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authorLei Yan2015-05-12 20:47:50 +0000
committerLei Yan2015-05-12 20:47:50 +0000
commitcb5684aa004d59585167804450f64ab74d3a3412 (patch)
tree31aedac7d1fd945c893f07e2e419b4361f00925b /wqflask/wqflask/templates
parentd11b71790f5f7c7eb9fe41704e1df7d8447371c9 (diff)
parentf228118ac112f3ebab5faf41ac9e1bc2a6e2c0fa (diff)
downloadgenenetwork2-cb5684aa004d59585167804450f64ab74d3a3412.tar.gz
Merge https://github.com/genenetwork/genenetwork2
Diffstat (limited to 'wqflask/wqflask/templates')
-rwxr-xr-xwqflask/wqflask/templates/base.html19
-rwxr-xr-xwqflask/wqflask/templates/collections/view.html118
-rwxr-xr-xwqflask/wqflask/templates/index_page.html136
-rwxr-xr-xwqflask/wqflask/templates/interval_mapping.html234
-rwxr-xr-xwqflask/wqflask/templates/new_security/login_user.html62
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html74
-rwxr-xr-xwqflask/wqflask/templates/search_result_page.html44
-rw-r--r--wqflask/wqflask/templates/show_image.html5
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html30
-rwxr-xr-xwqflask/wqflask/templates/show_trait_calculate_correlations.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_details.html6
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html184
-rwxr-xr-xwqflask/wqflask/templates/show_trait_statistics_new.html24
-rwxr-xr-xwqflask/wqflask/templates/whats_new.html13
14 files changed, 575 insertions, 376 deletions
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 240481cc..462a59a2 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -42,7 +42,6 @@
{% macro flash_me() -%}
{% with messages = get_flashed_messages(with_categories=true) %}
{% if messages %}
- <br />
<div class="container">
{% for category, message in messages %}
<div class="alert {{ category }}">{{ message }}</div>
@@ -72,7 +71,14 @@
<div>
<ul class="nav navbar-nav">
<li class="">
- <a href="/">Home</a>
+ <a href="/">Search</a>
+ </li>
+ <li class="">
+ <a href="/collections/list">Collections
+ {% if g.user_session.user_ob %}
+ <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
+ {% endif %}
+ </a>
</li>
<li class="">
<a href="/help">Help</a>
@@ -93,14 +99,6 @@
<a href="/environments">Environments</a>
</li>
<li class="">
- <a href="/collections/list">Collections
- {% if g.user_session.user_ob %}
- <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
- {% endif %}
- </a>
- </li>
-
- <li class="">
{% if g.user_session.logged_in %}
<a id="login_out" title="Signed in as {{ g.user_session.user_ob.name_and_org }}." href="/n/logout">Sign out</a>
{% else %}
@@ -143,7 +141,6 @@
<a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
<a href="http://www.python.org/">python</a> and good intentions.
</p>
- <p>Special thanks to CYP1A2 and AHR.</p>
<br />
<p>GeneNetwork is supported by:</p>
<UL>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 237a0d4e..fc1edf2a 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -1,5 +1,10 @@
{% extends "base.html" %}
{% block title %}View Collection{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+{% endblock %}
{% block content %}
<!-- Start of body -->
{% if uc %}
@@ -10,13 +15,7 @@
'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }}
{% endif %}
<div class="container">
- <div class="page-header">
- <h1>Your Collection</h1>
- {% if uc %}
- <h2>{{ uc.name }}</h2>
- {% endif %}
-
- <div class="form-group">
+ <div>
{% if uc %}
<form action="/collections/delete" method="post">
{% if uc %}
@@ -51,40 +50,18 @@
<input type="submit" class="btn btn-primary" value="Heatmap" />
</div>
</form>
- </div>
-
- <!--
- <form action="/corr_matrix" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <input type="submit"
- class="btn btn-small"
- value="Correlation Matrix" />
- </form>
- <form action="/heatmap" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <input type="submit"
- class="btn btn-small"
- value="Heatmap" />
- </form>
- -->
</div>
-
-
- <div class="bs-docs-example">
- <table class="table table-hover" id='trait_table'>
+ <div>
+ <br />
+ <br />
+ <br />
+ <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
+ <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
+ <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
+ <br />
+ <br />
+ <table class="table table-hover table-striped" id='trait_table'>
<thead>
<tr>
<th></th>
@@ -92,9 +69,9 @@
<th>Description</th>
<th>Location</th>
<th>Mean</th>
- <th>Max LRS</th>
+ <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
<th>Max LRS Location</th>
- <th>Additive Effect</th>
+ <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
</tr>
</thead>
@@ -126,15 +103,7 @@
</tbody>
</table>
-
<br />
-
- <button class="btn" id="select_all"><i class="icon-ok"></i> Select All</button>
- <button class="btn" id="deselect_all"><i class="icon-remove"></i> Deselect All</button>
- <button class="btn" id="invert"><i class="icon-resize-vertical"></i> Invert</button>
- <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
- <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
- <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
</div>
</div>
@@ -144,4 +113,55 @@
{% block js %}
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript">
+ $(document).ready( function () {
+
+ $('#trait_table tr').click(function(event) {
+ if (event.target.type !== 'checkbox') {
+ $(':checkbox', this).trigger('click');
+ }
+ });
+
+ console.time("Creating table");
+ $('#trait_table').dataTable( {
+ "aoColumns": [
+ { "bSortable": false },
+ { "sType": "natural" },
+ { "sType": "natural",
+ "sWidth": "35%" },
+ { "sType": "natural",
+ "sWidth": "15%" },
+ { "sType": "cust-txt" },
+ { "sType": "natural",
+ "sWidth": "12%" },
+ { "sType": "natural",
+ "sWidth": "15%" },
+ { "sType": "cust-txt" }
+ ],
+ "columns": [
+ { "width": "50%" },
+ null,
+ null,
+ null,
+ null,
+ null
+ ],
+ "sDom": "tir",
+ "iDisplayLength": -1,
+ "autoWidth": true,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+
+ </script>
+
+
{% endblock %}
+
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 1caca702..5e0a92e3 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -16,9 +16,9 @@
{{ flash_me() }}
- <div class="row" style="width: 1200px !important;">
+ <div class="row" style="width: 1400px !important;">
- <div class="col-xs-5 col-xs-5">
+ <div class="col-xs-5">
<section id="search">
<div class="page-header">
<h1>Select and search</h1>
@@ -29,31 +29,42 @@
<div class="form-group">
<label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
- <div class="col-xs-4 controls">
- <select name="species" id="species" class="form-control selectpicker span3" style="width: 300px !important;"></select>
+ <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
+ <div class="col-xs-8">
+ <select name="species" id="species" class="form-control selectpicker span3" style="width: 280px !important;"></select>
+ </div>
+ <div class="col-xs-4">
+ <input id="make_default" class="btn btn-primary form-control" value="Make Default">
+ </div>
</div>
</div>
<div class="form-group">
<label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
- <div class="col-xs-4 controls input-append">
- <select name="group" id="group" class="form-control selectpicker span3" style="width: 300px !important;"></select>
- <i class="icon-question-sign"></i>
+ <div class="col-xs-10 controls input-append">
+ <div class="col-xs-8">
+ <select name="group" id="group" class="form-control selectpicker span3" style="width: 280px !important;"></select>
+ <i class="icon-question-sign"></i>
+ </div>
</div>
</div>
<div class="form-group">
<label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
- <div class="col-xs-4 controls">
- <select name="type" id="type" class="form-control selectpicker span3" style="width: 300px !important;"></select>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-8">
+ <select name="type" id="type" class="form-control selectpicker span3" style="width: 280px !important;"></select>
+ </div>
</div>
</div>
<div class="form-group">
<label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
- <div class="col-xs-4 controls input-append">
- <select name="dataset" id="dataset" class="form-control selectpicker span5" style="width: 450px !important;"></select>
- <i class="icon-question-sign"></i>
+ <div class="col-xs-10 controls input-append">
+ <div class="col-xs-8">
+ <select name="dataset" id="dataset" class="form-control selectpicker span5" style="width: 450px !important;"></select>
+ <i class="icon-question-sign"></i>
+ </div>
</div>
</div>
@@ -65,34 +76,33 @@
<!-- GET ANY SEARCH -->
<div class="form-group">
- <label for="tfor" class="col-xs-1 control-label" style="width: 65px !important;">Search:</label>
+ <label for="tfor" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Search for:</label>
<div class="col-xs-10 controls">
- <textarea name="search_terms" rows="2" class="form-control search-query" style="width: 450px !important;" id="tfor"></textarea>
+ <div class="col-xs-8">
+ <textarea name="search_terms" rows="2" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="tfor"></textarea>
+ </div>
</div>
</div>
<!-- GET ANY HELP -->
+ <div class="form-group">
+ <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-2 controls" style="width: 100px !important;">
+ <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
+ </div>
+ <div class="col-xs-9 controls">
+ Enter terms, genes, ID numbers in the <b>Search</b> field
+ Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*)
+ Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>
+ </div>
+ </div>
+ </div>
- <p>Enter terms, genes, ID numbers in the
- <b>Search</b> field<br>
- Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
- synap*)<br>
- Use <b>quotes</b> for terms such as <i>"tyrosine
- kinase"</i></p>
- <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+ <!-- SEARCH, MAKE DEFAULT -->
<div class="form-group">
-
- <div class="col-xs-3 controls" style="width: 100px !important;">
- <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
- </div>
- <div class="col-xs-4 controls" style="width: 150px !important;">
- <input id="make_default" type="submit" class="btn btn-default form-control" value="Make Default">
- </div>
- <div class="col-xs-5 controls" style="width: 200px !important;">
- <input type="submit" class="btn btn-default form-control" value="Advanced Search">
- </div>
</div>
<input type="hidden" name="FormID" value="searchResult" class="form-control">
@@ -101,11 +111,9 @@
</fieldset>
</form>
</section>
- </div>
- <div style="padding-left:120px" class="col-xs-6" style="width: 600px !important;">
<section id="advanced">
<div class="page-header">
- <h1>Advanced commands</h1>
+ <h2>Advanced commands</h2>
</div>
<p>GeneNetwork supports a variety of advanced searches.</p>
@@ -113,12 +121,16 @@
<p>To try them out copy these examples into the search field:</p>
<ul>
- <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+ <!--<li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
chromosome 1 between 25 and 30 Mb.</li>
<li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
- linkage between 23 and 46.</li>
+ linkage between 23 and 46.</li>-->
+
+ <li><b>MEAN=(15 16)</b> finds highly expressed genes (15 to 16 log2 units).</li>
+
+ <li><b>LRS=(23 46)</b> finds genes with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a> linkage between 23 and 46.</li>
<li><b>RIF=mitochondrial</b> searches RNA databases for <a href="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
GeneRIF</a> links.</li>
@@ -127,7 +139,7 @@
GeneWiki</a> for genes that you or other users have annotated
with the word <i>nicotine</i>.</li>
- <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
+ <!--<li><b>GO:0045202</b> searches for synapse-associated genes listed in the
<a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
Gene Ontology</a>.</li>
@@ -139,9 +151,12 @@
<li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
- scores between 9 and 999.</li>
+ scores between 9 and 999.</li>-->
</ul>
</section>
+ </div>
+ <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
+ <!--
<section id="tour-info">
<div class="page-header">
<h1>Tour and more info</h1>
@@ -167,6 +182,7 @@
and advice on their use and citation.</p>
</section>
+ -->
<section id="websites">
<div class="page-header">
@@ -187,44 +203,16 @@
<li>GeneNetwork Source Code at <a href="https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
</ul>
- <h3>Mirror and development sites</h3>
- <ul>
- <li><a href="http://www.genenetwork.org/" target="_blank">
- Main GN site</a> at UTHSC</li>
-
- <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
- Australia</a> at the UWA</li>
-
- <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
- California</a> at UCLA</li>
-
- <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
- Germany</a> at the HZI</li>
-
- <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
- Netherlands</a> at the Hubrecht
- (development)</li>
+ <h3>GN1 Mirror and development sites</h3>
- <li><a href="http://genenetwork.memphis.edu/" target="_blank">
- Memphis</a> at the U of M</li>
-
- <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
- Singapore</a> at the NUS</li>
-
- <li><a href="http://genenetwork.epfl.ch/" target="_blank">
- Switzerland</a> at the EPFL</li>
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN1 site at UTHSC</a> (main site)</li>
+ <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+ <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
+ <li><a href="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
</ul>
- <h3>History and archive</h3>
-
- <p>The
- <a href="http://artemis.uthsc.edu" target="_blank">
- time machine</a>
- has earlier versions that correspond to specific publication dates.
- </p>
-
- <h3>The next generation</h3>
- <p>Try the <a href="http://alexandria.uthsc.edu/" target="_blank">
- development</a> site to explore experimental data and features.</p>
</section>
<!--<section id="getting-started">
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
index 7a03ce34..82a96ba1 100755
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -1,120 +1,116 @@
-{% extends "base.html" %}
-{% block title %}Interval Mapping{% endblock %}
-{% block css %}
-<!-- <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-{% endblock %}
-{% block content %} <!-- Start of body -->
-
- {{ header("Mapping",
- '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-
- <div class="container">
- <div>
- <h2>
- Whole Genome Mapping
- </h2>
- <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">
- <input type="hidden" id="data" name="data" value="">
- <input type="hidden" id="filename" name="filename" value="">
- <input type="submit" id="export" value="Download SVG">
- </form>
- <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">
- <input type="hidden" id="data" name="data" value="">
- <input type="hidden" id="filename" name="filename" value="">
- <input type="submit" id="export_pdf" value="Download PDF">
- </form>
- </div>
- <div id="chart_container">
- <div class="qtlcharts" id="topchart">
-
- </div>
- </div>
- <div>
- <h2>
- Results
- </h2>
- </div>
- <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <td>Index</td>
- <td>LRS Score</td>
- <td>Chr</td>
- <td>Mb</td>
- <td>Locus</td>
- <td>Additive Effect</td>
- </tr>
- </thead>
- <tbody>
- {% for marker in qtl_results %}
- <tr>
- <td>{{ loop.index }}</td>
- <td>{{ marker.lrs_value|float }}</td>
- <td>{{ marker.chr|int }}</td>
- <td>{{ marker.Mb|float }}</td>
- <td>{{ marker.name }}</td>
- <td>{{ marker.additive|float }}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
-
- </div>
-
- <!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script>
- js_data = {{ js_data | safe }}
- </script>
-
- <!--[if lt IE 9]>
-<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
- <![endif]-->
- <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_interval_map.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
- <script type="text/javascript" charset="utf-8">
- $(document).ready( function () {
- console.time("Creating table");
- $('#qtl_results').dataTable( {
- //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
- "sDom": "lTftipr",
- "oTableTools": {
- "aButtons": [
- "copy",
- "print",
- {
- "sExtends": "collection",
- "sButtonText": 'Save <span class="caret" />',
- "aButtons": [ "csv", "xls", "pdf" ]
- }
- ],
- "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
- },
- "iDisplayLength": 50,
- "bLengthChange": true,
- "bDeferRender": true,
- "bSortClasses": false
- } );
- console.timeEnd("Creating table");
- });
- </script>
+{% block css %}
+<!-- <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+
+ <div id="mapping_results" class="container">
+ <div>
+ <h2>
+ Whole Genome Mapping
+ </h2>
+ <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">
+ <input type="hidden" id="data" name="data" value="">
+ <input type="hidden" id="filename" name="filename" value="">
+ <input type="submit" id="export" value="Download SVG">
+ </form>
+ <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">
+ <input type="hidden" id="data" name="data" value="">
+ <input type="hidden" id="filename" name="filename" value="">
+ <input type="submit" id="export_pdf" value="Download PDF">
+ </form>
+ </div>
+ <div id="chart_container">
+ <div class="qtlcharts" id="topchart">
+
+ </div>
+ </div>
+ <div>
+ <h2>
+ Results
+ </h2>
+ </div>
+ <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <td>Index</td>
+ <td>LRS Score</td>
+ <td>Chr</td>
+ <td>Mb</td>
+ <td>Locus</td>
+ <td>Additive Effect</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in qtl_results %}
+ <tr>
+ <td>{{ loop.index }}</td>
+ <td>{{ marker.lrs_value|float }}</td>
+ <td>{{ marker.chr|int }}</td>
+ <td>{{ marker.Mb|float }}</td>
+ <td>{{ marker.name }}</td>
+ <td>{{ marker.additive|float }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+
+ </div>
+
+ <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script>
+ js_data = {{ js_data | safe }}
+ </script>
+
+ <!--[if lt IE 9]>
+<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
+ <![endif]-->
+ <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_interval_map.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#qtl_results').dataTable( {
+ //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+ "sDom": "lTftipr",
+ "oTableTools": {
+ "aButtons": [
+ "copy",
+ "print",
+ {
+ "sExtends": "collection",
+ "sButtonText": 'Save <span class="caret" />',
+ "aButtons": [ "csv", "xls", "pdf" ]
+ }
+ ],
+ "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+ },
+ "iDisplayLength": 50,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+ </script>
{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 61df445c..a66a85d6 100755
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -3,8 +3,11 @@
{% block content %}
<div class="container">
+
+ {{ flash_me() }}
+
<div class="page-header">
- <h1>Login</h1>
+ <h1>&nbsp;&nbsp;&nbsp;&nbsp;Login</h1>
</div>
@@ -13,7 +16,7 @@
<h4>Don't have an account?</h4>
- <a href="/n/register" class="btn btn-info modalize">Create a new account</a>
+ <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
<hr />
@@ -21,18 +24,18 @@
<h4>Already have an account? Sign in here.</h4>
- <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form">
+ <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form" id="loginUserForm">
<fieldset>
<div class="form-group">
- <label class="col-xs-2 control-label" for="email_address">Email&nbsp;Address</label>
- <div class="col-xs-10">
+ <label style="text-align:left;" class="col-xs-1 control-label" for="email_address">Email&nbsp;Address</label>
+ <div style="margin-left:20px;" class="col-xs-4">
<input id="email_address" class="focused" name="email_address" type="text" value="">
</div>
</div>
<div class="form-group">
- <label class="col-xs-2 control-label" for="password">Password</label>
- <div class="col-xs-3 controls">
+ <label style="text-align:left;" class="col-xs-1 control-label" for="password">Password</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<input id="password" name="password" type="password" value="">
<br />
<a href="/n/forgot_password">Forgot your password?</a><br/>
@@ -41,17 +44,15 @@
<div class="form-group">
- <label class="col-xs-2 control-label" for="remember"></label>
- <div class="col-xs-3 controls">
- <label class="checkbox">
- <input id="remember" name="remember" type="checkbox" value="y"> Remember me
- </label>
+ <label class="col-xs-1 control-label" for="remember"></label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+ <input id="remember" name="remember" type="checkbox" value="y"> <b>Remember me</b>
</div>
</div>
<div class="form-group">
- <label class="col-xs-2 control-label" for="submit"></label>
- <div class="col-xs-3 controls">
+ <label class="col-xs-1 control-label" for="submit"></label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<input id="next" name="next" type="hidden" value="">
<input class="btn btn-primary" id="submit" name="submit" type="submit" value="Sign in">
</div>
@@ -65,9 +66,42 @@
{% endblock %}
+{% block css %}
+<style type="text/css">
+input.error{
+ border:1px solid #FF0000 !important;
+}
+
+label.error,div.error{
+ font-weight:normal;
+ color:#FF0000 !important;
+}
+</style>
+{% endblock %}
+
{% block js %}
<!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
+ <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
+ <script>
+ $(document).ready(function () {
+ $("#loginUserForm").validate({
+ onkeyup: false,
+ onsubmit: true,
+ onfocusout: function(element) { $(element).valid(); },
+ rules: {
+ email_address: {
+ required: true,
+ email: true
+ },
+ password: {
+ required: true
+ }
+ }
+ });
+ });
+ </script>
+
{% include "new_security/_scripts.html" %}
{% endblock %}
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
new file mode 100644
index 00000000..f46d7cbf
--- /dev/null
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -0,0 +1,74 @@
+{% extends "base.html" %}
+{% block title %}Pair Scan{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+{% endblock %}
+
+{% block content %} <!-- Start of body -->
+
+ {{ header("Mapping",
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
+ <div class="container">
+ <div>
+ <h2>
+ Pair Scan
+ </h2>
+ </div>
+ <div id="chart_container">
+ <div class="pair_scan_figure" id="pair_scan_figure">
+ <a href="/tmp/{{ pair_scan_filename }}">
+ <img alt="Embedded Image" src="data:image/png;base64,
+ {% for elem in pair_scan_array -%}
+ {% print("%c"|format(elem)) %}
+ {%- endfor %}
+ " /></a>
+ </div>
+ </div>
+ <div>
+ <h2>
+ Results
+ </h2>
+ <table cellpadding="0" cellspacing="0" border="0" id="pair_scan_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <td>Index</td>
+ <td>Locus</td>
+ <td>Chr 1</td>
+ <td>Mb</td>
+ <td>Chr 2</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in pair_scan_results %}
+ <tr>
+ <td>{{loop.index}}</td>
+ <td>{{marker.name}}</td>
+ <td>{{marker.chr1}}</td>
+ <td>{{marker.Mb}}</td>
+ <td>{{marker.chr2}}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ </div>
+
+{% endblock %}
+
+{% block js %}
+
+ <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5e63a237..c7c2a62f 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -14,9 +14,15 @@
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
- <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a></p>
+ <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
+ to find all records that match
+ {% for word in search_terms %}
+ <strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}
+ {% endfor %}.
+
+ </p>
- <p>To find all records that match:</p>
+ <!--
<ul>
{% if search_terms %}
<li>
@@ -26,9 +32,9 @@
</li>
{% endif %}
</ul>
+ -->
- <p>To study a record, click on its ID below.<br />
- Check records below and click Add button to add to selection.</p>
+ <p>To study a record, click on its ID below. Check records below and click Add button to add to selection.</p>
<div>
<br />
@@ -36,14 +42,20 @@
<button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
<button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
<button class="btn btn-default" id="add"><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
- <button class="btn btn-primary pull-right"><span class="glyphicon glyphicon-download"></span> Download Table</button>
+ <button class="btn btn-primary"><span class="glyphicon glyphicon-download"></span> Download Table</button>
<br />
<br />
<table class="table table-hover table-striped" id='trait_table'>
<thead>
<tr>
{% for header in header_fields %}
+ {% if header == 'Max LRS' %}
+ <th>{{header}}<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ {% elif header == 'Additive Effect' %}
+ <th>{{header}}<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ {% else %}
<th>{{header}}</th>
+ {% endif %}
{% endfor %}
</tr>
</thead>
@@ -134,17 +146,11 @@
$(document).ready( function () {
- /*num_columns = $('#trait_table').find('tr:first th').length;
-
- nul_cols = []
- for (i=0; i<num_columns - 1, i++) {
- $('#trait_table > tbody > tr').each(function() {
- if ($(this).find('td:eq(i)').html()){
- continue;
- }
- });
- nul_cols.push(i)
- }*/
+ $('#trait_table tr').click(function(event) {
+ if (event.target.type !== 'checkbox') {
+ $(':checkbox', this).trigger('click');
+ }
+ });
console.time("Creating table");
{% if dataset.type == 'ProbeSet' %}
@@ -160,7 +166,7 @@
"sWidth": "15%" },
{ "sType": "cust-txt" },
{ "sType": "natural",
- "sWidth": "10%" },
+ "sWidth": "12%" },
{ "sType": "natural",
"sWidth": "15%" },
{ "sType": "cust-txt" }
@@ -174,7 +180,7 @@
null,
null
],
- "sDom": "ftir",
+ "sDom": "tir",
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
@@ -205,7 +211,7 @@
null,
null
],
- "sDom": "ftir",
+ "sDom": "tir",
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
diff --git a/wqflask/wqflask/templates/show_image.html b/wqflask/wqflask/templates/show_image.html
new file mode 100644
index 00000000..521f5414
--- /dev/null
+++ b/wqflask/wqflask/templates/show_image.html
@@ -0,0 +1,5 @@
+<img alt="Embedded Image" src="data:image/png;base64,
+{% for elem in img_base64 -%}
+ {% print("%c"|format(elem)) %}
+{%- endfor %}
+" /> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 5d0437df..d6f22f41 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -6,14 +6,19 @@
<link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
{% endblock %}
{% block content %} <!-- Start of body -->
- {{ header("{}".format(this_trait.symbol),
- '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+ {% if this_trait.dataset.type != 'Geno' %}
+ {{ header("{}".format(this_trait.name_header_fmt),
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+ {% else %}
+ {{ header("{}".format(this_trait.name_header_fmt)) }}
+ {% endif %}
<form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
@@ -30,7 +35,7 @@
<div class="page-header">
<h1>{{ dataset.group.species.capitalize() }} -
{{ dataset.group.name }} -
- {{ this_trait.symbol }}
+ {{ this_trait.name_header_fmt }}
</h1>
</div>
@@ -40,7 +45,7 @@
<div class="panel-heading">
<h3 class="panel-title">
<a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">
- Statistics
+ <span class="glyphicon glyphicon-chevron-down"></span> Statistics
</a>
</h3>
</div>
@@ -54,7 +59,7 @@
<div class="panel-heading">
<h3 class="panel-title">
<a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">
- Calculate Correlations
+ <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations
</a>
</h3>
</div>
@@ -68,7 +73,7 @@
<div class="panel-heading">
<h3 class="panel-title">
<a data-toggle="collapse" data-parent="#accordion" href="#collapseThree">
- Mapping Tools
+ <span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools
</a>
</h3>
</div>
@@ -82,7 +87,7 @@
<div class="panel-heading">
<h3 class="panel-title">
<a data-toggle="collapse" data-parent="#accordion" href="#collapseFour" aria-expanded="true">
- Review and Edit Data
+ <span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data
</a>
</h3>
</div>
@@ -122,6 +127,7 @@
<script type="text/javascript" src="/static/new/javascript/histogram.js"></script>
<script type="text/javascript" src="/static/new/javascript/box_plot.js"></script>
<script type="text/javascript" src="/static/new/javascript/scatterplot.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/scatter-matrix.js"></script>
<script type="text/javascript" src="/static/new/javascript/draw_probability_plot.js"></script>
<script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script>
@@ -162,6 +168,16 @@
};
$(document).ready( function () {
+
+ $('.panel-heading').find('a').click(function () {
+ if ($(this).hasClass('collapsed')){
+ $(this).find('.glyphicon-chevron-down').removeClass('glyphicon-chevron-down').addClass('glyphicon-chevron-up');
+ }
+ else {
+ $(this).find('.glyphicon-chevron-up').removeClass('glyphicon-chevron-up').addClass('glyphicon-chevron-down');
+ }
+ });
+
console.time("Creating table");
{% if sample_groups[0].se_exists() %}
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 63bbd7b6..f02d1705 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -2,7 +2,7 @@
<div style="padding: 20px" class="form-horizontal">
<div class="form-group">
- <label for="corr_method" class="col-xs-1 control-label">Method</label>
+ <label for="corr_type" class="col-xs-1 control-label">Method</label>
<div class="col-xs-2 controls">
<select name="corr_type" class="form-control">
<option value="sample">Sample r</option>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 0afac1f7..e1780e42 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,9 +1,13 @@
<dl class="dl-horizontal">
+ {% if this_trait.dataset.type == 'ProbeSet' %}
<dt>Aliases</dt>
<dd>{{ this_trait.alias_fmt }}</dd>
+ {% endif %}
+ {% if this_trait.dataset.type != 'Publish' %}
<dt>Location</dt>
<dd>{{ this_trait.location_fmt }}</dd>
+ {% endif %}
<dt>Database</dt>
<dd>
@@ -16,7 +20,7 @@
<dt>
<a href="/blatInfo.html" target="_blank"
title="Values higher than 2 for the specificity are good">
- BLAT Specifity
+ BLAT Specificity
</a>
</dt>
<dd>{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}</dd>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 84ddfd53..27504e51 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,5 +1,7 @@
<div>
+ <div class="col-xs-6">
<div class="tabbable"> <!-- Only required for left/right tabs -->
+
<ul class="nav nav-pills">
<li class="active">
<a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
@@ -27,22 +29,22 @@
<div class="tab-pane active" id="interval_mapping">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
+ <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
- <label for="mapping_bootstraps" class="col-xs-1 control-label" title="Bootstrapping Resamples">Bootstrap</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
+ <label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="mapping_bootstraps" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-2 control-label">Display Additive Effect</label>
- <div class="col-xs-4 controls" id="display_additive_effect">
+ <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
+ <div class="col-xs-12 controls" id="display_additive_effect">
<label class="radio-inline">
<input type="radio" name="display_additive" id="display_additive" value="yes" checked="">
Yes
@@ -55,8 +57,8 @@
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-2 control-label">Manhattan Plot</label>
- <div class="col-xs-4 controls">
+ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+ <div class="col-xs-12 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_reaper" value="true">
Yes
@@ -67,32 +69,42 @@
</label>
</div>
</div>
- </div>
- <div class="form-group">
- <label for="interval_mapping_submit" class="col-xs-1 control-label"></label>
- <div style="margin-left:35px;" class="col-xs-4 controls">
- <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+ <div class="form-group">
+ <div style="padding-left:15px;" class="controls">
+ <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
+ <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ </button>
+ </div>
</div>
</div>
- <div id="alert_placeholder"></div>
</div>
<div class="tab-pane" id="pylmm">
+
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
- <input name="num_perm_pylmm" value="2000" type="text" class="form-control">
+ <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <input name="num_pylmm" value="2000" type="text" class="form-control">
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-1 control-label">Manhattan Plot</label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
+ <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
+ <input name="control_pylmm" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
+ {% else %}
+ <input name="control_pylmm" value="" type="text" />
+ {% endif %}
+ </div>
+ </div>
+
+ <div class="mapping_method_fields form-group">
+ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+ <div class="col-xs-12 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_pylmm" value="true">
Yes
@@ -103,50 +115,82 @@
</label>
</div>
</div>
- <!--<div class="form-group" id="suggestive">
- <label for="suggestive_reaper" class="control-label" title="Control Locus">LOD score greater than: </label>
- <div class="controls">
- <input name="suggestive_reaper" type="text" value="0" class="form-control">
+ <div class="form-group">
+ <div style="padding-left:15px;" class="controls">
+ <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ </button>
</div>
- </div>-->
- </div>
-
- <div class="form-group">
- <label for="marker_regression_submit" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
- Compute
- </button>
</div>
</div>
- <div id="alert_placeholder"></div>
-
</div>
<div class="tab-pane" id="rqtl_geno">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
- <input name="num_perm_rqtl_geno" value="500" type="text" class="form-control">
+ <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
+ <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
- <input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
+ <input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
- <input name="control_rqtl_geno" value="" type="text" />
+ <input name="control_rqtl_geno" value="" type="text" class="form-control" />
{% endif %}
</div>
</div>
+
+ <div class="mapping_method_fields form-group">
+ <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-2 control-label">Method</label>
+ <div class="col-xs-4 controls">
+ <select name="mapmethod_rqtl_geno" class="form-control">
+ <option value="em">em</option>
+ <option value="imp">imp</option>
+ <option value="hk">hk</option>
+ <option value="ehk">ehk</option>
+ <option value="mr">mr</option>
+ <option value="mr-imp">mr-imp</option>
+ <option value="mr-argmax">mr-argmax</option>
+ </select>
+ </div>
+ </div>
+
+ <div class="mapping_method_fields form-group">
+ <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-2 control-label">Model</label>
+ <div class="col-xs-4 controls">
+ <select name="mapmodel_rqtl_geno" class="form-control">
+ <option value="normal">normal</option>
+ <option value="binary">binary</option>
+ <option value="2part">2part</option>
+ <option value="np">np</option>
+ </select>
+ </div>
+ </div>
+
+ <div class="mapping_method_fields form-group">
+ <label style="text-align:left;" class="col-xs-12 control-label">Pair Scan</label>
+ <div class="col-xs-12 controls">
+ <label class="radio-inline">
+ <input type="radio" name="pair_scan" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="pair_scan" value="false" checked="">
+ No
+ </label>
+ </div>
+ </div>
+
<div class="mapping_method_fields form-group">
- <label class="col-xs-1 control-label">Manhattan&nbsp;Plot</label>
- <div style="margin-left:35px;" class="col-xs-4 controls">
+ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+ <div class="col-xs-12 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_rqtl" value="true">
Yes
@@ -157,18 +201,15 @@
</label>
</div>
</div>
- </div>
-
- <div class="form-group">
- <label for="marker_regression_submit" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+
+ <div class="form-group">
+ <div style="padding-left:15px;" class="controls">
+ <button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ </button>
+ </div>
</div>
</div>
- <div id="alert_placeholder"></div>
-
</div>
{% if dataset.group.species == 'human' %}
@@ -176,46 +217,57 @@
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
<label for="maf_plink" class="col-xs-2 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-1 controls">
+ <div style="margin-left: 20px;" class="col-xs-2 controls">
<input name="maf_plink" value="0.01" type="text" class="form-control">
</div>
</div>
</div>
<div class="form-group">
- <label for="gemma_compute" class="col-xs-1 control-label"></label>
+ <label for="plink_compute" class="col-xs-1 control-label"></label>
<div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
</div>
</div>
- <div id="alert_placeholder"></div>
-
</div>
<div class="tab-pane" id="gemma">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
<label for="maf_gemma" class="col-xs-2 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-1 controls">
+ <div style="margin-left: 20px;" class="col-xs-2 controls">
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
</div>
<div class="form-group">
- <label for="plink_compute" class="col-xs-1 control-label"></label>
+ <label for="gemma_compute" class="col-xs-1 control-label"></label>
<div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
</div>
</div>
- <div id="alert_placeholder"></div>
-
</div>
{% endif %}
</div>
</div>
-</div> \ No newline at end of file
+ </div>
+ <div class="col-xs-6">
+ <dl>
+ <dt>Interval Mapping</dt>
+ <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
+ <dt>pyLMM</dt>
+ <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
+ <dt>R/qtl</dt>
+ <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+ </dl>
+ </div>
+ <div id="alert_placeholder"></div>
+ <div id="mapping_result_holder_wrapper" style="display:none;">
+ <div id="mapping_result_holder"></div>
+ </div>
+</div>
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
index 11f5ba68..f2ebbbef 100755
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -78,10 +78,28 @@
<i class="icon-tint"></i> Color by Trait
</button>
</div>
- <div id="bar_chart_container">
+ </div>
+ <div class="row" style="height: 0px">
+ <div id="bar_chart_legend" style="margin-left: 900px; margin-top:50px; positive: relative;">
+ <span id="legend-left"></span>
+ <span id="legend-colors">
+ <!--
+ <svg height="10" width="90">
+ <rect x="0" width="15" height="10" style="fill: rgb(0, 0, 0);"></rect>
+ <rect x="15" width="15" height="10" style="fill: rgb(50, 0, 0);"></rect>
+ <rect x="30" width="15" height="10" style="fill: rgb(100, 0, 0);"></rect>
+ <rect x="45" width="15" height="10" style="fill: rgb(150, 0, 0);"></rect>
+ <rect x="60" width="15" height="10" style="fill: rgb(200, 0, 0);"></rect>
+ <rect x="75" width="15" height="10" style="fill: rgb(255, 0, 0);"></rect>
+ </svg>
+ -->
+ </span>
+ <span id="legend-right"></span>
+ </div>
+ </div>
+ <div style="margin-left: 20px; margin-right: 20px;" class="row" id="bar_chart_container">
<div id="bar_chart" class="barchart"></div>
</div>
- </div>
</div>
<div class="tab-pane" id="probability_plot">
<div id="probability_plot_container">
@@ -103,7 +121,7 @@
</div>-->
<div class="tab-pane" id="scatterplot_matrix">
- <div class="btn-group">
+ <div style="margin-bottom:40px;" class="btn-group">
<button type="button" class="btn btn-default" id="select_compare_trait">
<i class="icon-th-large"></i> Select Traits
</button>
diff --git a/wqflask/wqflask/templates/whats_new.html b/wqflask/wqflask/templates/whats_new.html
index dca9e7b3..753c0d7d 100755
--- a/wqflask/wqflask/templates/whats_new.html
+++ b/wqflask/wqflask/templates/whats_new.html
@@ -3,25 +3,14 @@
{% block content %}
<!-- Start of body -->
- <TR>
- <TD bgColor=#eeeeee class="solidBorder">
- <Table width= "100%" cellSpacing=0 cellPadding=5><TR>
<!-- Body Start from Here -->
- <TD valign="top" height="200" width="100%" bgcolor="#eeeeee">
-
- <P class="title">Latest Updates and News from Genenetwork <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P>
-
-
+ <P class="title">Latest Updates and News from Genenetwork </P>
{% for news_item in news_items %}
<h4>{{ news_item.title }} ({{ news_item.date }})</h4>
{{ news_item.details | safe }}
<br /><br />
{% endfor %}
- <p />
-
- </TD>
- </TR>
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-02 22:27:01 +0000