From 2b782327281dc9ca586d1303a44418f8d42f76dd Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 13 Oct 2020 16:32:11 -0500 Subject: Changed styling in show_trait.html to use CSS instead * wqflask/wqflask/static/new/css/main.css - Added CSS for min-height in table cells with checkboxes, since this would apply to all tables throughout the site * wqflask/wqflask/static/new/css/show_trait.css - Added CSS for styling that was previous in show_trait.html * wqflask/wqflask/templates/show_trait.html - Replaced directly styling with classes --- wqflask/wqflask/static/new/css/main.css | 4 ++ wqflask/wqflask/static/new/css/show_trait.css | 32 ++++++++++++- wqflask/wqflask/templates/show_trait.html | 69 ++++++++++----------------- 3 files changed, 61 insertions(+), 44 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css index 097cd997..d5fb8a61 100644 --- a/wqflask/wqflask/static/new/css/main.css +++ b/wqflask/wqflask/static/new/css/main.css @@ -33,4 +33,8 @@ .collapsing { overflow: hidden!important; } +} + +.checkbox { + min-height: 20px; } \ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 92deab20..a9e85ee7 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -35,8 +35,13 @@ 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: 4px 15px 2px 10px; + padding: 2px 15px 0px 10px; } table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { @@ -51,4 +56,29 @@ table.dataTable.cell-border tbody tr td:first-child { .glyphicon { position: relative; top: 2px; +} + +.trait_page_main_div { + min-width: 700px; +} + +table.dataTable tbody td.column_name-Checkbox { + padding: 3px 0px 0px 9px; + text-align: center; +} + +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; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index ea881917..3d34b331 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -37,7 +37,7 @@ -
+
@@ -237,30 +237,22 @@ if (data.outlier) { $(row).addClass("outlier"); } - $('td', row).eq(0).attr("align", "center"); - $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;"); + $('td', row).eq(0).addClass("column_name-Checkbox") $('td', row).eq(1).addClass("column_name-Index") - $('td', row).eq(1).attr("align", "right"); - $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;"); $('td', row).eq(2).addClass("column_name-Sample") $('td', row).eq(3).addClass("column_name-Value") - $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% if sample_groups[0].se_exists() %} - $('td', row).eq(4).attr("align", "center"); - $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;"); - $('td', row).eq(5).addClass("column_name-SE") - $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); + $('td', row).eq(4).addClass("column_name-PlusMinus") + $('td', row).eq(5).addClass("column_name-SE value_column") {% if has_num_cases %} $('td', row).eq(6).addClass("column_name-num_cases") - $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% else %} {% if has_num_cases %} $('td', row).eq(4).addClass("column_name-num_cases") - $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% endif %} {% if sample_groups[0].attributes|length > 0 %} {% for attribute in sample_groups[0].attributes|sort() %} $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[0].attributes[attribute].name }}") - $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;") + $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }};") {% endfor %} {% endif %} }, @@ -271,7 +263,7 @@ 'orderDataType': "dom-checkbox", 'searchable' : false, 'render': function(data, type, row, meta) { - return '' + return '' } }, { @@ -289,15 +281,15 @@ } }, { - 'title': "
Value
", + 'title': "
Value
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.value == null) { - return '' + return '' } else { - return '' + return '' } } }{% if sample_groups[0].se_exists() %}, @@ -311,28 +303,28 @@ } }, { - 'title': "
SE
", + 'title': "
SE
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.variance == null) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if has_num_cases %}, { - 'title': "
N
", + 'title': "
N
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.num_cases == null || data.num_cases == undefined) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %}, @@ -387,25 +379,16 @@ if (data.outlier) { $(row).addClass("outlier"); } - $('td', row).eq(0).attr("align", "center"); - $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;"); $('td', row).eq(1).addClass("column_name-Index") - $('td', row).eq(1).attr("align", "right"); - $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;"); $('td', row).eq(2).addClass("column_name-Sample") $('td', row).eq(3).addClass("column_name-Value") - $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% if sample_groups[1].se_exists() %} - $('td', row).eq(4).attr("align", "center"); - $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;"); + $('td', row).eq(4).addClass("column_name-PlusMinus") $('td', row).eq(5).addClass("column_name-SE") - $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% if has_num_cases %} $('td', row).eq(6).addClass("column_name-num_cases") - $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% else %} {% if has_num_cases %} $('td', row).eq(4).addClass("column_name-num_cases") - $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% endif %} {% if sample_groups[1].attributes|length > 0 %} {% for attribute in sample_groups[1].attributes|sort() %} @@ -421,7 +404,7 @@ 'orderDataType': "dom-checkbox", 'searchable' : false, 'render': function(data, type, row, meta) { - return '' + return '' } }, { @@ -439,15 +422,15 @@ } }, { - 'title': "
Value
", + 'title': "
Value
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.value == null) { - return '' + return '' } else { - return '' + return '' } } }{% if sample_groups[1].se_exists() %}, @@ -461,28 +444,28 @@ } }, { - 'title': "
SE
", + 'title': "
SE
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.variance == null) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if has_num_cases %}, { - 'title': "
N
", + 'title': "
N
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.num_cases == null) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if sample_groups[1].attributes|length > 0 %}{% for attribute in sample_groups[1].attributes|sort() %}, -- cgit 1.4.1 From 794b176384dbe5a8c837a913f9a86f4d36adadcd Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 13 Oct 2020 16:41:32 -0500 Subject: Added styling from show_trait_details.html to show_trait.css * wqflask/wqflask/static/new/css/show_trait.css - Added the bottom margin styling for the div containing the buttons * wqflask/wqflask/templates/show_trait_details.html - Removed some unnecessary styling and moved the styling for .btn_toolbar to show_trait.css --- wqflask/wqflask/static/new/css/show_trait.css | 4 ++++ wqflask/wqflask/templates/show_trait_details.html | 12 ++++++------ 2 files changed, 10 insertions(+), 6 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index a9e85ee7..671b3cf7 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -81,4 +81,8 @@ table.dataTable tbody td.column_name-PlusMinus { 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; +} + +.btn_toolbar { + margin-bottom:15px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 4aced50c..d2999eef 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -1,20 +1,20 @@ - +
- + {% if this_trait.dataset.type == 'Publish' %} - + - + - + @@ -213,7 +213,7 @@ {% endif %}
GroupGroup {{ this_trait.dataset.group.species[0]|upper }}{{ this_trait.dataset.group.species[1:] }}: {{ this_trait.dataset.group.name }} group
Phenotype
{{ this_trait.description_fmt }}
{{ this_trait.description_fmt }}
Authors
{{ this_trait.authors }}
{{ this_trait.authors }}
Title
{{ this_trait.title }}
{{ this_trait.title }}
Journal
-
+
{% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %} -- cgit 1.4.1 From c32766556222b9f8167496268bc4011f77b60138 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 14 Oct 2020 14:43:23 -0500 Subject: Moved show_trait_statistics.html styling to show_trait.css and fixed a minor issue where not all figures had "Select Group:" before the group selection drop-down * wqflask/wqflask/static/new/css/show_trait.css - Moved styling from show_trait_statistic.html here * wqflask/wqflask/templates/show_trait_statistics.html - Replaced styling with classes, removed some unnecessary/unused styling, and added some missing label text --- wqflask/wqflask/static/new/css/show_trait.css | 14 +- .../wqflask/templates/show_trait_statistics.html | 247 ++++++++++----------- 2 files changed, 131 insertions(+), 130 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 671b3cf7..ade7128c 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -83,6 +83,18 @@ table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name text-align: right; } -.btn_toolbar { +div.btn_toolbar { margin-bottom:15px; +} + +div.padding-20 { + padding: 20px; +} + +table.left-float { + float: left; +} + +div.margin-b-40 { + margin-bottom:40px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 7bdb3ef9..f7d93447 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -1,148 +1,137 @@
-
- - -
-
-
-
-
-
-
-
- {% if sample_groups|length != 1 %} - -

- {% endif %} -
-
-
-
+
+ +
+
+
+
- {% if num_values < 256 %} -
-
- {% if sample_groups|length != 1 %} - - {% endif %} - {% if sample_groups[0].attributes %} -
- -
- {% endif %} -
- - -
- -
-
-
+
+
+
+ {% if sample_groups|length != 1 %} + Select Group: + +

+ {% endif %} +
+
- {% endif %} -
-
- {% if sample_groups|length != 1 %} - Select Group: - + {% for group, pretty_group in sample_group_types.items() %} + + {% endfor %} + + {% endif %} + {% if sample_groups[0].attributes %} +
+ -
-
- {% endif %} - -
-
-
-
-
- More about Normal Probability Plots and more - about interpreting these plots from the glossary -
-
- -
-
-
-
+ {% endif %} +
+ +
-
-
-
-
+
+
-
- -
- - +
+ {% endif %} +
+
+ {% if sample_groups|length != 1 %} + Select Group: + +
+
+ {% endif %} + +
+
-
-
+
+
+ More about Normal Probability Plots and more + about interpreting these plots from the glossary
+
+
+
+
+
+
+
+
+
+
+
+
+ + +
+
+
+
+
- +
-
-- cgit 1.4.1 From fa79f3b05688a59cdf1c46170b63ebdd6e2ebf4b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 14 Oct 2020 14:50:32 -0500 Subject: Changed a couple class names because it's probably dumb to include the pixels in the name since that might change later * wqflask/wqflask/static/new/css/show_trait.css - Changed a couple class names * wqflask/wqflask/templates/show_trait_statistics.html - Changed a couple class names --- wqflask/wqflask/static/new/css/show_trait.css | 4 ++-- wqflask/wqflask/templates/show_trait_statistics.html | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index ade7128c..68aa34e2 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -87,7 +87,7 @@ div.btn_toolbar { margin-bottom:15px; } -div.padding-20 { +div.stats_form_div { padding: 20px; } @@ -95,6 +95,6 @@ table.left-float { float: left; } -div.margin-b-40 { +div.scatterplot_btn_div { margin-bottom:40px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index f7d93447..7f50b7bc 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -27,12 +27,12 @@
-
+
-
+
{% if sample_groups|length != 1 %} Select Group: -- cgit 1.4.1 From 64158e2ff7df3f7d177a4a3a0b8d7ff9c8f7cfe5 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 14 Oct 2020 17:26:45 -0500 Subject: Converted show_trait_calculate_correlations.html to use CSS instead of styling in the template * wqflask/wqflask/static/new/css/show_trait.css - Added styling for elements in show_trait_calculate_correlations.html and changed a few existing class names to be more reasonable * wqflask/wqflask/templates/show_trait.html - Changed the class name for the main div * wqflask/wqflask/templates/show_trait_calculate_correlations.html - Substituted direct styling with CSS and changing some styling to make the correlation method descriptions keep a reasonable width and position * wqflask/wqflask/templates/show_trait_statistics.html - Changed some class names to be better --- wqflask/wqflask/static/new/css/show_trait.css | 57 +++- wqflask/wqflask/templates/show_trait.html | 2 +- .../show_trait_calculate_correlations.html | 295 ++++++++++----------- .../wqflask/templates/show_trait_statistics.html | 10 +- 4 files changed, 202 insertions(+), 162 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 68aa34e2..f20b840e 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -1,17 +1,17 @@ tr .outlier { - background-color: #ffff99; + background-color: #ffff99; } table.dataTable tbody tr.selected { - background-color: #ffee99; + background-color: #ffee99; } #bar_chart_container { - overflow-x:scroll; + overflow-x:scroll; } div.sample_group { - overflow: auto; # needed because it contains float dataTable wrapper + overflow: auto; # needed because it contains float dataTable wrapper } .js-plotly-plot .plotly .modebar { @@ -58,7 +58,7 @@ table.dataTable.cell-border tbody tr td:first-child { top: 2px; } -.trait_page_main_div { +.showtrait-main-div { min-width: 700px; } @@ -83,11 +83,12 @@ table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name text-align: right; } -div.btn_toolbar { +div.btn-toolbar { margin-bottom:15px; } -div.stats_form_div { +/* div containing the form options for each segment of the trait page - correlations, statistics, mapping, etc */ +div.section-form-div { padding: 20px; } @@ -95,6 +96,46 @@ table.left-float { float: left; } -div.scatterplot_btn_div { +div.scatterplot-btn-div { margin-bottom:40px; +} + +div.correlation-main { + min-width: 1200px; +} + +div.correlation-options { + min-width: 700px; +} + +.min-expr-field { + width: 70px; +} + +span.p-range-container { + display: inline; +} + +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; +} + +.corr-location { + width: 50px; + display: inline; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 3d34b331..599cef42 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -37,7 +37,7 @@ -
+
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 9420c9c6..00fdfc21 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,149 +1,148 @@ -
-
-
- -
- -
- -
-
- -
- -
- -
-
- -
- -
- -
-
- -
- -
- -
-
- -
- -
- -
-
- {% if dataset.type != "Publish" %} -
- -
- -
-
-
- -
- - Chr:     - Mb:  to  - -
-
-
- {% endif %} -
- -
- - - -
- -                                     - - -
-
- -
- -
- -
-
+
+
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ {% if dataset.type != "Publish" %} +
+ +
+ +
+
+
+ +
+ + Chr:     + Mb:  to  + +
+
+
+ {% endif %} +
+ +
+ + + +
+ + + +
+
+ +
+ +
+ +
+
+
-
-
- - The Sample Correlation - is computed - between trait data and any - other traits in the sample database selected above. Use - Spearman - Rank - when the sample size is small (<20) or when there are influential outliers. - - - -
-
\ No newline at end of file +
+ + The Sample Correlation + is computed + between trait data and any + other traits in the sample database selected above. Use + Spearman + Rank + when the sample size is small (<20) or when there are influential outliers. + + + +
+
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 7f50b7bc..4f347d4e 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -27,12 +27,12 @@
-
+
-
+
{% if sample_groups|length != 1 %} Select Group: @@ -84,7 +84,7 @@
{% endif %}
-
+
{% if sample_groups|length != 1 %} Select Group: {% endif %} Yes   No -
@@ -338,22 +328,6 @@
- -
-- cgit 1.4.1 From 9d94339ea0fe9f04d1f5f5fcb70c743ab720086e Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 15 Oct 2020 14:04:53 -0500 Subject: Replaced styling from show_trait_transform_and_filter.html with CSS * wqflask/wqflask/static/new/css/show_trait.css - Added styles for elements in show_trait_transform_and_filter.html * wqflask/wqflask/templates/show_trait_transform_and_filter.html - Replaced styling in template with classes --- wqflask/wqflask/static/new/css/show_trait.css | 13 ++++++++++ .../templates/show_trait_transform_and_filter.html | 28 +++++++++++----------- 2 files changed, 27 insertions(+), 14 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index f20b840e..f9c3dcd9 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -138,4 +138,17 @@ span.p-range-upper { .corr-location { width: 50px; display: inline; +} + +div.block-by-index-div { + margin-bottom: 10px; +} + +div.block-by-attribute-div { + margin-top:10px; + margin-bottom:10px; +} + +div.normalize-div { + margin-top:10px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index b4118b04..3956a34f 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -5,7 +5,7 @@ needed.

-
+
{% for attribute in sample_groups[0].attributes %} @@ -47,18 +47,18 @@
-
- - +
+ +
    {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} -
  • +
  • GEMMA
    • {% elif mapping_method == "R/qtl" %} -
  • +
  • R/qtl
    • {% elif mapping_method == "QTLReaper" %} -
  • +
  • Haley-Knott Regression
    • {% endif %} {% endfor %} -
{% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %}
-
+
- -
- {% for item in chr_list %} {% endfor %} @@ -41,8 +38,8 @@
{% if genofiles and genofiles|length>0 %}
- -
+ +
+ +
+
- -
+ +
-
- - Select covariate(s) from a collection -
-
+ +
{% if g.user_session.num_collections < 1 %} No collections available. Please add traits to a collection to use them as covariates. {% else %} -
- - +
+ +
- + {% endif %}
-
+
@@ -97,20 +91,20 @@
{% elif mapping_method == "QTLReaper" %}
-
+
- -
-
- -
- {% for item in chr_list %} {% endfor %} @@ -119,9 +113,9 @@
{% if genofiles and genofiles|length>0 %}
- -
- {% for item in scales_in_geno[genofiles[0]['location']] %} {% endfor %} @@ -129,8 +123,8 @@
- -
+ +
+ +
+
- -
- -
-
-
- -
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - - {% else %} - - {% endif %} - Yes   No -
-
- -
- -
+ +
-
+
@@ -221,11 +194,11 @@
{% elif mapping_method == "R/qtl" %}
-
+
- -
- {% for item in chr_list %} {% endfor %} @@ -234,9 +207,9 @@
{% if genofiles and genofiles|length > 0 %}
- -
- {% for item in scales_in_geno[genofiles[0]['location']] %} {% endfor %} @@ -244,8 +217,8 @@
- -
+ +
{% if sample_groups[0].attributes|length > 0 %}
- -
+ +
{% endif %}
- -
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - - {% else %} - - {% endif %} - - + +
+ + +
- -
+ +
@@ -319,8 +288,8 @@
-
-
- {% for mapping_method in dataset.group.mapping_names %} - {% if mapping_method == "GEMMA" %} -
GEMMA
-
Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (PMID: 2453419, and GitHub code). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.
- {% elif mapping_method == "R/qtl" %} -
R/qtl (version 1.44.9
-
The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (PMID: 12724300). Both R/qtl as implemented here, and R/qtl2 (PMID: 30591514) are available as R suites.
- {% elif mapping_method == "QTLReaper" %} -
Haley-Knott Regression
-
Fast linear mapping method (PMID 16718932) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (QTL Reaper code).
- {% endif %} - {% endfor %} -
-