Fixed the scrollable data tables for the show trait page

Added the option to display the rqtl results (and soon other mapping results)
as either a manhattan plot or "interval map" style curve chart

Removed a couple unnecessary javascript imports

Changed the function in helper_functions.py that creates the trait and dataset
objects, making it to where the trait object also gets qtl info

Fixed color by trait after it was broken by the "scatterplot matrix" function

5 files changed, 55 insertions, 10 deletions

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 61d17a22..88f6d65a 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,6 +1,5 @@
 {% extends "base.html" %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.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" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 451b3754..51aab95c 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -88,7 +88,8 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.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_manhattan_plot.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.js"></script>

+<!--    <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.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_manhattan_plot.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>

diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5bd6534c..0baac2d3 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -1,5 +1,10 @@
 {% extends "base.html" %}
 {% block title %}Search Results{% 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 -->
     {{ header("Search Results",
@@ -27,7 +32,7 @@
         Check records below and click Add button to add to selection.</p>
 
         <div class="bs-docs-example">
-            <table class="table table-hover" id='trait_table'>
+            <table class="table table-hover table-striped" id='trait_table'>
                 <thead>
                     <tr>
                     {% for header in header_fields %}
@@ -78,7 +83,8 @@
             </table>
 
             <br />
-
+            <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>
@@ -95,4 +101,24 @@
 
 {% 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 type="text/javascript" charset="utf-8">
+        $(document).ready( function () {
+            console.time("Creating table");
+            $('#trait_table').dataTable( {
+                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+                "sDom": "lftipr",
+                "iDisplayLength": 50,
+                "bLengthChange": true,
+                "bDeferRender": true,
+                "bSortClasses": false
+            } );
+            console.timeEnd("Creating table");
+        });
+    </script>
+    
 {% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index cbb06285..7bbebd72 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -109,7 +109,8 @@
                 console.time("Creating table");
                 
                 {% if sample_groups[0].se_exists() %}
-                    $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow').dataTable( {
+                    $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow')
+                    $('#samples_primary, #samples_other').dataTable( {
                         //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
                         "aoColumns": [
                             { "sType": "natural" },
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c58b7729..e5d96490 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -135,14 +135,14 @@
                 
                 <div class="tab-pane" id="pylmm">
                     <div class="control-group" id="display_all_div">
-                        <label class="control-label">Display all</label>
+                        <label class="control-label">Manhattan Plot</label>
                         <div class="controls">                      
                             <label class="radio inline">
-                                <input type="radio" name="display_all_pylmm" value="True" checked>
+                                <input type="radio" name="manhattan_plot_pylmm" value=true checked>
                                 Yes
                             </label>
                             <label class="radio inline">
-                                <input type="radio" name="display_all_pylmm" value="False">
+                                <input type="radio" name="manhattan_plot_pylmm" value=false>
                                 No
                             </label>
                         </div>
@@ -185,9 +185,27 @@
                     <div class="control-group">
                         <label for="control_rqtl_geno" class="control-label">Control Marker</label>
                         <div class="controls">
-                            <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" />
+                            {% if dataset.type == 'ProbeSet' %}
+                            <input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
+                            {% else %}
+                            <input name="control_rqtl_geno" value="" type="text" />
+                            {% endif %}
                         </div>
                     </div>
+                    <div class="control-group mapping_method_fields">
+                        <label class="control-label">Manhattan Plot</label>
+                        <div class="controls">                      
+                            <label class="radio inline">
+                                <input type="radio" name="manhattan_plot_rqtl" value=true checked>
+                                Yes
+                            </label>
+                            <label class="radio inline">
+                                <input type="radio" name="manhattan_plot_rqtl" value=false>
+                                No
+                            </label>
+                        </div>
+                    </div>
+
                     
                     <div class="control-group">
                         <div class="controls">
@@ -199,7 +217,7 @@
                             </button>
                         </div>
                     </div>
-                    
+       
                 </div>
                 
                 {% if dataset.group.species == 'human' %}