From 738326ffa7b8fedc765e0a8b3fc80cc9acea6891 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 Apr 2016 18:16:50 +0000
Subject: Permutation figure and x-axis label should change to correctly
 reflect the mapping scale (lrs or lod)

Fixed bug where broken image link would appear if you ran R/qtl with no permutations
---
 wqflask/wqflask/marker_regression/marker_regression_gn1.py | 11 +++++++++--
 wqflask/wqflask/templates/marker_regression_gn1.html       |  2 +-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 3e08f7ae..ec4f79aa 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -2541,12 +2541,19 @@ class MarkerRegression(object):
             heading2.append(HT.Strong("Trait Name: "), fd.identification)
         return HT.TD(intMapHeading, heading2, valign="top")
 
-    def drawPermutationHistogram(self, x_label='LRS'):
+    def drawPermutationHistogram(self):
         #########################################
         #      Permutation Graph
         #########################################
         myCanvas = pid.PILCanvas(size=(400,300))
-        Plot.plotBar(myCanvas, self.perm_output, XLabel='LRS', YLabel='Frequency', title=' Histogram of Permutation Test')
+        if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS":
+            perm_output = [value*4.16 for value in self.perm_output]
+        elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD":
+            perm_output = [value/4.16 for value in self.perm_output]
+        else:
+            perm_output = self.perm_output
+            
+        Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test')
         filename= webqtlUtil.genRandStr("Reg_")
         myCanvas.save(webqtlConfig.IMGDIR+filename, format='gif')
         
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index cc881011..67f5e010 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -139,7 +139,7 @@
                   <br>
                   <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span>
                   {% endif %}
-                  {% if permChecked|upper == "ON" %}
+                  {% if nperm > 0 %}
                   <br><br>
                   <img src="/static/output/{{ perm_filename }}.gif">
                   {% endif %}
-- 
cgit v1.2.3