' + table).DataTable(); + val_nodes = tableApi.column(3).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0]; + if(!isNaN(this_node.value)) { + if (0 <= this_node.value && this_node.value < 1){ + return true + } + } + } + } + } + return false +} + +log2Data = function(this_node) { + current_value = this_node.value; + original_value = this_node.attributes['data-value'].value; + if(!isNaN(current_value) && !isNaN(original_value)) { + if (zeroToOneValsExist){ + original_value = parseFloat(original_value) + 1; + } + this_node.value = Math.log2(original_value).toFixed(3); + } +}; + +log10Data = function() { + current_value = this_node.value; + original_value = this_node.attributes['data-value'].value; + if(!isNaN(current_value) && !isNaN(original_value)) { + if (zeroToOneValsExist){ + original_value = parseFloat(original_value) + 1; + } + this_node.value = Math.log10(original_value).toFixed(3); + } +}; + +sqrtData = function() { + current_value = this_node.value; + original_value = this_node.attributes['data-value'].value; + if(!isNaN(current_value) && !isNaN(original_value)) { + if (zeroToOneValsExist){ + original_value = parseFloat(original_value) + 1; + } + this_node.value = Math.sqrt(original_value).toFixed(3); + } +}; + +invertData = function() { + current_value = this_node.value; + if(!isNaN(current_value)) { + this_node.value = parseFloat(-(current_value)).toFixed(3); + } +}; + +qnormData = function() { + current_value = this_node.value; + qnorm_value = this_node.attributes['data-qnorm'].value; + if(!isNaN(current_value)) { + this_node.value = qnorm_value; + } +}; + +zScoreData = function() { + current_value = this_node.value; + zscore_value = this_node.attributes['data-zscore'].value; + if(!isNaN(current_value)) { + this_node.value = zscore_value; + } +}; + +doTransform = function(transform_type) { + tables = ['samples_primary', 'samples_other']; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + tableApi = $('#' + table).DataTable(); + val_nodes = tableApi.column(3).nodes().to$(); + for (i = 0; i < val_nodes.length; i++) { + this_node = val_nodes[i].childNodes[0] + if (transform_type == "log2"){ + log2Data(this_node) + } + if (transform_type == "log10"){ + log10Data(this_node) + } + if (transform_type == "sqrt"){ + sqrtData(this_node) + } + if (transform_type == "invert"){ + invertData(this_node) + } + if (transform_type == "qnorm"){ + qnormData(this_node) + } + if (transform_type == "zscore"){ + zScoreData(this_node) + } + } + } + } +} + +normalizeData = function() { + if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){ + if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') { + doTransform("log2") + $('input[name="transform"]').val("log2") + $('span[name="transform_text"]').text(" - log2 Transformed") + } else { + if ($('input[name="transform"]').val() != "log10" && $('#norm_method option:selected').val() == 'log10'){ + doTransform("log10") + $('input[name="transform"]').val("log10") + $('span[name="transform_text"]').text(" - log10 Transformed") + } + } + } + else if ($('#norm_method option:selected').val() == 'sqrt'){ + if ($('input[name="transform"]').val() != "sqrt") { + doTransform("sqrt") + $('input[name="transform"]').val("sqrt") + $('span[name="transform_text"]').text(" - Square Root Transformed") + } + } + else if ($('#norm_method option:selected').val() == 'invert'){ + doTransform("invert") + $('input[name="transform"]').val("inverted") + if ($('span[name="transform_text"]:eq(0)').text() != ""){ + current_text = $('span[name="transform_text"]:eq(0)').text(); + $('span[name="transform_text"]').text(current_text + " and Inverted"); + } else { + $('span[name="transform_text"]').text(" - Inverted") + } + } + else if ($('#norm_method option:selected').val() == 'qnorm'){ + if ($('input[name="transform"]').val() != "qnorm") { + doTransform("qnorm") + $('input[name="transform"]').val("qnorm") + $('span[name="transform_text"]').text(" - Quantile Normalized") + } + } + else if ($('#norm_method option:selected').val() == 'zscore'){ + if ($('input[name="transform"]').val() != "zscore") { + doTransform("zscore") + $('input[name="transform"]').val("zscore") + $('span[name="transform_text"]').text(" - Z-Scores") + } + } +} + +zeroToOneValsExist = checkForZeroToOneVals(); + +showTransformWarning = function() { + transform_type = $('#norm_method option:selected').val() + if (transform_type == "log2" || transform_type == "log10"){ + if (zeroToOneValsExist){ + $('#transform_alert').css("display", "block") + } + } else { + $('#transform_alert').css("display", "none") + } +} + +$('#norm_method').change(function(){ + showTransformWarning() +}); +$('#normalize').hover(function(){ + showTransformWarning() +}); + +$('#normalize').click(normalizeData) + +switchQNormData = function() { + return $('.trait-value-input').each((function(_this) { + return function(_index, element) { + transform_val = $(element).data('transform') + if (transform_val != "") { + $(element).val(transform_val.toFixed(3)); + } + return transform_val + }; + })(this)); +}; +$('#qnorm').click(switchQNormData); + +getSampleTableData = function(tableName, attributesAsList, includeNAs=false) { + var samples = []; + + if ($('#' + tableName).length){ + tableApi = $('#' + tableName).DataTable(); + attrCol = 4 + + nameNodes = tableApi.column(2).nodes().to$(); + valNodes = tableApi.column(3).nodes().to$(); + if (js_data.se_exists){ + varNodes = tableApi.column(5).nodes().to$(); + attrCol = 6 + if (js_data.has_num_cases) { + nNodes = tableApi.column(6).nodes().to$(); + attrCol = 7 + } + } else { + if (js_data.has_num_cases){ + nNodes = tableApi.column(4).nodes().to$(); + attrCol = 5 + } + } + + attributeNodes = [] + for (_i = 0; _i < attributesAsList.length; _i++){ + attributeNodes.push(tableApi.column(attrCol + _i).nodes().to$()) + } + + checkedRows = getCheckedRows(tableName) + + for (_j = 0; _j < valNodes.length; _j++){ + if (!checkedRows.includes(_j) && checkedRows.length > 0) { + continue + } + sampleVal = valNodes[_j].childNodes[0].value + sampleName = $.trim(nameNodes[_j].childNodes[0].textContent) + if (isNumber(sampleVal) && sampleVal !== "") { + sampleVal = parseFloat(sampleVal); + } else { + sampleVal = 'x' + } + if (typeof varNodes == 'undefined'){ + sampleVar = null; + } else { + sampleVar = varNodes[_j].childNodes[0].value; + if (isNumber(sampleVar)) { + sampleVar = parseFloat(sampleVar); + } else { + sampleVar = 'x'; + } + } + if (typeof nNodes == 'undefined'){ + sampleN = null; + } else { + sampleN = nNodes[_j].childNodes[0].value; + if (isNumber(sampleN)) { + sampleN = parseInt(sampleN); + } else { + sampleN = 'x'; + } + } + + rowDict = { + name: sampleName, + value: sampleVal, + se: sampleVar, + num_cases: sampleN + } + + for (_k = 0; _k < attributeNodes.length; _k++){ + rowDict[attributesAsList[_k]] = attributeNodes[_k][_j].textContent; + } + if (includeNAs || sampleVal != 'x') { + samples.push(rowDict) + } + } + } + + return samples; +}; +exportSampleTableData = function() { + var format, json_sample_data, sample_data; + + var attributesAsList = Object.keys(js_data.attributes).map(function(key) { + return js_data.attributes[key].name; + }); + + sample_data = {}; + sample_data.primary_samples = getSampleTableData('samples_primary', attributesAsList, true); + sample_data.other_samples = getSampleTableData('samples_other', attributesAsList, true); + sample_data.attributes = attributesAsList; + json_sample_data = JSON.stringify(sample_data); + $('input[name=export_data]').val(json_sample_data); + format = $('input[name=export_format]').val(); + if (format === "excel") { + $('#trait_data_form').attr('action', '/export_trait_excel'); + } else { + $('#trait_data_form').attr('action', '/export_trait_csv'); + } + return $('#trait_data_form').submit(); +}; + +$('.export_format').change(function() { + if (this.value == "csv"){ + $('#export_code').css("display", "block") + } else{ + $('#export_code').css("display", "none") + } + $('input[name=export_format]').val( this.value ); + $('.export_format').val( this.value ); +}); + +$('.export').click(exportSampleTableData); +$('#blockOutliers').click(blockOutliers); +_.mixin(_.str.exports()); + +getSampleVals = function(sample_list) { + var sample; + return this.sample_vals = (function() { + var i, len, results; + results = []; + for (i = 0, len = sample_list.length; i < len; i++) { + sample = sample_list[i]; + if (sample.value !== null) { + results.push(sample.value); + } + } + return results; + })(); +}; + +getSampleErrors = function(sample_list) { + var sample; + return this.sample_vals = (function() { + var i, len, results; + variance_exists = false; + results = []; + for (i = 0, len = sample_list.length; i < len; i++) { + sample = sample_list[i]; + if (sample.variance !== null) { + results.push(sample.variance); + variance_exists = true; + } + } + return [results, variance_exists]; + })(); +}; + +getSampleNames = function(sample_list) { + var sample; + return this.sampleNames = (function() { + var i, len, results; + results = []; + for (i = 0, len = sample_list.length; i < len; i++) { + sample = sample_list[i]; + if (sample.value !== null) { + results.push(sample.name); + } + } + return results; + })(); +}; + +getBarBottomMargin = function(sample_list){ + bottomMargin = 80 + maxLength = 0 + sampleNames = getSampleNames(sample_list) + for (i=0; i < sampleNames.length; i++){ + if (sampleNames[i].length > maxLength) { + maxLength = sampleNames[i].length + } + } + + if (maxLength > 6){ + bottomMargin += 11*(maxLength - 6) + } + + return bottomMargin; +} + +root.stats_group = 'samples_primary'; + +if (Object.keys(js_data.sample_group_types).length > 1) { + fullSampleLists = [sampleLists[0], sampleLists[1], sampleLists[0].concat(sampleLists[1])] + sampleGroupList = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']] +} else { + fullSampleLists = [sampleLists[0]] + sampleGroupList = [js_data.sample_group_types['samples_primary']] +} + +// Define Plotly Options (for the options bar at the top of each figure) + +root.modebar_options = { + displayModeBar: true, + modeBarButtonsToAdd:[{ + name: 'Export as SVG', + icon: Plotly.Icons.disk, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'svg'}) + } + }, + { + name: 'Export as JPEG', + icon: Plotly.Icons.camera, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'jpeg'}) + } + }], + showEditInChartStudio: true, + plotlyServerURL: "https://chart-studio.plotly.com", + modeBarButtonsToRemove:['zoom2d', 'pan2d', 'toImage', 'hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines', 'resetScale2d'], + displaylogo: false + //modeBarButtons:['toImage2', 'zoom2d', 'pan2d', 'select2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d'], +} + +// Bar Chart + +root.errors_exist = getSampleErrors(sampleLists[0])[1] +var barTrace = { + x: getSampleNames(sampleLists[0]), + y: getSampleVals(sampleLists[0]), + error_y: { + type: 'data', + array: getSampleErrors(sampleLists[0])[0], + visible: root.errors_exist + }, + type: 'bar' +} + +root.bar_data = [barTrace] + +getBarRange = function(sample_vals, sampleErrors = null){ + positiveErrorVals = [] + negativeErrorVals = [] + for (i = 0;i < sample_vals.length; i++){ + if (sampleErrors[i] != undefined) { + positiveErrorVals.push(sample_vals[i] + sampleErrors[i]) + negativeErrorVals.push(sample_vals[i] - sampleErrors[i]) + } else { + positiveErrorVals.push(sample_vals[i]) + negativeErrorVals.push(sample_vals[i]) + } + } + + minYVal = Math.min(...negativeErrorVals) + maxYVal = Math.max(...positiveErrorVals) + + if (minYVal == 0) { + rangeTop = maxYVal + Math.abs(maxYVal)*0.1 + rangeBottom = 0; + } else { + rangeTop = maxYVal + Math.abs(maxYVal)*0.1 + rangeBottom = minYVal - Math.abs(minYVal)*0.1 + if (minYVal > 0) { + rangeBottom = minYVal - 0.1*Math.abs(minYVal) + } else if (minYVal < 0) { + rangeBottom = minYVal + 0.1*minYVal + } else { + rangeBottom = 0 + } + } + + return [rangeBottom, rangeTop] +} + +root.chart_range = getBarRange(getSampleVals(sampleLists[0]), getSampleErrors(sampleLists[0])[0]) +valRange = root.chart_range[1] - root.chart_range[0] + +if (valRange < 0.05){ + tickDigits = '.3f' + leftMargin = 80 +} else if (valRange < 0.5) { + tickDigits = '.2f' + leftMargin = 70 +} else if (valRange < 5){ + tickDigits = '.1f' + leftMargin = 60 +} else { + tickDigits = 'f' + leftMargin = 55 +} + +if (js_data.num_values < 256) { + barChartWidth = 25 * getSampleVals(sampleLists[0]).length + + // Set bottom margin dependent on longest sample name length, since those can get long + bottomMargin = getBarBottomMargin(sampleLists[0]) + + root.bar_layout = { + title: { + x: 0, + y: 10, + xanchor: 'left', + text: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", + }, + xaxis: { + type: 'category', + titlefont: { + size: 16 + }, + showline: true, + ticklen: 4, + tickfont: { + size: 16 + }, + }, + yaxis: { + title: "<b>" + js_data.unit_type + "</b>", + range: root.chart_range, + titlefont: { + size: 16 + }, + showline: true, + ticklen: 4, + tickfont: { + size: 16 + }, + tickformat: tickDigits, + fixedrange: true + }, + width: barChartWidth, + height: 600, + margin: { + l: leftMargin, + r: 30, + t: 100, + b: bottomMargin + }, + dragmode: false + }; + + $('.bar_chart_tab').click(function() { + updateBarChart(); + }); +} + +total_sample_count = 0 +for (i = 0, i < sampleLists.length; i++;) { + total_sample_count += getSampleVals(sampleLists[i]).length +} + +// Histogram +var hist_trace = { + x: getSampleVals(sampleLists[0]), + type: 'histogram' +}; +root.histogram_data = [hist_trace]; +root.histogram_layout = { + bargap: 0.05, + title: { + x: 0, + y: 10, + xanchor: 'left', + text: "<b> Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", + }, + xaxis: { + autorange: true, + title: js_data.unit_type, + titlefont: { + family: "arial", + size: 16 + }, + ticklen: 4, + tickfont: { + size: 16 + } + }, + yaxis: { + autorange: true, + title: "<b>count</b>", + titlefont: { + family: "arial", + size: 16 + }, + showline: true, + ticklen: 4, + tickfont: { + size: 16 + }, + automargin: true, + fixedrange: true + }, + width: 500, + height: 600, + margin: { + l: 100, + r: 30, + t: 100, + b: 50 + } +}; + +$('.histogram_tab').click(function() { + updateHistogram(); + updateHistogram_width(); +}); + +$('.histogram_samples_group').val(root.stats_group); +$('.histogram_samples_group').change(function() { + root.stats_group = $(this).val(); + return updateHistogram(); +}); + +// Violin Plot + +root.violin_layout = { + title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", + xaxis: { + showline: true, + titlefont: { + family: "arial", + size: 16 + }, + tickfont: { + family: "arial", + size: 16 + } + }, + yaxis: { + title: { + text: "<b>"+js_data.unit_type+"</b>" + }, + titlefont: { + family: "arial", + size: 16 + }, + autorange: true, + showline: true, + ticklen: 4, + tickfont: { + size: 16 + }, + tickformat: tickDigits, + zeroline: false, + automargin: true + }, + margin: { + l: 100, + r: 30, + t: 100, + b: 80 + }, + dragmode: false, + showlegend: false +}; + +if (fullSampleLists.length > 1) { + root.violin_layout['width'] = 600; + root.violin_layout['height'] = 500; + var trace1 = { + y: getSampleVals(fullSampleLists[2]), + type: 'violin', + points: 'none', + box: { + visible: true + }, + line: { + color: 'blue', + }, + meanline: { + visible: true + }, + name: "<b>" + sampleGroupList[2] + "</b>", + x0: "<b>" + sampleGroupList[2] + "</b>" + } + var trace2 = { + y: getSampleVals(fullSampleLists[1]), + type: 'violin', + points: 'none', + box: { + visible: true + }, + line: { + color: 'red', + }, + meanline: { + visible: true + }, + name: "<b>" + sampleGroupList[1] + "</b>", + x0: "<b>" + sampleGroupList[1] + "</b>" + } + var trace3 = { + y: getSampleVals(fullSampleLists[0]), + type: 'violin', + points: 'none', + box: { + visible: true + }, + line: { + color: 'green', + }, + meanline: { + visible: true + }, + name: "<b>" + sampleGroupList[0] + "</b>", + x0: "<b>" + sampleGroupList[0] + "</b>" + } + root.violin_data = [trace1, trace2, trace3] +} else { + root.violin_layout['width'] = 320; + root.violin_layout['height'] = 400; + root.violin_data = [ + { + y: getSampleVals(fullSampleLists[0]), + type: 'violin', + points: 'none', + box: { + visible: true + }, + meanline: { + visible: true + }, + name: "<b>Trait " + js_data.trait_id + "</b>", + x0: "<b>density</b>" + } + ] +} + +$('.violin_plot_tab').click(function() { + updateViolinPlot(); +}); + +if (getSampleVals(sampleLists[0]).length < 256) { + $('.bar_chart_samples_group').change(function() { + root.stats_group = $(this).val(); + return updateBarChart(); + }); + root.bar_sort = "name" +} +$('.sort_by_name').click(function() { + root.bar_sort = "name" + return updateBarChart(); +}); +$('.sort_by_value').click(function() { + root.bar_sort = "value" + return updateBarChart(); +}); + +root.prob_plot_group = 'samples_primary'; +$('.prob_plot_samples_group').val(root.prob_plot_group); +$('.prob_plot_tab').click(function() { + return updateProbPlot(); +}); +$('.prob_plot_samples_group').change(function() { + root.prob_plot_group = $(this).val(); + return updateProbPlot(); +}); + +function isEmpty( el ){ + return !$.trim(el.html()) +} + +$('.stats_panel').click(function() { + if (isEmpty($('#stats_table'))){ + makeTable(); + editDataChange(); + } else { + editDataChange(); + } +}); + +$('#block_by_index').click(function(){ + blockByIndex(); + editDataChange(); +}); + +$('#filter_by_study').click(function(){ + filter_by_study(); + editDataChange(); +}) + +$('#filter_by_value').click(function(){ + filter_by_value(); + editDataChange(); +}) + +$('.edit_sample_value').change(function() { + editDataChange(); +}); + +$('#exclude_group').click(editDataChange); +$('#blockOutliers').click(editDataChange); +$('#reset').click(editDataChange); +$('#qnorm').click(editDataChange); +$('#normalize').click(editDataChange); + +Number.prototype.countDecimals = function () { + if(Math.floor(this.valueOf()) === this.valueOf()) return 0; + return this.toString().split(".")[1].length || 0; +} diff --git a/gn2/wqflask/static/new/javascript/show_trait_mapping_tools.js b/gn2/wqflask/static/new/javascript/show_trait_mapping_tools.js new file mode 100644 index 00000000..a4e6dafc --- /dev/null +++ b/gn2/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -0,0 +1,329 @@ +var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining; + +update_time_remaining = function(percent_complete) { + var minutes_remaining, now, period, total_seconds_remaining; + now = new Date(); + period = now.getTime() - root.start_time; + console.log("period is:", period); + if (period > 8000) { + total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000; + minutes_remaining = Math.round(total_seconds_remaining / 60); + if (minutes_remaining < 3) { + return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining"); + } else { + return $('#time_remaining').text(minutes_remaining + " minutes remaining"); + } + } +}; + +get_progress = function() { + var params, params_str, temp_uuid, url; + console.log("temp_uuid:", $("#temp_uuid").val()); + temp_uuid = $("#temp_uuid").val(); + params = { + key: temp_uuid + }; + params_str = $.param(params); + url = "/get_temp_data?" + params_str; + console.log("url:", url); + $.ajax({ + type: "GET", + url: url, + success: (function(_this) { + return function(progress_data) { + var percent_complete; + percent_complete = progress_data['percent_complete']; + console.log("in get_progress data:", progress_data); + $('#marker_regression_progress').css("width", percent_complete + "%"); + if (root.start_time) { + if (!isNaN(percent_complete)) { + return update_time_remaining(percent_complete); + } + } else { + return root.start_time = new Date().getTime(); + } + }; + })(this) + }); + return false; +}; + +block_outliers = function() { + return $('.outlier').each((function(_this) { + return function(_index, element) { + return $(element).find('.trait_value_input').val('x'); + }; + })(this)); +}; + +do_ajax_post = function(url, form_data) { + $.ajax({ + type: "POST", + url: url, + data: form_data, + error: (function(_this) { + return function(xhr, ajaxOptions, thrownError) { + alert("Sorry, an error occurred"); + console.log(xhr); + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return $("body").html("We got an error."); + }; + })(this), + success: (function(_this) { + return function(data) { + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return open_mapping_results(data); + }; + })(this) + }); + console.log("settingInterval"); + this.my_timer = setInterval(get_progress, 1000); + return false; +}; + +open_mapping_results = function(data) { + return $.colorbox({ + html: data, + href: "#mapping_results_holder", + height: "90%", + width: "90%", + onComplete: (function(_this) { + return function() { + var filename, getSvgXml; + root.create_lod_chart(); + filename = "lod_chart_" + js_data.this_trait; + getSvgXml = function() { + var svg; + svg = $("#topchart").find("svg")[0]; + return (new XMLSerializer).serializeToString(svg); + }; + $("#exportform > #export").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + return $("#exportpdfform > #export_pdf").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + }; + })(this) + }); +}; + +outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results."; +showalert = function(message, alerttype) { + return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); +}; + +$('#suggestive').hide(); + +$('input[name=display_all]').change((function(_this) { + return function() { + if ($('input[name=display_all]:checked').val() === "False") { + return $('#suggestive').show(); + } else { + return $('#suggestive').hide(); + } + }; +})(this)); + +// This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', + 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', + 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', + 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', + 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', + 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', + 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', + 'mapmethod_rqtl', 'mapmodel_rqtl', 'temp_trait', 'group', 'species', + 'reaper_version', 'primary_samples'] + +$(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=pair_scan]').val("false"); + $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); + $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); + $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); + $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_geno').val()); + $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_geno').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); + $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$(".rqtl-pair-tab, #rqtl_pair_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_pair_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=pair_scan]').val("true"); + $('input[name=genofile]').val($('#genofile_rqtl_pair').val()); + $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_pair').val()); + $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_pair').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_pair]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=control_marker]').val($('input[name=control_rqtl_pair]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl_pair]:checked').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$(".gemma-tab, #gemma_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("gemma"); + $('input[name=mapping_scale]').val('physic'); + $('input[name=selected_chr]').val($('#chr_gemma').val()); + $('input[name=num_perm]').val(0); + $('input[name=genofile]').val($('#genofile_gemma').val()); + $('input[name=maf]').val($('input[name=maf_gemma]').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$(".reaper-tab, #interval_mapping_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ + var form_data, url; + console.log("In interval mapping"); + url = "/loading"; + $('input[name=method]').val("reaper"); + $('input[name=selected_chr]').val($('#chr_reaper').val()); + $('input[name=mapping_scale]').val($('#scale_reaper').val()); + $('input[name=genofile]').val($('#genofile_reaper').val()); + $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); + $('input[name=control_marker]').val($('input[name=control_reaper]').val()); + $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) { + return function() { + if ($(".outlier").length && $(".outlier-alert").length < 1) { + return showalert(outlier_text, "alert-success outlier-alert"); + } + }; +})(this)); + +composite_mapping_fields = function() { + return $(".composite_fields").toggle(); +}; + +mapping_method_fields = function() { + return $(".mapping_method_fields").toggle(); +}; + +$("#use_composite_choice").change(composite_mapping_fields); + +$("#mapping_method_choice").change(mapping_method_fields); + +$("#mapmodel_rqtl_geno,#mapmodel_rqtl_pair").change(function() { + if ($(this).val() == "np"){ + $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); + $("#missing_geno,#missing_geno_pair").attr('disabled', 'disabled'); + $("#missing_geno,#missing_geno_pair").css('background-color', '#CCC'); + } else { + $("#mapmethod_rqtl_geno").removeAttr('disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); + $("#missing_geno,#missing_geno_pair").removeAttr('disabled'); + $("#missing_geno,#missing_geno_pair").css('background-color', '#FFF'); + } +}); + +$("#mapmethod_rqtl_geno,#mapmethod_rqtl_pair").change(function() { + if ($(this).val() == "mr"){ + $("#missing_geno_div,#missing_geno_pair_div").css('display', 'block'); + } else { + $("#missing_geno_div,#missing_geno_pair_div").css('display', 'none'); + } +}); + +$("li.mapping-tab").click(function() { + if ($(this).hasClass("rqtl")){ + $(".rqtl_description").css("display", "block"); + } else { + $(".rqtl_description").css("display", "none"); + } +}); + +toggle_enable_disable = function(elem) { + return $(elem).prop("disabled", !$(elem).prop("disabled")); +}; + +$("#choose_closet_control").change(function() { + return toggle_enable_disable("#control_locus"); +}); + +$("#display_all_lrs").change(function() { + return toggle_enable_disable("#suggestive_lrs"); +}); + +$('#genofile_rqtl_geno').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_rqtl_geno').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); +$('#genofile_reaper').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_reaper').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); diff --git a/gn2/wqflask/static/new/javascript/stats.js b/gn2/wqflask/static/new/javascript/stats.js new file mode 100644 index 00000000..6c443ab3 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/stats.js @@ -0,0 +1,176 @@ +// Generated by CoffeeScript 1.8.0 +var Stats, bxd_only; + +Stats = (function() { + function Stats(the_values) { + this.the_values = the_values; + } + + Stats.prototype.add_value = function(value) { + return this.the_values.push(value); + }; + + Stats.prototype.n_of_samples = function() { + return this.the_values.length; + }; + + Stats.prototype.sum = function() { + var total, value, _i, _len, _ref; + total = 0; + _ref = this.the_values; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + value = _ref[_i]; + total += value; + } + return total; + }; + + Stats.prototype.mean = function() { + return this.sum() / this.n_of_samples(); + }; + + Stats.prototype.median = function() { + var is_odd, median_position, the_values_sorted; + is_odd = this.the_values.length % 2; + median_position = Math.floor(this.the_values.length / 2); + the_values_sorted = this.the_values.sort(function(a, b) { + return a - b; + }); + if (is_odd) { + return the_values_sorted[median_position]; + } else { + return (the_values_sorted[median_position] + the_values_sorted[median_position - 1]) / 2; + } + }; + + Stats.prototype.std_dev = function() { + var step_a, step_b, sum, value, _i, _len, _ref; + sum = 0; + _ref = this.the_values; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + value = _ref[_i]; + step_a = Math.pow(value - this.mean(), 2); + sum += step_a; + } + step_b = sum / this.the_values.length; + return Math.sqrt(step_b); + }; + + Stats.prototype.std_error = function() { + return this.std_dev() / Math.sqrt(this.n_of_samples()); + }; + + Stats.prototype.min = function() { + return Math.min.apply(Math, this.the_values); + }; + + Stats.prototype.max = function() { + return Math.max.apply(Math, this.the_values); + }; + + Stats.prototype.range = function() { + if (js_data.dataset_type == "ProbeSet"){ + if (js_data.data_scale == "linear_positive"){ + return Math.log2(this.max()) - Math.log2(this.min()); + } else { + return this.max() - this.min() + } + } else { + return this.max() - this.min() + } + }; + + Stats.prototype.range_fold = function() { + if (js_data.dataset_type == "ProbeSet"){ + return Math.pow(2, this.range()); + } else { + return this.range() + } + }; + + Stats.prototype.interquartile = function() { + var iq, length, q1, q3; + length = this.the_values.length; + if (js_data.dataset_type == "ProbeSet" && js_data.data_scale == "linear_positive") { + q1 = Math.log2(this.the_values[Math.floor(length * .25)]); + q3 = Math.log2(this.the_values[Math.floor(length * .75)]); + } else { + q1 = this.the_values[Math.floor(length * .25)]; + q3 = this.the_values[Math.floor(length * .75)]; + } + iq = q3 - q1; + if (js_data.dataset_type == "ProbeSet") { + return Math.pow(2, iq); + } else { + return iq; + } + }; + + Stats.prototype.skewness = function() { + var len = this.the_values.length, + delta = 0, + delta_n = 0, + term1 = 0, + N = 0, + mean = 0, + M2 = 0, + M3 = 0, + g; + + for ( var i = 0; i < len; i++ ) { + N += 1; + + delta = this.the_values[ i ] - mean; + delta_n = delta / N; + + term1 = delta * delta_n * (N-1); + + M3 += term1*delta_n*(N-2) - 3*delta_n*M2; + M2 += term1; + mean += delta_n; + } + // Calculate the population skewness: + g = Math.sqrt( N )*M3 / Math.pow( M2, 3/2 ); + + // Return the corrected sample skewness: + return Math.sqrt( N*(N-1))*g / (N-2); + }; + + Stats.prototype.kurtosis = function() { + var len = this.the_values.length, + delta = 0, + delta_n = 0, + delta_n2 = 0, + term1 = 0, + N = 0, + mean = 0, + M2 = 0, + M3 = 0, + M4 = 0, + g; + + for ( var i = 0; i < len; i++ ) { + N += 1; + + delta = this.the_values[ i ] - mean; + delta_n = delta / N; + delta_n2 = delta_n * delta_n; + + term1 = delta * delta_n * (N-1); + + M4 += term1*delta_n2*(N*N - 3*N + 3) + 6*delta_n2*M2 - 4*delta_n*M3; + M3 += term1*delta_n*(N-2) - 3*delta_n*M2; + M2 += term1; + mean += delta_n; + } + // Calculate the population excess kurtosis: + g = N*M4 / (M2*M2) - 3; + //Return the corrected sample excess kurtosis: + return (N-1) / ( (N-2)*(N-3) ) * ( (N+1)*g + 6 ); + }; + + return Stats; + +})(); + +window.Stats = Stats; diff --git a/gn2/wqflask/static/new/javascript/table_functions.js b/gn2/wqflask/static/new/javascript/table_functions.js new file mode 100644 index 00000000..62888cd9 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/table_functions.js @@ -0,0 +1,90 @@ +recheckRows = function(theTable, checkedRows){ + // This is meant to recheck checkboxes after columns are resized + checkCells = theTable.column(0).nodes().to$(); + for (let i = 0; i < checkCells.length; i++) { + if (checkedRows.includes(i)){ + checkCells[i].childNodes[0].checked = true; + } + } + + checkRows = traitTable.rows().nodes(); + for (let i =0; i < checkRows.length; i++) { + if (checkedRows.includes(i)){ + checkRows[i].classList.add("selected") + } + } +} + +getCheckedRows = function(tableId){ + let checkedRows = [] + $("#" + tableId + " input.checkbox").each(function(index){ + if ($(this).prop("checked") == true){ + checkedRows.push(index); + } + }); + + return checkedRows +} + +function setUserColumnsDefWidths(tableId, columnDefs) { + var userColumnDef; + + // Get the settings for this table from localStorage + var userColumnDefs = JSON.parse(localStorage.getItem(tableId)) || []; + + if (userColumnDefs.length === 0 ) return; + + columnDefs.forEach( function(columnDef) { + // Check if there is a width specified for this column + userColumnDef = userColumnDefs.find( function(column) { + return column.targets === columnDef.targets; + }); + + // If there is, set the width of this columnDef in px + if ( userColumnDef ) { + + columnDef.sWidth = userColumnDef.width + 'px'; + columnDef.width = userColumnDef.width + 'px'; + + $('.toggle-vis').each(function(){ + if ($(this).attr('data-column') == columnDef.targets){ + if ($(this).hasClass("active")){ + columnDef.bVisible = false + } else { + columnDef.bVisible = true + } + } + }) + } + }); + + return columnDefs +} + +function saveColumnSettings(tableId, traitTable) { + var userColumnDefs = JSON.parse(localStorage.getItem(tableId)) || []; + var width, header, existingSetting; + + traitTable.columns().every( function ( targets ) { + // Check if there is a setting for this column in localStorage + existingSetting = userColumnDefs.findIndex( function(column) { return column.targets === targets;}); + + // Get the width of this column + header = this.header(); + width = $(header).width(); + + if ( existingSetting !== -1 ) { + // Update the width + userColumnDefs[existingSetting].width = width; + } else { + // Add the width for this column + userColumnDefs.push({ + targets: targets, + width: width, + }); + } + }); + + // Save (or update) the settings in localStorage + localStorage.setItem(tableId, JSON.stringify(userColumnDefs)); +} diff --git a/gn2/wqflask/static/new/javascript/thank_you.js b/gn2/wqflask/static/new/javascript/thank_you.js new file mode 100644 index 00000000..deb68211 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/thank_you.js @@ -0,0 +1,6 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + console.log("Starting transform"); + $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize'); + return console.log("Transformed to sign out I hope"); +}); diff --git a/gn2/wqflask/static/new/javascript/typeahead_rn6.json b/gn2/wqflask/static/new/javascript/typeahead_rn6.json new file mode 100644 index 00000000..1889d8a2 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/typeahead_rn6.json @@ -0,0 +1 @@ +var rat_genes = 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\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/validation.js b/gn2/wqflask/static/new/javascript/validation.js new file mode 100644 index 00000000..2cacacfa --- /dev/null +++ b/gn2/wqflask/static/new/javascript/validation.js @@ -0,0 +1,42 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + var remove_samples_is_valid, validate_remove_samples; + remove_samples_is_valid = function(input) { + var new_splats, pattern, splat, splats, _i, _len; + if (_.trim(input).length === 0) { + return true; + } + splats = input.split(","); + new_splats = (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = splats.length; _i < _len; _i++) { + input = splats[_i]; + _results.push(_.trim(input)); + } + return _results; + })(); + pattern = /^\d+\s*(?:-\s*\d+)?\s*$/; + for (_i = 0, _len = new_splats.length; _i < _len; _i++) { + splat = new_splats[_i]; + if (!splat.match(pattern)) { + return false; + } + } + return true; + }; + validate_remove_samples = function() { + + /* + Check if input for the remove samples function is valid and notify the user if not + */ + var input; + input = $('#remove_samples_field').val(); + if (remove_samples_is_valid(input)) { + return $('#remove_samples_invalid').hide(); + } else { + return $('#remove_samples_invalid').show(); + } + }; + return $('#remove_samples_field').change(validate_remove_samples); +}); |
