Haplotype Analyst now works for GN1 mapping figure

Chromosome drop-down select and Mb range text fields now are set to the values the user last selected

4 files changed, 51 insertions, 38 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 745cdfaa..9f61ee3c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -94,6 +94,8 @@ class MarkerRegression(object):
             self.endMb = start_vars['endMb']
         if "graphWidth" in start_vars:
             self.graphWidth = start_vars['graphWidth']
+        if "haplotypeAnalystCheck" in start_vars:
+            self.haplotypeAnalystCheck = start_vars['haplotypeAnalystCheck']
         if "startMb" in start_vars: #ZS: This is to ensure showGenes, Legend, etc are checked the first time you open the mapping page, since startMb will only not be set during the first load
             if "showGenes" in start_vars:
                 self.showGenes = start_vars['showGenes']
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 0a4846fe..b53d5b1e 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -37,9 +37,9 @@ from flask import Flask, g
 from htmlgen import HTMLgen2 as HT
 
 from base import webqtlConfig
+from base.GeneralObject import GeneralObject
 #from base.webqtlTrait import webqtlTrait
 #from base.templatePage import templatePage
-#from base.GeneralObject import GeneralObject
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot
@@ -271,10 +271,12 @@ class MarkerRegression(object):
 
 ## BEGIN HaplotypeAnalyst
         #self.haplotypeAnalystChecked = fd.formdata.getvalue('haplotypeAnalystCheck')
-        self.haplotypeAnalystChecked = False
+        if 'haplotypeAnalystCheck' in start_vars.keys():
+            self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck']
+        else:
+            self.haplotypeAnalystChecked = False
 ## END HaplotypeAnalyst
 
-
         self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
         self.manhattan_plot = start_vars['manhattan_plot']
         self.additiveChecked = False
@@ -415,20 +417,21 @@ class MarkerRegression(object):
 
 ## BEGIN HaplotypeAnalyst
 ## count the amount of individuals to be plotted, and increase self.graphHeight
-        #if self.haplotypeAnalystChecked and self.selectedChr > -1:
-        #    thisTrait = self.traitList[0]
-        #    _strains, _vals, _vars = thisTrait.exportInformative()
-        #    smd=[]
-        #    for ii, _val in enumerate(_vals):
-        #        temp = GeneralObject(name=_strains[ii], value=_val)
-        #        smd.append(temp)
-        #    bxdlist=list(self.genotype.prgy)
-        #    for j,_geno in enumerate (self.genotype[0][1].genotype):
-        #        for item in smd:
-        #            if item.name == bxdlist[j]:
-        #                self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
-## default:
-        #    self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
+        if self.haplotypeAnalystChecked and self.selectedChr > -1:
+           #thisTrait = self.traitList[0]
+           thisTrait = self.this_trait
+           _strains, _vals, _vars = thisTrait.export_informative()
+           smd=[]
+           for ii, _val in enumerate(_vals):
+               temp = GeneralObject(name=_strains[ii], value=_val)
+               smd.append(temp)
+           samplelist = list(self.genotype.prgy)
+           for j,_geno in enumerate (self.genotype[0][1].genotype):
+               for item in smd:
+                   if item.name == samplelist[j]:
+                       self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
+# default:
+           self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
 ## for paper:
         #    #self.graphHeight = self.graphHeight + 1 * self.NR_INDIVIDUALS * self.EACH_GENE_HEIGHT - 180
 ## END HaplotypeAnalyst
@@ -526,7 +529,7 @@ class MarkerRegression(object):
         #    showLocusForm =  webqtlUtil.genRandStr("fm_")
         #else:
         showLocusForm = ""
-        intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
+        intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight))
         gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)    
 
         self.gifmap = gifmap.__str__()
@@ -1267,7 +1270,11 @@ class MarkerRegression(object):
                 canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1)
 
                 #draw the arrows
-                for xCoord in range(0, geneEndPix-geneStartPix):
+                if geneEndPix - geneStartPix < 1:
+                    genePixRange = 1
+                else:
+                    genePixRange = int(geneEndPix - geneStartPix)
+                for xCoord in range(0, genePixRange):
 
                     if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0:
                         if strand == "+":
@@ -1347,7 +1354,6 @@ class MarkerRegression(object):
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
             return
 
-
         fpText = open(os.path.join(webqtlConfig.TMPDIR, "hallo") + '.txt','wb')
 
         clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
@@ -1363,18 +1369,21 @@ class MarkerRegression(object):
 
         exprdrawn = 0
 
-        thisTrait = self.traitList[0]
-        _strains, _vals, _vars = thisTrait.exportInformative()
+        #thisTrait = self.traitList[0]
+        thisTrait = self.this_trait
+        _strains, _vals, _vars = thisTrait.export_informative()
 
         smd=[]
         for ii, _val in enumerate(_vals):
-            temp = GeneralObject(name=_strains[ii], value=_val)
-            smd.append(temp)
+            if _strains[ii] in self.dataset.group.samplelist:
+                temp = GeneralObject(name=_strains[ii], value=_val)
+                smd.append(temp)
+            
 
         smd.sort(lambda A, B: cmp(A.value, B.value))
         smd.reverse()
 
-        bxdlist=list(self.genotype.prgy)
+        samplelist = list(self.genotype.prgy)
 
         oldgeneEndPix = -1
         #Initializing plotRight, error before
@@ -1473,7 +1482,7 @@ class MarkerRegression(object):
 
                         plotbxd=0
                         for item in smd:
-                            if item.name == bxdlist[j]:
+                            if item.name == samplelist[j]:
                                 plotbxd=1
 
                         if (plotbxd == 1):
@@ -1481,7 +1490,7 @@ class MarkerRegression(object):
                             counter = 0
                             for item in smd:
                                 counter = counter + 1
-                                if item.name == bxdlist[j]:
+                                if item.name == samplelist[j]:
                                     ind = counter
                             maxind=max(ind,maxind)
 
@@ -1504,7 +1513,7 @@ class MarkerRegression(object):
 
 
                             COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
-                            TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (bxdlist[j], self.genotype[0][i].name, float(txStart))
+                            TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (samplelist[j], self.genotype[0][i].name, float(txStart))
                             HREF = ''
                             gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
 
@@ -1524,14 +1533,14 @@ class MarkerRegression(object):
                     firstGene = 0
                 else:
                     lastGene = 0
-
-        for j,_geno in enumerate (self.genotype[0][1].genotype):
+                     
+        for j, _geno in enumerate (self.genotype[0][1].genotype):
 
             plotbxd=0
             for item in smd:
-                if item.name == bxdlist[j]:
-                    plotbxd=1
-
+                if item.name == samplelist[j]:
+                    plotbxd=1    
+                    
             if (plotbxd == 1):
 
                 ind = 0
@@ -1539,12 +1548,12 @@ class MarkerRegression(object):
                 expr = 0
                 for item in smd:
                     counter = counter + 1
-                    if item.name == bxdlist[j]:
+                    if item.name == samplelist[j]:
                         ind = counter
                         expr = item.value
 
                 # Place where font is hardcoded
-                canvas.drawString("%s" % (bxdlist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+                canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
                 canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
 
         fpText.close()
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index ab75d5e3..3be9ad01 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -47,7 +47,7 @@
                   <td>
                     <select name="chromosomes" size="1">
                         {% for chr in ChrList %}
-                        <option value="{{ chr[1] }}">{{ chr[0] }}</option>
+                        <option value="{{ chr[1] }}" {% if (chr[1] + 1) == selectedChr %}selected{% endif %}>{{ chr[0] }}</option>
                         {% endfor %}
                     </select>&nbsp;
                     <button type="button" class="btn btn-primary" style="padding-bottom: 2px; padding-top: 2px;" onclick="javascript:remap();">Remap</button>
@@ -56,7 +56,7 @@
                 <tr>
                   <td><b>View:&nbsp;</b></td>
                   <td style="padding: 5px;">
-                    <input type="text" name="startMb" size="10"> to <input type="text" name="endMb" size="10">
+                    <input type="text" name="startMb" size="10" value="{{ startMb }}"> to <input type="text" name="endMb" size="10" value="{{ endMb }}">
                   </td>
                 </tr>
                 <tr>
@@ -69,7 +69,8 @@
               </div>
               <div class="col-xs-4" style="padding: 0px;">
                   <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> 
+                  <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>
+                  <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> 
               </div>
           </div>
         </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index f1b55b51..de04a758 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -359,6 +359,7 @@ def marker_regression_page():
         'graphWidth',
         'showGenes',
         'viewLegend',
+        'haplotypeAnalystCheck',
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno'
     )