From 5a1f69aa85809768577069ae63d92c9ef6aecc02 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 23 Oct 2020 16:13:48 -0500
Subject: Fixed bootstrap results when using interval mapping for the full
 genome view; still need to fix for single chromosome or Mb range view

* wqflask/wqflask/marker_regression/display_mapping_results.py - Fixed bootstrap results by iterating through qtlresults instead of self.genotype (the latter didn't have intervals added, resulting in the bootstrap result positions being wrong)
---
 .../marker_regression/display_mapping_results.py   | 54 ++++++++++------------
 1 file changed, 25 insertions(+), 29 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 79266df2..de751907 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -656,7 +656,7 @@ class DisplayMappingResults(object):
         plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
 
         #draw bootstap
-        if self.bootChecked and not self.multipleInterval and not self.manhattan_plot:
+        if self.bootChecked and not self.multipleInterval:
             self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
 
         # Draw clickable region and gene band if selected
@@ -703,31 +703,34 @@ class DisplayMappingResults(object):
         #break bootstrap result into groups
         BootCoord = []
         i = 0
+        previous_chr = None
+        previous_chr_as_int = 0
         startX = xLeftOffset
 
+        BootChrCoord = []
         if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
-            for j, _chr in enumerate(self.genotype):
-                BootCoord.append( [])
-                for _locus in _chr:
+            for i, result in enumerate(self.qtlresults):
+                if result['chr'] != previous_chr:
+                    previous_chr = result['chr']
+                    previous_chr_as_int += 1
+                    if previous_chr_as_int != 1:
+                        BootCoord.append(BootChrCoord)
+                        BootChrCoord = []
+                        startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval)*plotXScale
+                if self.plotScale == 'physic':
+                    Xc = startX + (result['Mb']-self.startMb)*plotXScale
+                else:
+                    Xc = startX + (result['cM']-self.qtlresults[0]['cM'])*plotXScale
+                BootChrCoord.append([Xc, self.bootResult[i]])
+        else:
+            for i, result in enumerate(self.qtlresults):
+                if result['chr'] == self.ChrList[self.selectedChr][0]:
                     if self.plotScale == 'physic':
-                        Xc = startX + (_locus.Mb-self.startMb)*plotXScale
+                        Xc = startX + (result['Mb']-self.startMb)*plotXScale
                     else:
-                        Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
-                    BootCoord[-1].append([Xc, self.bootResult[i]])
-                    i += 1
-                startX += (self.ChrLengthDistList[j] + self.GraphInterval)*plotXScale
-        else:
-            for j, _chr in enumerate(self.genotype):
-                if _chr.name == self.ChrList[self.selectedChr][0]:
-                    BootCoord.append( [])
-                for _locus in _chr:
-                    if _chr.name == self.ChrList[self.selectedChr][0]:
-                        if self.plotScale == 'physic':
-                            Xc = startX + (_locus.Mb-startMb)*plotXScale
-                        else:
-                            Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
-                        BootCoord[-1].append([Xc, self.bootResult[i]])
-                    i += 1
+                        Xc = startX + (result['cM']-self.qtlresults[0]['cM'])*plotXScale
+                    BootChrCoord.append([Xc, self.bootResult[i]])
+            BootCoord = [BootChrCoord]
 
         #reduce bootResult
         if self.selectedChr > -1:
@@ -1687,9 +1690,6 @@ class DisplayMappingResults(object):
             for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
 
                 calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
-                if pixel == (xLeftOffset + pixelStep*2):
-                  logger.debug("CALBASE:", calBase)
-                  logger.debug("FLANKING:", flankingWidthInBases)
 
                 xBrowse1 = pixel
                 xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
@@ -2074,11 +2074,7 @@ class DisplayMappingResults(object):
                         pass
 
             if self.permChecked and self.nperm > 0 and not self.multipleInterval:
-                if self.significant > LRS_LOD_Max:
-                    LRS_LOD_Max = self.significant * 1.1
-                #LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
-            else:
-                LRS_LOD_Max = 1.15*LRS_LOD_Max
+                LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
 
             #genotype trait will give infinite LRS
             LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS)
-- 
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