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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py54
1 files 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)