From 8d7f923631cc3578aa9fb8116b31dbfd773e3b59 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 Apr 2016 17:58:49 +0000
Subject: SNP Track option should now work for GN1 mapping figure

Fixed typo in show_trait html that caused the p-value slider to not work for correlations
---
 wqflask/utility/Plot.py                                    |  1 +
 wqflask/wqflask/marker_regression/marker_regression.py     |  8 +++++++-
 wqflask/wqflask/marker_regression/marker_regression_gn1.py | 13 ++++++++-----
 wqflask/wqflask/templates/marker_regression_gn1.html       |  6 ++++++
 wqflask/wqflask/templates/show_trait.html                  |  2 +-
 wqflask/wqflask/views.py                                   |  1 +
 6 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index ad11a81e..444c71c9 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -497,6 +497,7 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
     xLow, xTop, stepX = detScale(min_D, max_D)
 
     #reduce data
+    #ZS: Used to determine number of bins for permutation output
     step = ceil((xTop-xLow)/50.0)
     j = xLow
     dataXY = []
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 86fced39..26ba212d 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -104,7 +104,12 @@ class MarkerRegression(object):
             self.num_perm = int(start_vars['num_perm'])
         
             self.LRSCheck = start_vars['LRSCheck']
-        
+            
+            if "showSNP" in start_vars:
+                self.showSNP = start_vars['showSNP']
+            else:
+                self.showSNP = False 
+                
             if "showGenes" in start_vars:
                 self.showGenes = start_vars['showGenes']
             else:
@@ -125,6 +130,7 @@ class MarkerRegression(object):
             
             self.LRSCheck = self.score_type
             self.permCheck = "ON"
+            self.showSNP = "ON"
             self.showGenes = "ON"
             self.viewLegend = "ON"
  
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 45d98554..3e08f7ae 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -304,11 +304,14 @@ class MarkerRegression(object):
             self.legendChecked = start_vars['viewLegend']
         else:
             self.legendChecked = False
+        if 'showSNP' in start_vars.keys():
+            self.SNPChecked = start_vars['showSNP']
+        else:
+            self.SNPChecked = False  
         if 'showGenes' in start_vars.keys():
             self.geneChecked = start_vars['showGenes']
         else:
             self.geneChecked = False
-        self.SNPChecked  = False
         self.draw2X = False
         self.lrsMax = 0
         try:
@@ -1047,14 +1050,14 @@ class MarkerRegression(object):
         SNPCounts = []
 
         while startMb<endMb:
-            self.cursor.execute("""
+            snp_count = g.db.execute("""
                     select
                             count(*) from BXDSnpPosition
                     where
                             Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
                             StrainId1 = %d AND StrainId2 = %d
-                    """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2))
-            SNPCounts.append(self.cursor.fetchone()[0])
+                    """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2)).fetchone()[0]
+            SNPCounts.append(snp_count)
             startMb += stepMb
 
         if (len(SNPCounts) > 0):
@@ -2538,7 +2541,7 @@ class MarkerRegression(object):
             heading2.append(HT.Strong("Trait Name: "), fd.identification)
         return HT.TD(intMapHeading, heading2, valign="top")
 
-    def drawPermutationHistogram(self):
+    def drawPermutationHistogram(self, x_label='LRS'):
         #########################################
         #      Permutation Graph
         #########################################
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 11c0f859..cc881011 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -104,6 +104,12 @@
                     </a>
                   <br>
                   {% endif %}
+                  <input type="checkbox" name="showSNP" class="checkbox" style="display: inline; margin-top: 0px;" {% if SNPChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">SNP Track </span>
+                    <a href="http://genenetwork.org/glossary.html#snpSeismograph" target="_blank">
+                      <sup style="color:#f00"> ?</sup>
+                    </a>
+                    <span style="color:red;">*</span>
+                  <br>
                   <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>
                   {% if plotScale != "morgan" %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 73bd8e4b..62a08d85 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -151,7 +151,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
     <script type="text/javascript" charset="utf-8">
             
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2e846066..acc46137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -365,6 +365,7 @@ def marker_regression_page():
         'endMb',
         'graphWidth',
         'additiveCheck',
+        'showSNP',
         'showGenes',
         'viewLegend',
         'haplotypeAnalystCheck',
-- 
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