The option to switch between LRS and LOD for the GN1 mapping figure should now work correctly.

The correct value (LRS or LOD) will now be displayed in the results table

Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)

4 files changed, 123 insertions, 66 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 112dcd5c..86fced39 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -103,10 +103,13 @@ class MarkerRegression(object):
                 self.permCheck = False
             self.num_perm = int(start_vars['num_perm'])
         
+            self.LRSCheck = start_vars['LRSCheck']
+        
             if "showGenes" in start_vars:
                 self.showGenes = start_vars['showGenes']
             else:
                 self.showGenes = False 
+                
             if "viewLegend" in start_vars:
                 self.viewLegend = start_vars['viewLegend']
             else:
@@ -120,6 +123,7 @@ class MarkerRegression(object):
             except:
                 self.num_perm = 0
             
+            self.LRSCheck = self.score_type
             self.permCheck = "ON"
             self.showGenes = "ON"
             self.viewLegend = "ON"
@@ -660,18 +664,18 @@ class MarkerRegression(object):
             if samples[i] in self.dataset.group.samplelist:
                 trimmed_samples.append(samples[i])
                 trimmed_values.append(values[i])
-                
-        self.lrs_array = genotype.permutation(strains = trimmed_samples,
-                                              trait = trimmed_values, 
-                                              nperm= self.num_perm)
-        
-        self.suggestive = self.lrs_array[int(self.num_perm*0.37-1)]
-        self.significant = self.lrs_array[int(self.num_perm*0.95-1)]
+
+        if self.num_perm < 100:
+            self.suggestive = 0
+            self.significant = 0
+        else:
+            self.perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=self.num_perm)
+            self.suggestive = self.perm_output[int(self.num_perm*0.37-1)]
+            self.significant = self.perm_output[int(self.num_perm*0.95-1)]
+            
         self.json_data['suggestive'] = self.suggestive
         self.json_data['significant'] = self.significant
 
-        #print("samples:", trimmed_samples)
-
         if self.control_marker != "" and self.do_control == "true":
             reaper_results = genotype.regression(strains = trimmed_samples,
                                                  trait = trimmed_values,
@@ -706,14 +710,6 @@ class MarkerRegression(object):
                 self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
                                                             trait = trimmed_values,
                                                             nboot = self.num_bootstrap)
-                                                            
-        if self.num_perm < 100:
-            self.suggestive = 0
-            self.significant = 0
-        else:
-            self.perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=self.num_perm)
-            self.suggestive = self.perm_output[int(self.num_perm*0.37-1)]
-            self.significant = self.perm_output[int(self.num_perm*0.95-1)]
 
         self.json_data['chr'] = []
         self.json_data['pos'] = []
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 692e381b..45d98554 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -293,7 +293,7 @@ class MarkerRegression(object):
         self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
         self.manhattan_plot = start_vars['manhattan_plot']
         self.dominanceChecked = False
-        self.LRS_LOD = start_vars['score_type']
+        self.LRS_LOD = start_vars['LRSCheck']
         self.cutoff = start_vars['cutoff']
         self.intervalAnalystChecked = False
         if 'additiveCheck' in start_vars.keys():
@@ -1108,7 +1108,6 @@ class MarkerRegression(object):
         if zoom == 2:
             fontZoom = 1.5
 
-
         labelFont=pid.Font(ttf="trebuc",size=12*fontZoom, bold=1)
         startPosY = 15
         stepPosY = 12*fontZoom
@@ -1146,10 +1145,8 @@ class MarkerRegression(object):
             lod = 1
             if self.LRS_LOD == 'LOD':
                 lod = self.LODFACTOR
-            canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant/lod),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
-            canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive/lod),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
-
-
+            canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
+            canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
 
         labelFont=pid.Font(ttf="verdana",size=12*fontZoom)
         labelColor = pid.black
@@ -1865,46 +1862,66 @@ class MarkerRegression(object):
 
         #draw the LRS scale
         #We first determine whether or not we are using a sliding scale.
-        #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax.
-        #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment.
-        #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter.
+        #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max.
+        #LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment.
+        #if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter.
 
         #ZS: I'm not sure what this if statement is supposed to do. It appears to work correctly for both LOD and LRS if I just set lodm to 1.0
-        #if self.LRS_LOD == 'LRS':
-        #    lodm = self.LODFACTOR
-        #else:
-        #     lodm = 1.0
-        lodm = 1.0
+        # if self.LRS_LOD == 'LRS':
+            # lodm = self.LODFACTOR
+        # else:
+            # lodm = 1.0
  
+        #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD
         if self.lrsMax <= 0:  #sliding scale
-            if self.LRS_LOD == "LRS" and "lrs_value" in self.qtlresults[0]:
-                LRSMax = max([result['lrs_value'] for result in self.qtlresults])
-                #LRSMax = max(map(max, self.qtlresults)).lrs_value
-            else: 
-                LRSMax = max([result['lod_score'] for result in self.qtlresults])
-                #LRSMax = max(map(max, self.qtlresults)).lod_score
-            #genotype trait will give infinite LRS
-            LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
+            if "lrs_value" in self.qtlresults[0]:
+                LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults])
+                if self.LRS_LOD == "LOD":
+                    LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR
+                    if self.permChecked and self.nperm > 0 and not self.multipleInterval:
+                        self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS)
+                        self.suggestive = min(self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS)
+                else:
+                    if self.permChecked and self.nperm > 0 and not self.multipleInterval:
+                        self.significant = min(self.significant, webqtlConfig.MAXLRS)
+                        self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)                    
+                    else:
+                        pass
+            else:
+                LRS_LOD_Max = max([result['lod_score'] for result in self.qtlresults])
+                if self.LRS_LOD == "LRS":
+                    LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR
+                    if self.permChecked and self.nperm > 0 and not self.multipleInterval:
+                        self.significant = min(self.significant * self.LODFACTOR, webqtlConfig.MAXLRS)
+                        self.suggestive = min(self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS)
+                else:
+                    if self.permChecked and self.nperm > 0 and not self.multipleInterval:
+                        self.significant = min(self.significant, webqtlConfig.MAXLRS)
+                        self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)  
+                    else:
+                        pass
+                        
             if self.permChecked and self.nperm > 0 and not self.multipleInterval:
-                self.significant = min(self.significant, webqtlConfig.MAXLRS)
-                self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
-                LRSMax = max(self.significant, LRSMax)
+                LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
+
+            #genotype trait will give infinite LRS
+            LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS)
         else:
-            LRSMax = self.lrsMax*lodm
+            LRS_LOD_Max = self.lrsMax
 
-        if LRSMax/lodm > 100:
+        if LRS_LOD_Max > 100:
             LRSScale = 20.0
-        elif LRSMax/lodm > 20:
+        elif LRS_LOD_Max > 20:
             LRSScale = 5.0
-        elif LRSMax/lodm > 7.5:
+        elif LRS_LOD_Max > 7.5:
             LRSScale = 2.5
         else:
             LRSScale = 1.0
            
-        LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale)
+        LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale)
         #make sure the user's value appears on the y-axis
-        #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460
-        LRSAxisList.append(round(LRSMax/lodm))
+        #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460
+        LRSAxisList.append(round(LRS_LOD_Max))
 
         #draw the "LRS" or "LOD" string to the left of the axis
         LRSScaleFont=pid.Font(ttf="verdana", size=16*zoom, bold=0)
@@ -1915,17 +1932,17 @@ class MarkerRegression(object):
                                           yZero - 150 - 300*(zoom - 1), font=LRSLODFont, color=pid.black, angle=90)
 
         for item in LRSAxisList:
-            if LRSMax == 0.0:
-                LRSMax = 0.000001
-            yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh
+            if LRS_LOD_Max == 0.0:
+                LRS_LOD_Max = 0.000001
+            yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
             canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom)
             scaleStr = "%2.1f" % item
             #Draw the LRS/LOD Y axis label
             canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)
 
         if self.permChecked and self.nperm > 0 and not self.multipleInterval:
-            significantY = yZero - self.significant*LRSHeightThresh/LRSMax
-            suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax
+            significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max
+            suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRS_LOD_Max
             startPosX = xLeftOffset
 
             #"Significant" and "Suggestive" Drawing Routine
@@ -2025,21 +2042,30 @@ class MarkerRegression(object):
                     # 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 self.LRS_LOD == "LRS":
-                        if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
-                            Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+                    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)
                         else:
-                            Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
+                            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
                     else:
                         if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf':
-                            Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+                            Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
                         else:
-                            Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSMax
+                            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/LRSMax
+                    #    Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
                     #else:
-                    #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
+                    #    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)
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 8ec8a104..11c0f859 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -61,6 +61,20 @@
                   </td>
                 </tr>
                 <tr>
+                  <td><b>Units:&nbsp;</b></td>
+                  <td style="padding: 5px;">
+                    <label class="radio-inline">
+                      <input type="radio" name="LRSCheck" value="LRS" {% if LRS_LOD == "LRS" %}checked{% endif %}>LRS
+                    </label>
+                    <label class="radio-inline">
+                      <input type="radio" name="LRSCheck" value="LOD" {% if LRS_LOD == "LOD" %}checked{% endif %}>LOD
+                    </label>
+                    <a href="http://genenetwork.org/glossary.html#LOD" target="_blank">
+                      <sup style="color:#f00"> ?</sup>
+                    </a>
+                  </td>
+                </tr>
+                <tr>
                   <td><b>Width:&nbsp;</b></td>
                   <td>
                     <input type="text" name="graphWidth" value="{% if graphWidth is defined %}{{ graphWidth }}{% else %}1600{% endif %}" size="5"><span style="font-size: 11px;"> pixels (minimum=900)</span>
@@ -70,13 +84,25 @@
               </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 <br>
+                  <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">
+                      <sup style="color:#f00"> ?</sup>
+                    </a>
+                  <br>
                   {% endif %}
                   {% if mapping_method == "reaper" and nboot > 0 %}
-                  <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test <br>
+                  <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test 
+                    <a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank">
+                      <sup style="color:#f00"> ?</sup>
+                    </a>
+                  <br>
                   {% endif %}
                   {% if mapping_method == "reaper" %}
-                  <input type="checkbox" name="additiveCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if additiveChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Allele Effects<br>
+                  <input type="checkbox" name="additiveCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if additiveChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Allele Effects
+                    <a href="http://genenetwork.org/glossary.html#additive" target="_blank">
+                      <sup style="color:#f00"> ?</sup>
+                    </a>
+                  <br>
                   {% endif %}
                   <input type="checkbox" name="showGenes" class="checkbox" style="display: inline; margin-top: 0px;" {% if geneChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Gene Track </span> <span style="color:red;">*</span><br>
                   <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span><br>
@@ -151,12 +177,20 @@
                                        class="checkbox edit_sample_checkbox"
                                        value="{{ marker.name }}" checked="checked">
                             </td>
-                            <Td align="right">{{ loop.index }}</Td>
+                            <td align="right">{{ loop.index }}</td>
                             {% if LRS_LOD == "LOD" %}
+                            {% if 'lod_score' in marker %}
                             <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td>
                             {% else %}
+                            <td>{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}</td>
+                            {% endif %}
+                            {% else %}
+                            {% if 'lod_score' in marker %}
+                            <td>{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}</td>
+                            {% else %}
                             <td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
                             {% endif %}
+                            {% endif %}
                             <td>{{marker.chr}}</td>
                             <td>{{ '%0.6f' | format(marker.Mb|float) }}</td>
                             <td>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index acfc5fc6..2e846066 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -354,6 +354,7 @@ def marker_regression_page():
         'num_bootstrap',
         'bootCheck',
         'bootstrap_results',
+        'LRSCheck',
         'maf',
         'manhattan_plot',
         'control_marker',