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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py185
1 files changed, 103 insertions, 82 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 9ac4946b..25846099 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -27,7 +27,7 @@
import datetime
import string
from math import *
-import piddle as pid
+from PIL import (ImageColor)
import sys,os
import cPickle
import httplib
@@ -49,6 +49,27 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
+RED = ImageColor.getrgb("red")
+BLUE = ImageColor.getrgb("blue")
+GRAY = ImageColor.getrgb("gray")
+GOLD = ImageColor.getrgb("gold")
+BLACK = ImageColor.getrgb("black")
+GREEN = ImageColor.getrgb("green")
+PURPLE = ImageColor.getrgb("purple")
+ORANGE = ImageColor.getrgb("orange")
+YELLOW = ImageColor.getrgb("yellow")
+DARKRED = ImageColor.getrgb("darkred")
+DARKBLUE = ImageColor.getrgb("darkblue")
+DARKGRAY = ImageColor.getrgb("darkgray")
+DEEPPINK = ImageColor.getrgb("deeppink")
+DARKGREEN = ImageColor.getrgb("darkgreen")
+GAINSBORO = ImageColor.getrgb("gainsboro")
+LIGHTBLUE = ImageColor.getrgb("lightblue")
+DARKORANGE = ImageColor.getrgb("darkorange")
+DARKVIOLET = ImageColor.getrgb("darkviolet")
+MEDIUMPURPLE = ImageColor.getrgb("mediumpurple")
+# ---- END: Define common colours ---- #
+
#########################################
# Inteval Mapping Plot Page
#########################################
@@ -96,47 +117,47 @@ class DisplayMappingResults(object):
LODFACTOR = 4.61
- SNP_COLOR = pid.orange # Color for the SNP "seismograph"
- TRANSCRIPT_LOCATION_COLOR = pid.mediumpurple
+ SNP_COLOR = ORANGE # Color for the SNP "seismograph"
+ TRANSCRIPT_LOCATION_COLOR = MEDIUMPURPLE
- BOOTSTRAP_BOX_COLOR = pid.yellow
- LRS_COLOR = pid.HexColor(0x0000FF)
- SIGNIFICANT_COLOR = pid.HexColor(0xEBC7C7)
- SUGGESTIVE_COLOR = pid.gainsboro
+ BOOTSTRAP_BOX_COLOR = YELLOW
+ LRS_COLOR = ImageColor.getrgb("#0000FF")
+ SIGNIFICANT_COLOR = ImageColor.getrgb("#EBC7C7")
+ SUGGESTIVE_COLOR = GAINSBORO
SIGNIFICANT_WIDTH = 5
SUGGESTIVE_WIDTH = 5
- ADDITIVE_COLOR_POSITIVE = pid.green
- ADDITIVE_COLOR_NEGATIVE = pid.orange
- DOMINANCE_COLOR_POSITIVE = pid.darkviolet
- DOMINANCE_COLOR_NEGATIVE = pid.red
+ ADDITIVE_COLOR_POSITIVE = GREEN
+ ADDITIVE_COLOR_NEGATIVE = ORANGE
+ DOMINANCE_COLOR_POSITIVE = DARKVIOLET
+ DOMINANCE_COLOR_NEGATIVE = RED
## BEGIN HaplotypeAnalyst
- HAPLOTYPE_POSITIVE = pid.green
- HAPLOTYPE_NEGATIVE = pid.red
- HAPLOTYPE_HETEROZYGOUS = pid.blue
- HAPLOTYPE_RECOMBINATION = pid.darkgray
+ HAPLOTYPE_POSITIVE = GREEN
+ HAPLOTYPE_NEGATIVE = RED
+ HAPLOTYPE_HETEROZYGOUS = BLUE
+ HAPLOTYPE_RECOMBINATION = DARKGRAY
## END HaplotypeAnalyst
- TOP_RIGHT_INFO_COLOR = pid.black
+ TOP_RIGHT_INFO_COLOR = BLACK
- CLICKABLE_WEBQTL_REGION_COLOR = pid.HexColor(0xF5D3D3)
- CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9)
- CLICKABLE_WEBQTL_TEXT_COLOR = pid.HexColor(0x912828)
+ CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3")
+ CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FCE9E9")
+ CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828")
- CLICKABLE_PHENOGEN_REGION_COLOR = pid.HexColor(0xA2FB94)
- CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = pid.HexColor(0xCEFEC7)
- CLICKABLE_PHENOGEN_TEXT_COLOR = pid.HexColor(0x1FD504)
+ CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94")
+ CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = ImageColor.getrgb("#CEFEC7")
+ CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504")
- CLICKABLE_UCSC_REGION_COLOR = pid.HexColor(0xDDDDEE)
- CLICKABLE_UCSC_REGION_OUTLINE_COLOR = pid.HexColor(0xEDEDFF)
- CLICKABLE_UCSC_TEXT_COLOR = pid.HexColor(0x333366)
+ CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE")
+ CLICKABLE_UCSC_REGION_OUTLINE_COLOR = ImageColor.getrgb("#EDEDFF")
+ CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366")
- CLICKABLE_ENSEMBL_REGION_COLOR = pid.HexColor(0xEEEEDD)
- CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = pid.HexColor(0xFEFEEE)
- CLICKABLE_ENSEMBL_TEXT_COLOR = pid.HexColor(0x555500)
+ CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD")
+ CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FEFEEE")
+ CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500")
- GRAPH_BACK_LIGHT_COLOR = pid.HexColor(0xFBFBFF)
- GRAPH_BACK_DARK_COLOR = pid.HexColor(0xF1F1F9)
+ GRAPH_BACK_LIGHT_COLOR = ImageColor.getrgb("#FBFBFF")
+ GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9")
HELP_PAGE_REF = '/glossary.html'
@@ -698,23 +719,23 @@ class DisplayMappingResults(object):
bootOffset = 50*fontZoom
bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0)
- canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow)
- canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black)
- canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black)
+ canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = YELLOW)
+ canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=BLACK)
+ canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=BLACK)
for item in bootScale:
if item == 0:
continue
bootY = yZero-bootHeightThresh*item/highestPercent
- canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=pid.black)
- canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=pid.black)
+ canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=BLACK)
+ canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=BLACK)
if self.legendChecked:
startPosY = 30
nCol = 2
smallLabelFont = pid.Font(ttf="trebuc", size=12*fontZoom, bold=1)
leftOffset = xLeftOffset+(nCol-1)*200
- canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=pid.yellow)
- canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=pid.black)
+ canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=YELLOW)
+ canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=BLACK)
def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
if len(self.traitList) != 1:
@@ -784,7 +805,7 @@ class DisplayMappingResults(object):
break
if locPixel >= 0 and self.plotScale == 'physic':
traitPixel = ((locPixel, yZero), (locPixel-7, yZero+14), (locPixel+7, yZero+14))
- canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
+ canvas.drawPolygon(traitPixel, edgeColor=BLACK, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
if self.legendChecked:
startPosY = 15
@@ -794,7 +815,7 @@ class DisplayMappingResults(object):
leftOffset = xLeftOffset
else:
leftOffset = xLeftOffset+(nCol-1)*200*fontZoom
- canvas.drawPolygon(((leftOffset+7, startPosY-7), (leftOffset, startPosY+7), (leftOffset+14, startPosY+7)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
+ canvas.drawPolygon(((leftOffset+7, startPosY-7), (leftOffset, startPosY+7), (leftOffset+14, startPosY+7)), edgeColor=BLACK, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR)
def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -863,7 +884,7 @@ class DisplayMappingResults(object):
nameWidths.append(nameWidth)
canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor)
- canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black)
+ canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=BLACK)
if thisTrait.db:
COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
@@ -884,21 +905,21 @@ class DisplayMappingResults(object):
stepPosY = 12*fontZoom
if self.manhattan_plot != True:
canvas.drawLine(xLeftOffset,startPosY,xLeftOffset+32,startPosY,color=self.LRS_COLOR, width=2)
- canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=pid.black)
+ canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=BLACK)
startPosY += stepPosY
if self.additiveChecked:
startPosX = xLeftOffset
canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.ADDITIVE_COLOR_POSITIVE, width=2)
canvas.drawLine(startPosX+18,startPosY,startPosX+32,startPosY,color=self.ADDITIVE_COLOR_NEGATIVE, width=2)
- canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=pid.black)
+ canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=BLACK)
if self.genotype.type == 'intercross' and self.dominanceChecked:
startPosX = xLeftOffset
startPosY += stepPosY
canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.DOMINANCE_COLOR_POSITIVE, width=4)
canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.DOMINANCE_COLOR_NEGATIVE, width=4)
- canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=pid.black)
+ canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=BLACK)
if self.haplotypeAnalystChecked:
startPosY += stepPosY
@@ -907,18 +928,18 @@ class DisplayMappingResults(object):
canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.HAPLOTYPE_NEGATIVE, width=4)
canvas.drawLine(startPosX+36,startPosY,startPosX+53,startPosY,color=self.HAPLOTYPE_HETEROZYGOUS, width=4)
canvas.drawLine(startPosX+54,startPosY,startPosX+67,startPosY,color=self.HAPLOTYPE_RECOMBINATION, width=4)
- canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=pid.black)
+ canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=BLACK)
if self.permChecked and self.nperm > 0:
startPosY += stepPosY
startPosX = xLeftOffset
canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
- canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
- canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
+ canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=BLACK)
+ canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=BLACK)
labelFont = pid.Font(ttf="verdana",size=12*fontZoom)
- labelColor = pid.black
+ labelColor = BLACK
if self.dataset.type == "Publish" or self.dataset.type == "Geno":
dataset_label = self.dataset.fullname
else:
@@ -1042,19 +1063,19 @@ class DisplayMappingResults(object):
densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
if SNPdensity < densities[0]:
- myColor = pid.black
+ myColor = BLACK
elif SNPdensity < densities[1]:
- myColor = pid.purple
+ myColor = PURPLE
elif SNPdensity < densities[2]:
- myColor = pid.darkblue
+ myColor = DARKBLUE
elif SNPdensity < densities[3]:
- myColor = pid.darkgreen
+ myColor = DARKGREEN
elif SNPdensity < densities[4]:
- myColor = pid.gold
+ myColor = GOLD
elif SNPdensity < densities[5]:
- myColor = pid.darkorange
+ myColor = DARKORANGE
else:
- myColor = pid.darkred
+ myColor = DARKRED
outlineColor = myColor
fillColor = myColor
@@ -1086,14 +1107,14 @@ class DisplayMappingResults(object):
elif (geneStartPix < xLeftOffset):
geneStartPix = xLeftOffset; # clip the first in-range gene
- outlineColor = pid.darkblue
- fillColor = pid.darkblue
+ outlineColor = DARKBLUE
+ fillColor = DARKBLUE
TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand)
# NL: 06-02-2011 Rob required to change this link for gene related
HREF=geneNCBILink %geneSymbol
else:
- outlineColor = pid.orange
- fillColor = pid.orange
+ outlineColor = ORANGE
+ fillColor = ORANGE
TITLE = "Gene: %s" % geneSymbol
#Draw Genes
@@ -1287,7 +1308,7 @@ class DisplayMappingResults(object):
drawit = 1
if drawit == 1:
- myColor = pid.darkblue
+ myColor = DARKBLUE
outlineColor = myColor
fillColor = myColor
@@ -1335,8 +1356,8 @@ class DisplayMappingResults(object):
canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
- fillColor=pid.black
- outlineColor=pid.black
+ fillColor=BLACK
+ outlineColor=BLACK
if lastGene == 0:
canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor)
@@ -1355,7 +1376,7 @@ class DisplayMappingResults(object):
if lastGene == 0:
- canvas.drawString("%s" % (_chr[j].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90)
+ canvas.drawString("%s" % (_chr[j].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=BLACK, angle=-90)
oldgeneEndPix = geneEndPix;
oldgeno = _chr[j].genotype
@@ -1384,8 +1405,8 @@ class DisplayMappingResults(object):
expr = item.value
# Place where font is hardcoded
- canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
- canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+ canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=BLACK)
+ canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=BLACK)
## END HaplotypeAnalyst
@@ -1487,14 +1508,14 @@ class DisplayMappingResults(object):
chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1)
traitFont = pid.Font(ttf="verdana", size=14, bold=0)
chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)
- canvas.drawString("Chr %s" % self.ChrList[self.selectedChr][0], chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray)
+ canvas.drawString("Chr %s" % self.ChrList[self.selectedChr][0], chrX, ensemblPaddingTop-5, font=chrFont, color=GRAY)
# end of drawBrowserClickableRegions
else:
#draw the gray text
chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1)
traitFont = pid.Font(ttf="verdana", size=14, bold=0)
chrX = xLeftOffset + (plotWidth - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont))/2
- canvas.drawString("Chr %s" % currentChromosome, chrX, 32, font=chrFont, color=pid.gray)
+ canvas.drawString("Chr %s" % currentChromosome, chrX, 32, font=chrFont, color=GRAY)
# end of drawBrowserClickableRegions
pass
@@ -1517,8 +1538,8 @@ class DisplayMappingResults(object):
MBLabelFont = pid.Font(ttf="verdana", size=15*zoom, bold=0)
xMajorTickHeight = 10 * zoom # How high the tick extends below the axis
xMinorTickHeight = 5*zoom
- xAxisTickMarkColor = pid.black
- xAxisLabelColor = pid.black
+ xAxisTickMarkColor = BLACK
+ xAxisLabelColor = BLACK
fontHeight = 12*fontZoom # How tall the font that we're using is
spacingFromLabelToAxis = 5
@@ -1565,14 +1586,14 @@ class DisplayMappingResults(object):
else:
distScale = 5
for j, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)):
- canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
+ canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=BLACK, width=1*zoom)
if j % 2 == 0:
- canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
+ canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=BLACK, font=MBLabelFont, angle=270)
startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
megabaseLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0)
canvas.drawString("Megabases", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
- strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=megabaseLabelFont, color=pid.black)
+ strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=megabaseLabelFont, color=BLACK)
pass
else:
strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont) + 8
@@ -1619,7 +1640,7 @@ class DisplayMappingResults(object):
LRectWidth = 10
LRectHeight = 3
offsetA = -stepA
- lineColor = pid.lightblue
+ lineColor = LIGHTBLUE
startPosX = xLeftOffset
for j, ChrInfo in enumerate(ChrAInfo):
@@ -1642,11 +1663,11 @@ class DisplayMappingResults(object):
yZero+25, color=lineColor)
canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\
yZero+40+Zorder*(LRectWidth+3),color=lineColor)
- rectColor = pid.orange
+ rectColor = ORANGE
else:
canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\
xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor)
- rectColor = pid.deeppink
+ rectColor = DEEPPINK
canvas.drawRect(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA-LRectHeight,yZero+40+Zorder*(LRectWidth+3)+LRectWidth,\
edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
@@ -1663,9 +1684,9 @@ class DisplayMappingResults(object):
centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0)
canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2,
- strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black)
+ strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=BLACK)
- canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself
+ canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1774,7 +1795,7 @@ class DisplayMappingResults(object):
#draw the "LRS" or "LOD" string to the left of the axis
canvas.drawString(self.LRS_LOD, xLeftOffset - max_lrs_width - 15*(zoom-1), \
- yZero - 150 - 300*(zoom - 1), font=LRSLODFont, color=pid.black, angle=90)
+ yZero - 150 - 300*(zoom - 1), font=LRSLODFont, color=BLACK, angle=90)
for item in LRSAxisList:
if LRS_LOD_Max == 0.0:
@@ -1955,9 +1976,9 @@ class DisplayMappingResults(object):
if self.manhattan_plot == True:
if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1):
- point_color = pid.red
+ point_color = RED
else:
- point_color = pid.blue
+ point_color = BLUE
final_x_pos = Xc-canvas.stringWidth("5",font=symbolFont)/2+1
if final_x_pos > (xLeftOffset + plotWidth):
@@ -2121,13 +2142,13 @@ class DisplayMappingResults(object):
#draw the shaded boxes and the sig/sug thick lines
canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \
- yBottom, edgeColor=pid.gainsboro,fillColor=theBackColor)
+ yBottom, edgeColor=GAINSBORO,fillColor=theBackColor)
chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont)
chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2
- canvas.drawString(_chr.name, chrStartPix, yTopOffset + 20 ,font = chrLabelFont,color=pid.black)
+ canvas.drawString(_chr.name, chrStartPix, yTopOffset + 20 ,font = chrLabelFont,color=BLACK)
COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
#add by NL 09-03-2010
@@ -2379,4 +2400,4 @@ class DisplayMappingResults(object):
lCorr = lCorr[0]
break
except: raise #lCorr = None
- return lCorr \ No newline at end of file
+ return lCorr