Fixed issue where qtl lines in interval mapping wouldn't connect between chromosomes

Added text explaining what * indicates in the mapping options menu

Removed ranges (log2 and fold) from stats table for phenotype traits

6 files changed, 19 insertions, 15 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 63f62411..c10aac73 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -2015,6 +2015,9 @@ class MarkerRegression(object):
             thisLRSColor = self.colorCollection[0]
 
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
+                if self.manhattan_plot != True:
+                    canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                LRSCoordXY = []
                 previous_chr = qtlresult['chr']
                 previous_chr_as_int += 1
 
@@ -2032,7 +2035,6 @@ class MarkerRegression(object):
             else:
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
-                #LRSCoordXY = []
                 #AdditiveCoordXY = []
                 #DominanceCoordXY = []
                 #for k, _locus in enumerate(_chr):
@@ -2087,7 +2089,6 @@ class MarkerRegression(object):
                        # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax
                        # DominanceCoordXY.append((Xc, Yc))
                     m += 1
-        
                     #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
 
         lineWidth = 1
@@ -2151,9 +2152,6 @@ class MarkerRegression(object):
                             canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
                 
 
-        if self.manhattan_plot != True:
-		    canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-
         ###draw additive scale
         if not self.multipleInterval and self.additiveChecked:
             additiveScaleFont=pid.Font(ttf="verdana",size=16*zoom,bold=0)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fb03f027..a57bfffe 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -119,9 +119,9 @@ class SearchResultPage(object):
             
             #### Excel file needs to be generated ####
 
-            print("foo locals are:", locals())
+            #print("foo locals are:", locals())
             trait_id = result[0]
-            this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True)
+            this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
             self.trait_list.append(this_trait)
 
         self.dataset.get_trait_info(self.trait_list, species)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3cc6121f..2d4c952a 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -152,10 +152,11 @@ class ShowTrait(object):
 
         self.trait_table_width = get_trait_table_width(self.sample_groups)
 
-        js_data = dict(sample_group_types = self.sample_group_types,
-                        sample_lists = sample_lists,
-                        attribute_names = self.sample_groups[0].attributes,
-                        temp_uuid = self.temp_uuid)
+        js_data = dict(dataset_type = self.dataset.type,
+                       sample_group_types = self.sample_group_types,
+                       sample_lists = sample_lists,
+                       attribute_names = self.sample_groups[0].attributes,
+                       temp_uuid = self.temp_uuid)
         self.js_data = js_data
 
     def get_mapping_methods(self):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8d5982b7..663f7f3b 100755..100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -186,6 +186,9 @@
       the_rows = "<tbody>";
       for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
         row = Stat_Table_Rows[_i];
+        if ((row.vn == "range_fold" || row.vn == "range") && js_data.dataset_type == "Publish"){
+            continue;
+        }
         console.log("rowing");
         row_line = "<tr>";
         if (row.url != null) {
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index d7950754..c65948c0 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -87,8 +87,8 @@
                   </td>
                 </tr>
               </table>
-              </div>
-              <div class="col-xs-4" style="padding: 0px;">
+            </div>
+            <div class="col-xs-4" style="padding: 0px;">
                   {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %}
                   <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test 
                     <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank">
@@ -121,7 +121,10 @@
                   {% if plotScale != "morgan" %}
                   <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span>
                   {% endif %}
-              </div>
+            </div>
+            <div class="col-xs-12" align="center" style="padding: 5px;">
+              <span style="color:red;">*</span> <span style="font-size: 12px;">only apply to single chromosome physical mapping</span>
+            </div>
           </div>
         </div>
  
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 2183dd30..9c5c94b2 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -27,7 +27,6 @@
                 <div class="tab-pane active" id="stats_tab">
                     <div style="padding: 20px" class="form-horizontal">
                             <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table>
-
                     </div>
                 </div>   
                 <div class="tab-pane" id="histogram_tab">