diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 50 |
1 files changed, 25 insertions, 25 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 65eba7e3..7e43f6bd 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -342,7 +342,7 @@ class DisplayMappingResults(object): if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] if 'output_files' in start_vars: - self.output_files = ",".join(start_vars['output_files']) + self.output_files = ",".join([(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) self.categorical_vars = "" self.perm_strata = "" @@ -684,7 +684,7 @@ 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 @@ -731,31 +731,34 @@ 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 str(result['chr']) == str(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: @@ -1715,9 +1718,6 @@ 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)) |