diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 52 |
1 files changed, 36 insertions, 16 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index e74f35f5..66b5e25e 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1654,10 +1654,6 @@ class DisplayMappingResults(object): INTERCROSS = (self.genotype.type=="intercross") - LRSHeightThresh = drawAreaHeight - AdditiveHeightThresh = drawAreaHeight/2 - DominanceHeightThresh = drawAreaHeight/2 - #draw the LRS scale #We first determine whether or not we are using a sliding scale. #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max. @@ -1694,7 +1690,9 @@ class DisplayMappingResults(object): pass if self.permChecked and self.nperm > 0 and not self.multipleInterval: - LRS_LOD_Max = max(self.significant, LRS_LOD_Max) + 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 @@ -1715,6 +1713,12 @@ class DisplayMappingResults(object): LRSLODFont=pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) yZero = yTopOffset + plotHeight + #LRSHeightThresh = drawAreaHeight + #AdditiveHeightThresh = drawAreaHeight/2 + #DominanceHeightThresh = drawAreaHeight/2 + LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1)) + AdditiveHeightThresh = LRSHeightThresh/2 + DominanceHeightThresh = LRSHeightThresh/2 if LRS_LOD_Max > 100: LRSScale = 20.0 @@ -1728,7 +1732,7 @@ class DisplayMappingResults(object): LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) #make sure the user's value appears on the y-axis #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460 - LRSAxisList.append(round(LRS_LOD_Max)) + LRSAxisList.append(ceil(LRS_LOD_Max)) #ZS: Convert to int if all axis values are whole numbers all_int = True @@ -1751,7 +1755,9 @@ class DisplayMappingResults(object): for item in LRSAxisList: if LRS_LOD_Max == 0.0: LRS_LOD_Max = 0.000001 - yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh + yTopOffset + 30*(zoom - 1) + #yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh + yLRS = yZero - (item/LRSAxisList[-1]) * LRSHeightThresh canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom) if all_int: scaleStr = "%d" % item @@ -1761,8 +1767,10 @@ class DisplayMappingResults(object): canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR) if self.permChecked and self.nperm > 0 and not self.multipleInterval: - significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max - suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRS_LOD_Max + # significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max + # suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRS_LOD_Max + significantY = yZero - self.significant*LRSHeightThresh/LRSAxisList[-1] + suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSAxisList[-1] startPosX = xLeftOffset #"Significant" and "Suggestive" Drawing Routine @@ -1878,25 +1886,37 @@ class DisplayMappingResults(object): # updated by NL 06-18-2011: # fix the over limit LRS graph issue since genotype trait may give infinite LRS; # for any lrs is over than 460(LRS max in this system), it will be reset to 460 + + yLRS = yZero - (item/LRSAxisList[-1]) * (yZero - yTopOffset + 30*(zoom - 1)) + #yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh + + if 'lrs_value' in qtlresult: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)": if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) + #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) else: - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) + Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) + #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) else: if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] + #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max else: - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] + #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] + #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max else: if self.LRS_LOD == "LRS": - Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] + #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max else: - Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] + #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): |