From 99f56231b94583a64410a57b842f1d910c4e3f2e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 1 Sep 2015 16:33:22 +0000
Subject: Fixed issue that caused R/qtl mapping to not work

Removed bootstrap and additive effect options until I can get them working correctly
---
 wqflask/wqflask/interval_mapping/interval_mapping.py    | 9 +++++----
 wqflask/wqflask/marker_regression/marker_regression.py  | 6 ++++--
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 7 ++++---
 3 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 108bc747..46aac86c 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -92,10 +92,11 @@ class IntervalMapping(object):
             self.manhattan_plot = True
         else:
             self.manhattan_plot = False
-        if start_vars['display_additive'] == "yes":
-            self.additive = True
-        else:
-            self.additive = False
+        #ZS: Commenting this out until we can fix the issue with positive/negative additive effects being colored properly
+        #if start_vars['display_additive'] == "yes":
+        #    self.additive = True
+        #else:
+        self.additive = False
         if 'control_locus' in start_vars:
             self.control_locus = start_vars['control_locus']
         else:
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1c5757a6..757aeb72 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -73,9 +73,11 @@ class MarkerRegression(object):
         self.suggestive = ""
         self.significant = ""
         self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
+        self.score_type = "LRS" #ZS: LRS or LOD
  
         self.dataset.group.get_markers()
         if self.mapping_method == "gemma":
+            self.score_type = "LOD"
             included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
             self.dataset.group.get_specified_markers(markers = included_markers)
             self.dataset.group.markers.add_pvalues(p_values)
@@ -83,6 +85,7 @@ class MarkerRegression(object):
         elif self.mapping_method == "rqtl_plink":
             results = self.run_rqtl_plink()
         elif self.mapping_method == "rqtl_geno":
+            self.score_type = "LOD"
             if start_vars['num_perm'] == "":
                 self.num_perm = 0
             else:
@@ -136,7 +139,6 @@ class MarkerRegression(object):
             )
 
         else:
-            self.score_type = "LRS"
             self.cutoff = 2    
             self.qtl_results = []
             highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
@@ -165,7 +167,7 @@ class MarkerRegression(object):
                 else:
                     self.json_data['chr'].append(str(qtl['chr']))
                 self.json_data['pos'].append(qtl['Mb'])
-                if self.score_type == "LRS":
+                if 'lrs_value' in qtl:
                     self.json_data['lod.hk'].append(str(qtl['lrs_value']))
                 else:
                     self.json_data['lod.hk'].append(str(qtl['lod_score']))
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index b9ac80bf..7f26a252 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -9,7 +9,7 @@
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
                 <li>
-                    <a href="#rqtl_geno" data-toggle="tab">rqtl</a>
+                    <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
                 <li>
                     <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
@@ -169,14 +169,14 @@
                                 <input name="num_perm_reaper" value="2000" type="text" class="form-control">
                             </div>
                         </div>
-    
+<!-- 
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <input name="mapping_bootstraps" value="2000" type="text" class="form-control">
                             </div>
                         </div>
-                    
+
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
                             <div class="col-xs-12 controls" id="display_additive_effect">                      
@@ -190,6 +190,7 @@
                                 </label>
                             </div>
                         </div>
+-->
 
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
-- 
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