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authorzsloan2020-03-12 12:53:20 -0500
committerzsloan2020-03-12 12:53:20 -0500
commit9a4433a7fe6bab8298f58c42f54731d7ade18d4e (patch)
tree1b7ddc03e1a094c574beb483ee72656426de4217 /wqflask
parent79aec8e686e83d5f5ed3b65b450b44648c799d1e (diff)
downloadgenenetwork2-9a4433a7fe6bab8298f58c42f54731d7ade18d4e.tar.gz
Made some changes to how the mapping Y axis is determined/drawn; left in the commented-out old code until we're sure this works well
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py52
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):