Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into HEAD

8 files changed, 96 insertions, 77 deletions

diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 058e269c..825dfb84 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -11,22 +11,9 @@
             {% else %}
             <input type="hidden" name="hash" value="{{ hash }}" />
             {% endif %}
-            <fieldset>
-              <legend>1. Create a new collection</legend>
-              <div style="margin-left: 20px;">
-                <!--<label>Collection name:</label>-->
-                <input type="text" name="new_collection" placeholder=" Name of new collection..."
-                    data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%">
-                <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button>
-                {% if uc is not defined %}
-                <span class="help-block" style="color:red;">This collection will be saved to your computer for a year (or until you clear your cache).</span>
-                {% endif %}
-              </div>
-            </fieldset>
             {% if collections|length > 0 %}
-            <hr />
             <fieldset>
-              <legend>2. Add to an existing collection</legend>
+              <legend>1. Add to an existing collection</legend>
               <div style="margin-left: 20px;">  
                 <!--<label>Existing collection name:</label>-->
                 <select name="existing_collection" class="form-control">
@@ -44,6 +31,19 @@
               </div>
             </fieldset>
             {% endif %}
+            <hr />
+            <fieldset>
+              <legend>{% if collections|length > 0 %}2. {% else %}{% endif %}Create a new collection</legend>
+              <div style="margin-left: 20px;">
+                <!--<label>Collection name:</label>-->
+                <input type="text" name="new_collection" placeholder=" Name of new collection..."
+                    data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%">
+                <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button>
+                {% if uc is not defined %}
+                <span class="help-block">This collection will be saved to your computer for a year (or until you clear your cache).</span>
+                {% endif %}
+              </div>
+            </fieldset>
         </form>
     </div>
 </div>
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index a2f1a1f7..3829b950 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -28,7 +28,7 @@
         <br>
         <div id="collections_list" style="width:50%; margin-top: 20px; margin-bottom: 20px;">
         {% if collections|length > 0 %}
-        <table class="table-hover table-striped cell-border" id='trait_table'>
+        <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
             <thead>
                 <tr>
                     <th></th>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 3b7f9671..59936a8e 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -88,8 +88,9 @@
             <button class="btn btn-danger" id="remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button>
             <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
             </form>
-            <br />
-            <br />
+            <div style="margin-top: 10px; margin-bottom: 5px;">
+                <b>Show/Hide Columns:</b>
+            </div>
             <div>
                 <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
                     <thead>
@@ -127,6 +128,8 @@
                             </TD>
                             {% if this_trait.symbol %}
                             <TD data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</TD>
+                            {% elif this_trait.abbreviation %}
+                            <TD data-export="{{ this_trait.abbreviation }}">{{ this_trait.abbreviation }}</TD>
                             {% else %}
                             <TD data-export="N/A">N/A</TD>
                             {% endif %}
@@ -139,9 +142,17 @@
                             {% endif %}
                             <TD data-export="{{ this_trait.location_repr }}">{{ this_trait.location_repr }}</TD>
                             <TD data-export="{{ this_trait.mean }}" align="right">{{ '%0.3f' % this_trait.mean|float }}</TD>
+                            {% if this_trait.LRS_score_repr|float > 0 %}
                             <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
+                            {% else %}
+                            <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD>
+                            {% endif %}
                             <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
+                            {% if this_trait.additive|float > 0 %}
                             <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD>
+                            {% else %}
+                            <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD>
+                            {% endif %}
                         </TR>
                     {% endfor %}
                     </tbody>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 3e8baab6..03b03aa7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -29,46 +29,42 @@
                 {{ this_trait.name }}:{{ this_trait.dataset }},
             {% endfor %}" >
 
+            <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
+                Correlations
+            </button>
 
-                <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
-                    Correlation Matrix
-                </button>
+            <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
+                Networks
+            </button>
 
+            <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
+              WebGestalt
+            </button>
 
-                <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
-                    Network Graph
-                </button>
+            <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
+              GeneWeaver
+            </button>
 
+            <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+              BNW
+           </button>
 
-                <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
-                    WGCNA Analysis
-                </button>
+            <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+                WGCNA
+            </button>
 
+            <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+                CTL Maps
+            </button>
 
-                <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
-                    CTL Analysis
-                </button>
+            <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
+                MultiMap
+            </button>
 
+            <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+                Comparison Bar Chart
+            </button>
 
-                <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
-                    Heatmap
-                </button>
-
-                <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
-                    Comparison Bar Chart
-                </button>
-
-                <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
-                    WebGestalt
-                </button>
-
-                <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
-                    GeneWeaver
-                </button>
-
-                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
-                    BNW
-                </button>
           </form>
         </div>
         <br />
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index bc614e01..49bcbff7 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -9,7 +9,7 @@
       <div style="min-height: 80vh; display: flex; align-items: center; text-align: center;">
         <div style="margin-bottom: 5px; left: 50%; margin-right: -50%; margin-top: 10%; transform: translate(-50%, -50%); position: absolute;">
         {% if start_vars.tool_used == "Mapping" %}
-        <h1>Computing the Map</h1>
+        <h1>Computing the Maps</h1>
         <br>
         <i>n</i> = {{ start_vars.num_vals }}
         <br>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 162bde08..33221e0f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -8,7 +8,7 @@
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
-    <div style="padding-left: 10px; min-width: 1200px;">
+    <div style="padding-left: 10px; {% if dataset.type == 'Publish' %}min-width: 1000px;{% else %}min-width: 1200px;{% endif %}">
         <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
 
         <div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
@@ -68,45 +68,41 @@
 
 
                 <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
-                    Correlation Matrix
+                    Correlations
                 </button>
 
-
                 <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
-                    Network Graph
+                    Networks
                 </button>
 
+                <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
+                  WebGestalt
+                </button>
 
-                <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
-                    WGCNA Analysis
+                <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
+                  GeneWeaver
                 </button>
 
+                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+                  BNW
+               </button>
 
-                <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
-                    CTL Analysis
+                <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+                    WGCNA
                 </button>
 
+                <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+                    CTL Maps
+                </button>
 
                 <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
-                    Heatmap
+                    MultiMap
                 </button>
 
                 <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
                     Comparison Bar Chart
                 </button>
 
-                <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
-                    WebGestalt
-                </button>
-
-                <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
-                    GeneWeaver
-                </button>
-
-                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
-                    BNW
-                </button>
-
           </form>
         </div>
 
@@ -252,11 +248,13 @@
                     $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text());
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
                     $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text());
-                    $('td', row).slice(6,9).attr("align", "right");
+                    $('td', row).eq(4).attr('align', 'right');
+                    $('td', row).slice(6,10).attr("align", "right");
                     $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text());
                     $('td', row).eq(6).attr('data-export', $('td', row).eq(6).text());
                     $('td', row).eq(7).attr('data-export', $('td', row).eq(7).text());
                     $('td', row).eq(8).attr('data-export', $('td', row).eq(8).text());
+                    $('td', row).eq(9).attr('data-export', $('td', row).eq(8).text());
                     {% elif dataset.type == 'Geno' %}
                     $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text());
                     {% endif %}
@@ -339,7 +337,7 @@
                     {
                       'title': "Description",
                       'type': "natural",
-                      'width': "25%",
+                      'width': "800px",
                       'data': null,
                       'render': function(data, type, row, meta) {
 			                  try {
@@ -359,7 +357,7 @@
                     {
                       'title': "Authors",
                       'type': "natural",
-                      'width': "25%",
+                      'width': "500px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         author_list = data.authors.split(",")
@@ -398,7 +396,7 @@
                     {
                       'title': "Max LRS Location",
                       'type': "natural",
-                      'width': "160px",
+                      'width': "200px",
                       'data': "lrs_location"
                     },
                     {
@@ -430,7 +428,6 @@
                     }
                 ],
                 'sDom': "Bitir",
-                'autoWidth': false,
                 'deferRender': true,
                 'paging': false,
                 'orderClasses': true,
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 81661f86..27c3e398 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -364,7 +364,7 @@
                   }
                 } );
 
-                primary_table.on( 'order.dt search.dt', function () {
+                primary_table.on( 'order.dt search.dt draw.dt', function () {
                   primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
                     cell.innerHTML = i+1;
                   } );
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 01d90d21..777d4a2d 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -243,6 +243,21 @@
                                 <input name="num_perm_rqtl_geno" value="200" type="text" class="form-control">
                             </div>
                         </div>
+                        {% if sample_groups[0].attributes|length > 0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label style="text-align:right;" class="col-xs-3 control-label">Stratified</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                                <label class="radio-inline">
+                                    <input type="radio" name="perm_strata" value="True" checked=""> 
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="perm_strata" value="False" >
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                        {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
                             <div style="margin-left:20px;" class="col-xs-6 controls">
@@ -365,7 +380,7 @@
              <dd>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 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). 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.</dd>
              {% elif mapping_method == "R/qtl" %}
              <dt style="margin-top: 20px;">R/qtl</dt>
-             <dd>The original R/qtl mapping code that supports most classic experimental crosses provided that they  do not have complex kinship or admixture (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>). Both R/qtl, implemented here, and R/qtl2 are available as stand-alone R packages (<a href="https://kbroman.org/pages/software.html">R suite</a>).</dd>
+             <dd>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 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/12724300">PMID: 12724300</a>). Both R/qtl as implemented here, and R/qtl2 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>) are available as <a href="https://kbroman.org/pages/software.html">R suites</a>.</dd>
              {% elif mapping_method == "QTLReaper" %}
              <dt style="margin-top: 20px;">Haley-Knott Regression</dt>
              <dd>Fast linear mapping method (<a href="https://www.ncbi.nlm.nih.gov/pubmed/16718932">PMID 16718932</a>) 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 (<a href="https://github.com/pjotrp/QTLReaper">QTL Reaper code</a>).</dd>