diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 54 |
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) |