removed LOD text from index page until LOD search works and cleaned up mapping options appearance/text some

3 files changed, 18 insertions, 16 deletions

diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index a544f3cb..6a19fe08 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -17,7 +17,7 @@ var legendWidth = 140.0;
 if ('significant' in js_data) {
   var significant_score = parseFloat(js_data.significant)
 } else {
-  var significant_score = 4
+  var significant_score = js_data.max_score * 0.75
 }
 var score = { min: 0.0, max: js_data.max_score, sig: significant_score };
 var gwasPadding = { top: 35.0,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index bdf51bf8..3b008d83 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -150,14 +150,14 @@
                         <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). 
                         Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li>
 
-                        <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li>
+                        <li><b>LRS=(15 1000)</b> finds all traits with peak LRS scores between lower and upper limits.</li>
 
                         <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li>
 
-                        <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits,
+                        <li><b>cisLRS=(15 1000 5)</b> finds all cis eQTLs with peak LRS scores between lower and upper limits,
                             with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li>
 
-                        <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits,
+                        <li><b>transLRS=(15 1000 5)</b> finds all trans eQTLs with peak LRS scores between lower and upper limits,
                             with an <b>exclusion</b> zone of 5 Mb around the parent gene.</li>
 
                         <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 369bbe43..04480e69 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,6 +1,6 @@
 <div>
     {% if dataset.group.mapping_names|length > 0 %}
-    <div class="col-xs-5">
+    <div class="col-xs-4" style="min-width: 560px;">
         <div class="tabbable"> <!-- Only required for left/right tabs -->
 
             <ul class="nav nav-pills">
@@ -9,7 +9,7 @@
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
                 <li class="mapping_tab">
-                    <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
+                    <a href="#interval_mapping" data-toggle="tab">Haley-Knott Regression</a>
                 </li>
                 <li class="mapping_tab rqtl">
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
@@ -162,10 +162,12 @@
                             <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">
                                 {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
-                                <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
+                                <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px; display: inline-block;" class="form-control" />
                                 {% else %}
-                                <input name="control_reaper" value="" type="text" class="form-control" />
+                                <input name="control_reaper" value="" type="text" style="display: inline-block; padding-right: 10px;" class="form-control" />
                                 {% endif %}
+                                <input type="radio" name="do_control_reaper" value="true"> Yes&nbsp;&nbsp;<input type="radio" name="do_control_reaper" value="false" checked=""> No</span>
+                                <!--
                                 <label class="radio-inline">
                                     <input type="radio" name="do_control_reaper" value="true">
                                     Yes
@@ -174,6 +176,7 @@
                                     <input type="radio" name="do_control_reaper" value="false" checked="">
                                     No
                                 </label>
+                            -->
                             </div>
                         </div>
 
@@ -202,14 +205,14 @@
                         </div>
 -->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+                            <label style="text-align: right;" class="col-xs-3 control-label">Interval<br>Mapping</label>
                             <div style="margin-left:20px;" class="col-xs-6 controls">
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="True">
+                                    <input type="radio" name="manhattan_plot_reaper" value="False">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="False" checked="">
+                                    <input type="radio" name="manhattan_plot_reaper" value="True" checked="">
                                     No
                                </label>
                             </div>
@@ -351,15 +354,14 @@
             </div>
         </div>
     </div>
-    <div class="col-xs-5">
+    <div class="col-xs-6">
         <dl>
              <dt>GEMMA</dt>
              <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd>
              {% if dataset.group.mapping_id == "1" %}
-             <dt style="margin-top: 20px;">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.<br><br>
-                 The default option is a version of qtlrearper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.<br>
-                 <i>Please let us know if you encounter any issues while using the new version.</i></dd>
+             <dt style="margin-top: 20px;">Haley-Knott Regression</dt>
+             <dd>This method is implementing using the tool QTLReaper. Interval mapping (the last option) 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.<br><br>
+                 The default option is a version of QTLReaper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.</dd>
              <dt style="margin-top: 20px;">R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
              {% endif %}