From 1fcdd76716d76d6f24c62df3009b0a1fc648e692 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 22 Apr 2016 19:46:54 +0000
Subject: Fixed issue where manhattan plot setting wasn't being carried over to
 single chromosome view for mapping results

Removed a useless "if 1 == 1" line that was in marker_regression_gn1.py for testing.
---
 .../wqflask/marker_regression/marker_regression.py |  2 +-
 .../marker_regression/marker_regression_gn1.py     | 95 +++++++++++-----------
 .../wqflask/templates/marker_regression_gn1.html   |  2 +-
 .../templates/show_trait_mapping_tools.html        | 12 +--
 4 files changed, 55 insertions(+), 56 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 32cdb9af..fa439b55 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -68,7 +68,7 @@ class MarkerRegression(object):
             self.vals.append(value)
  
         self.mapping_method = start_vars['method']
-        if start_vars['manhattan_plot'] == "true":
+        if start_vars['manhattan_plot'] == "True":
             self.manhattan_plot = True
         else:
             self.manhattan_plot = False
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 01303b0f..b89f6b97 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -2066,63 +2066,62 @@ class MarkerRegression(object):
             if self.plotScale == "physic":
                 this_chr = str(self.ChrList[self.selectedChr][0])
             else:
-                this_chr = str(self.ChrList[self.selectedChr][1]+1)
+                this_chr = str(self.ChrList[self.selectedChr][1]+1)                                                                                                                    
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
                 #AdditiveCoordXY = []
                 #DominanceCoordXY = []
                 #for k, _locus in enumerate(_chr):
-                if 1 == 1:
-                    Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-                    #if self.plotScale == 'physic':
-                        #Xc = startPosX + (_locus.Mb-startMb)*plotXScale
-                        #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-                    #else:
-                        #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
-                        #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
-
-                    # updated by NL 06-18-2011:
-                    # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
-                    # for any lrs is over than 460(LRS max in this system), it will be reset to 460
-                    if 'lrs_value' in qtlresult:
-                        if self.LRS_LOD == "LOD":
-                            if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
-                                Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
-                            else:
-                                Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
+                Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+                #if self.plotScale == 'physic':
+                    #Xc = startPosX + (_locus.Mb-startMb)*plotXScale
+                    #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+                #else:
+                    #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
+                    #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
+
+                # updated by NL 06-18-2011:
+                # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
+                # for any lrs is over than 460(LRS max in this system), it will be reset to 460
+                if 'lrs_value' in qtlresult:
+                    if self.LRS_LOD == "LOD":
+                        if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+                            Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
                         else:
-                            if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
-                                Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
-                            else:
-                                Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
+                            Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
                     else:
-                        if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf':
+                        if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
                             Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
                         else:
-                            if self.LRS_LOD == "LRS":
-                                Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max
-                            else:
-                                Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max
-                    #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
-                    #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf':
-                    #    Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
-                    #else:
-                    #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
-
-                    if self.manhattan_plot == True:
-                        canvas.drawEllipse(Xc-1, Yc-1, Xc+1, Yc+1, fillColor=pid.black)
+                            Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
+                else:
+                    if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf':
+                        Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
                     else:
-                        LRSCoordXY.append((Xc, Yc))
-
-                    if not self.multipleInterval and self.additiveChecked:
-                       if additiveMax == 0.0:
-                           additiveMax = 0.000001
-                       Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax
-                       AdditiveCoordXY.append((Xc, Yc))
-                    # if not self.multipleInterval and INTERCROSS and self.additiveChecked:
-                       # 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))
+                        if self.LRS_LOD == "LRS":
+                            Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max
+                        else:
+                            Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max
+                #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+                #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf':
+                #    Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
+                #else:
+                #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
+
+                if self.manhattan_plot == True:
+                    canvas.drawEllipse(Xc-1, Yc-1, Xc+1, Yc+1, fillColor=pid.black)
+                else:
+                    LRSCoordXY.append((Xc, Yc))
+
+                if not self.multipleInterval and self.additiveChecked:
+                   if additiveMax == 0.0:
+                       additiveMax = 0.000001
+                   Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax
+                   AdditiveCoordXY.append((Xc, Yc))
+                # if not self.multipleInterval and INTERCROSS and self.additiveChecked:
+                   # 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))
 
         if self.manhattan_plot != True:
             canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index f3f33fad..7d34e88f 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -20,7 +20,7 @@
         {% endfor %}
         <input type="hidden" name="maf">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
-        <input type="hidden" name="manhattan_plot">
+        <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
         <input type="hidden" name="num_perm" value="{{ nperm }}">
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 5d9b0278..067dfc67 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -66,11 +66,11 @@
                             <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
                             <div class="col-xs-12 controls">                      
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_pylmm" value="true">
+                                    <input type="radio" name="manhattan_plot_pylmm" value="True">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_pylmm" value="false" checked="">
+                                    <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
                                     No
                                </label>
                             </div>
@@ -160,11 +160,11 @@
                             <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
                             <div class="col-xs-12 controls">                      
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_rqtl" value="true">
+                                    <input type="radio" name="manhattan_plot_rqtl" value="True">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_rqtl" value="false" checked="">
+                                    <input type="radio" name="manhattan_plot_rqtl" value="False" checked="">
                                     No
                                </label>
                             </div>
@@ -242,11 +242,11 @@
                             <label style="text-align:left;" class="col-xs-12 control-label">Marker Regr.</label>
                             <div class="col-xs-12 controls">                      
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="true">
+                                    <input type="radio" name="manhattan_plot_reaper" value="True">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
+                                    <input type="radio" name="manhattan_plot_reaper" value="False" checked="">
                                     No
                                </label>
                             </div>
-- 
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