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-rw-r--r--wqflask/utility/Plot.py87
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py757
2 files changed, 637 insertions, 207 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 9bc84d22..c557bcc6 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -26,7 +26,7 @@
from __future__ import print_function
-import piddle as pid
+from PIL import (Image, ImageColor, ImageDraw, ImageFont)
from pprint import pformat as pf
from math import *
@@ -42,6 +42,17 @@ from base import webqtlConfig
import utility.logger
logger = utility.logger.getLogger(__name__ )
+# ---- Define common colours ---- #
+BLUE = ImageColor.getrgb("blue")
+BLACK = ImageColor.getrgb("black")
+# ---- END: Define common colours ---- #
+
+# ---- FONT FILES ---- #
+VERDANA_FILE = "fonts/ttf/verdana.ttf"
+COUR_FILE = "fonts/ttf/courbd.ttf"
+TAHOMA_FILE = "fonts/ttf/tahoma.ttf"
+# ---- END: FONT FILES ---- #
+
def cformat(d, rank=0):
'custom string format'
strD = "%2.6f" % d
@@ -114,7 +125,8 @@ def find_outliers(vals):
# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
-def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+ im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -161,43 +173,67 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
if count:
xc = (dataXY[i]-xLow)*xScale+xLeftOffset
yc =-(count-yLow)*yScale+yTopOffset+plotHeight
- canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
+ im_drawer.rectangle(
+ xy=((xc+2,yc),(xc+barWidth-2,yTopOffset+plotHeight)),
+ outline=barColor, fill=barColor)
#draw drawing region
- canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+ im_drawer.rectangle(
+ xy=((xLeftOffset, yTopOffset), (xLeftOffset+plotWidth, yTopOffset+plotHeight))
+ )
#draw scale
- scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+ scaleFont=ImageFont.truetype(font=COUR_FILE,size=11)
x=xLow
for i in range(int(stepX)+1):
xc=xLeftOffset+(x-xLow)*xScale
- canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
+ im_drawer.line(
+ xy=((xc,yTopOffset+plotHeight),(xc,yTopOffset+plotHeight+5)),
+ fill=axesColor)
strX = cformat(d=x, rank=0)
- canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
+ im_drawer.text(
+ text=strX,
+ xy=(xc-im_drawer.textsize(strX,font=scaleFont)[0]/2,
+ yTopOffset+plotHeight+14),font=scaleFont)
x+= (xTop - xLow)/stepX
y=yLow
for i in range(int(stepY)+1):
yc=yTopOffset+plotHeight-(y-yLow)*yScale
- canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+ im_drawer.line(xy=((xLeftOffset,yc),(xLeftOffset-5,yc)), fill=axesColor)
strY = "%d" %y
- canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+ im_drawer.text(
+ text=strY,
+ xy=(xLeftOffset-im_drawer.textsize(strY,font=scaleFont)[0]-6,yc+5),
+ font=scaleFont)
y+= (yTop - yLow)/stepY
#draw label
- labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
+ labelFont=ImageFont.truetype(font=TAHOMA_FILE,size=17)
if XLabel:
- canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
- yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
+ im_drawer.text(
+ text=XLabel,
+ xy=(xLeftOffset+(
+ plotWidth-im_drawer.textsize(XLabel,font=labelFont)[0])/2.0,
+ yTopOffset+plotHeight+yBottomOffset-10),
+ font=labelFont,fill=labelColor)
if YLabel:
- canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
- font=labelFont,color=labelColor,angle=90)
-
- labelFont=pid.Font(ttf="verdana",size=16,bold=0)
+ im_drawer.text(
+ text=YLabel,
+ xy=(19,
+ yTopOffset+plotHeight-(plotHeight-im_drawer.textsize(
+ YLabel,font=labelFont)[0])/2.0),
+ font=labelFont,fill=labelColor,angle=90)
+
+ labelFont=ImageFont.truetype(font=VERDANA_FILE,size=16)
if title:
- canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
- 20,font=labelFont,color=labelColor)
+ im_drawer.text(
+ text=title,
+ xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
+ title,font=labelFont)[0])/2.0,
+ 20),
+ font=labelFont,fill=labelColor)
# This function determines the scale of the plot
def detScaleOld(min,max):
@@ -265,16 +301,21 @@ def greenfunc(x):
def colorSpectrum(n=100):
multiple = 10
if n == 1:
- return [pid.Color(1,0,0)]
+ return [ImageColor.getrgb("rgb(100%,0%,0%)")]
elif n == 2:
- return [pid.Color(1,0,0),pid.Color(0,0,1)]
+ return [ImageColor.getrgb("100%,0%,0%)"),
+ ImageColor.getrgb("rgb(0%,0%,100%)")]
elif n == 3:
- return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
+ return [ImageColor.getrgb("rgb(100%,0%,0%)"),
+ ImageColor.getrgb("rgb(0%,100%,0%)"),
+ ImageColor.getrgb("rgb(0%,0%,100%)")]
N = n*multiple
out = [None]*N;
for i in range(N):
x = float(i)/N
- out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
+ out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format(
+ *[int(i*100) for i in (
+ redfunc(x), greenfunc(x), bluefunc(x))]))
out2 = [out[0]]
step = N/float(n-1)
j = 0
@@ -290,4 +331,4 @@ def _test():
if __name__=="__main__":
- _test() \ No newline at end of file
+ _test()
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 25846099..39067fc5 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 *
-from PIL import (ImageColor)
+from PIL import (Image,ImageDraw,ImageFont,ImageColor)
import sys,os
import cPickle
import httplib
@@ -70,6 +70,13 @@ DARKVIOLET = ImageColor.getrgb("darkviolet")
MEDIUMPURPLE = ImageColor.getrgb("mediumpurple")
# ---- END: Define common colours ---- #
+# ---- FONT FILES ---- #
+VERDANA_FILE = "fonts/ttf/verdana.ttf"
+TREBUC_FILE = "fonts/ttf/trebucbd.ttf"
+FNT_BS_FILE = "fonts/ttf/fnt_bs.ttf"
+ARIAL_FILE = "fonts/ttf/arial.ttf"
+# ---- END: FONT FILES ---- #
+
#########################################
# Inteval Mapping Plot Page
#########################################
@@ -487,21 +494,28 @@ class DisplayMappingResults(object):
# Plots goes here
################################################################
showLocusForm = ""
- intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight))
+ intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
with Bench("Drawing Plot"):
gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
self.gifmap = gifmap.__str__()
self.filename= webqtlUtil.genRandStr("Itvl_")
- intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png')
+ intCanvas.save(
+ "{}.png".format(
+ os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename)),
+ format='png')
intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
#Scales plot differently for high resolution
if self.draw2X:
- intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2))
+ intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2))
gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
- intCanvasX2.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename+"X2"), format='png')
+ intCanvasX2.save(
+ "{}.png".format(
+ os.path.join(webqtlConfig.GENERATED_IMAGE_DIR,
+ self.filename+"X2")),
+ format='png')
################################################################
# Outputs goes here
@@ -529,6 +543,7 @@ class DisplayMappingResults(object):
btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
+ im_drawer = ImageDraw.Draw(canvas)
#calculating margins
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
if self.multipleInterval:
@@ -622,6 +637,7 @@ class DisplayMappingResults(object):
return gifmap
def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
@@ -708,8 +724,10 @@ class DisplayMappingResults(object):
if item[1] > xLeftOffset+plotWidth:
item[1] = xLeftOffset+plotWidth
if item[0] != item[1]:
- canvas.drawRect(item[0], yZero, item[1], yZero - item[2]*bootHeightThresh/maxBootCount,
- fillColor=self.BOOTSTRAP_BOX_COLOR)
+ im_drawer.rectangle(
+ xy=((item[0], yZero),
+ (item[1], yZero - item[2]*bootHeightThresh/maxBootCount)),
+ fill=self.BOOTSTRAP_BOX_COLOR)
###draw boot scale
highestPercent = (maxBootCount*100.0)/nboot
@@ -718,26 +736,43 @@ class DisplayMappingResults(object):
bootScale = bootScale[:-1] + [highestPercent]
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 = 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)
+ bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom)
+ im_drawer.rectangle(
+ xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh),
+ (canvas.size[0]-bootOffset-15*zoom,yZero)),
+ fill = YELLOW)
+ im_drawer.line(
+ xy=((canvas.size[0]-bootOffset+4, yZero),
+ (canvas.size[0]-bootOffset, yZero)),
+ fill=BLACK)
+ im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+5), text='0%',
+ font=bootScaleFont, fill=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=BLACK)
- canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=BLACK)
+ im_drawer.line(
+ xy=((canvas.size[0]-bootOffset+4,bootY),
+ (canvas.size[0]-bootOffset,bootY)),
+ fill=BLACK)
+ im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+5),
+ text='%2.1f'%item, font=bootScaleFont, color=BLACK)
if self.legendChecked:
startPosY = 30
nCol = 2
- smallLabelFont = pid.Font(ttf="trebuc", size=12*fontZoom, bold=1)
+ smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
leftOffset = xLeftOffset+(nCol-1)*200
- 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)
+ im_drawer.rectangle(
+ xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)),
+ fill=YELLOW)
+ im_drawer.text(xy=(leftOffset+ 20, startPosY+5),
+ text='Frequency of the Peak LRS',
+ font=smallLabelFont, color=BLACK)
def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ im_drawer = ImageDraw.Draw(canvas)
if len(self.traitList) != 1:
return
@@ -805,12 +840,15 @@ 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=BLACK, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
+ im_drawer.polygon(
+ xy=traitPixel, outline=BLACK,
+ fill=self.TRANSCRIPT_LOCATION_COLOR#, closed=1
+ )
if self.legendChecked:
startPosY = 15
nCol = 2
- smallLabelFont = pid.Font(ttf="trebuc", size=12*fontZoom, bold=1)
+ smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
if self.manhattan_plot:
leftOffset = xLeftOffset
else:
@@ -819,6 +857,7 @@ class DisplayMappingResults(object):
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):
+ im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
return
@@ -856,12 +895,15 @@ class DisplayMappingResults(object):
if maxCount>0:
for i in range(xLeftOffset, xLeftOffset + plotWidth):
snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount)
- canvas.drawLine(i, drawSNPLocationY+(snpDensity)*zoom, i, drawSNPLocationY-(snpDensity)*zoom, color=self.SNP_COLOR, width=1)
+ im_drawer.line(
+ xy=((i, drawSNPLocationY+(snpDensity)*zoom),
+ (i, drawSNPLocationY-(snpDensity)*zoom)),
+ fill=self.SNP_COLOR, width=1)
def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
nameWidths = []
yPaddingTop = 10
- colorFont=pid.Font(ttf="trebuc",size=12,bold=1)
+ colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12)
if len(self.qtlresults) >20 and self.selectedChr > -1:
rightShift = 20
rightShiftStep = 60
@@ -880,11 +922,16 @@ class DisplayMappingResults(object):
rightShift += rightShiftStep
name = thisTrait.displayName()
- nameWidth = canvas.stringWidth(name,font=colorFont)
+ nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont)
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=BLACK)
+ im_drawer.rectangle(
+ xy=((rightShift,yPaddingTop+kstep*15),
+ (rectWidth+rightShift,yPaddingTop+10+kstep*15)),
+ fill=thisLRSColor)
+ im_drawer.text(
+ text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15),
+ font=colorFont,fill=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)
@@ -892,6 +939,7 @@ class DisplayMappingResults(object):
gifmap.areas.append(Areas)
def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
+ im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
@@ -900,45 +948,80 @@ class DisplayMappingResults(object):
if zoom == 2:
fontZoom = 1.5
- labelFont=pid.Font(ttf="trebuc",size=12*fontZoom, bold=1)
+ labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom)
startPosY = 15
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=BLACK)
+ im_drawer.line(
+ xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)),
+ fill=self.LRS_COLOR, width=2)
+ im_drawer.text(
+ text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+5),
+ font=labelFont,fill=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=BLACK)
+ im_drawer.line(
+ xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+ fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
+ im_drawer.line(
+ xy=((startPosX+18,startPosY),(startPosX+32,startPosY)),
+ fill=self.ADDITIVE_COLOR_NEGATIVE, width=2)
+ im_drawer.text(
+ text='Additive Effect',xy=(startPosX+40,startPosY+5),
+ font=labelFont,fill=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=BLACK)
+ im_drawer.line(
+ xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+ fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
+ im_drawer.line(
+ xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+ fill=self.DOMINANCE_COLOR_NEGATIVE, width=4)
+ im_drawer.text(
+ text='Dominance Effect', xy=(startPosX+42,startPosY+5),
+ font=labelFont,fill=BLACK)
if self.haplotypeAnalystChecked:
startPosY += stepPosY
startPosX = xLeftOffset
- canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.HAPLOTYPE_POSITIVE, width=4)
- 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=BLACK)
+ im_drawer.line(
+ xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+ fill=self.HAPLOTYPE_POSITIVE, width=4)
+ im_drawer.line(
+ xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+ fill=self.HAPLOTYPE_NEGATIVE, width=4)
+ im_drawer.line(
+ xy=((startPosX+36,startPosY),(startPosX+53,startPosY)),
+ fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
+ im_drawer.line(
+ xy=((startPosX+54,startPosY),(startPosX+67,startPosY)),
+ fill=self.HAPLOTYPE_RECOMBINATION, width=4)
+ im_drawer.text(
+ text='Haplotypes (Pat, Mat, Het, Unk)',
+ xy=(startPosX+76,startPosY+5),font=labelFont,fill=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=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)
+ im_drawer.line(
+ xy=((startPosX, startPosY),( startPosX + 32, startPosY)),
+ fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
+ im_drawer.line(
+ xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)),
+ fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
+ im_drawer.text(
+ text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant),
+ xy=(xLeftOffset+42,startPosY +5),font=labelFont,fill=BLACK)
+ im_drawer.text(
+ text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
+ xy=(xLeftOffset+42,startPosY + 5 +stepPosY),font=labelFont,
+ fill=BLACK)
+
+ labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom)
labelColor = BLACK
if self.dataset.type == "Publish" or self.dataset.type == "Geno":
dataset_label = self.dataset.fullname
@@ -1000,20 +1083,32 @@ class DisplayMappingResults(object):
identification += "Trait: %s" % (self.this_trait.name)
identification += " with %s samples" % (self.n_samples)
- d = 4+ max(canvas.stringWidth(identification, font=labelFont), canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
- canvas.drawString(identification,canvas.size[0] - xRightOffset-d,20*fontZoom,font=labelFont,color=labelColor)
- else:
- d = 4+ max(canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
- canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35*fontZoom,font=labelFont,color=labelColor)
- canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50*fontZoom,font=labelFont,color=labelColor)
- canvas.drawString(string3,canvas.size[0] - xRightOffset-d,65*fontZoom,font=labelFont,color=labelColor)
- if string4 != '':
- canvas.drawString(string4,canvas.size[0] - xRightOffset-d,80*fontZoom,font=labelFont,color=labelColor)
- canvas.drawString("Created at: " + str(datetime.datetime.now()).split('.')[0], canvas.size[0] - xRightOffset-d,95*fontZoom,font=labelFont,color=labelColor)
+ d = 4+ max(
+ im_drawer.textsize(identification, font=labelFont)[0],
+ im_drawer.textsize(string1, font=labelFont)[0],
+ im_drawer.textsize(string2, font=labelFont)[0])
+ im_drawer.text(
+ text=identification,
+ xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont,
+ fill=labelColor)
else:
- canvas.drawString("Created at: " + str(datetime.datetime.now()).split('.')[0], canvas.size[0] - xRightOffset-d,80*fontZoom,font=labelFont,color=labelColor)
+ d = 4+ max(
+ im_drawer.textsize(string1, font=labelFont)[0],
+ im_drawer.textsize(string2, font=labelFont)[0])
+ im_drawer.text(
+ text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom),
+ font=labelFont,fill=labelColor)
+ im_drawer.text(
+ text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom),
+ font=labelFont,fill=labelColor)
+ if string3 != '':
+ im_drawer.text(
+ text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom),
+ font=labelFont,fill=labelColor)
+
def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
return
@@ -1126,11 +1221,15 @@ class DisplayMappingResults(object):
#draw the detail view
if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
- utrColor = pid.Color(0.66, 0.66, 0.66)
- arrowColor = pid.Color(0.7, 0.7, 0.7)
+ utrColor = ImageColor.getrgb("rgb(66%, 66%, 66%)")
+ arrowColor = ImageColor.getrgb("rgb(70%, 70%, 70%)")
#draw the line that runs the entire length of the gene
- canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1)
+ im_drawer.line(
+ xy=(
+ (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom),
+ ( geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom)),
+ fill=outlineColor, width=1)
#draw the arrows
if geneEndPix - geneStartPix < 1:
@@ -1141,11 +1240,30 @@ class DisplayMappingResults(object):
if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0:
if strand == "+":
- canvas.drawLine(geneStartPix + xCoord, geneYLocation, geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
- canvas.drawLine(geneStartPix + xCoord, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH, geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom, color=arrowColor, width=1)
+ im_drawer.line(
+ xy=((geneStartPix + xCoord, geneYLocation),
+ (geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
+ geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom)),
+ fill=arrowColor, width=1)
+ im_drawer.line(
+ xy=((geneStartPix + xCoord,
+ geneYLocation + self.EACH_GENE_HEIGHT*zoom),
+ (geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH,
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
+ fill=arrowColor, width=1)
else:
- canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation, geneStartPix + xCoord, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
- canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord, geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+ im_drawer.line(
+ xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
+ geneYLocation),
+ ( geneStartPix + xCoord,
+ geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom)),
+ fill=arrowColor, width=1)
+ im_drawer.line(
+ xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
+ geneYLocation + self.EACH_GENE_HEIGHT*zoom),
+ ( geneStartPix + xCoord,
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom)),
+ fill=arrowColor, width=1)
#draw the blocks for the exon regions
for i in range(0, len(exonStarts)):
@@ -1159,7 +1277,10 @@ class DisplayMappingResults(object):
exonEndPix = xLeftOffset + plotWidth
if (exonStartPix > xLeftOffset + plotWidth):
exonStartPix = xLeftOffset + plotWidth
- canvas.drawRect(exonStartPix, geneYLocation, exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
+ im_drawer.rectangle(
+ xy=((exonStartPix, geneYLocation),
+ (exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom))),
+ outline = outlineColor, fill = fillColor)
#draw gray blocks for 3' and 5' UTR blocks
if cdsStart and cdsEnd:
@@ -1173,14 +1294,16 @@ class DisplayMappingResults(object):
utrEndPix = xLeftOffset + plotWidth
if (utrStartPix > xLeftOffset + plotWidth):
utrStartPix = xLeftOffset + plotWidth
- #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
if strand == "-":
labelText = "3'"
else:
labelText = "5'"
- canvas.drawString(labelText, utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
+ im_drawer.text(
+ text=labelText,
+ xy=(utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT),
+ font=ImageFont.truetype(font=ARIAL_FILE, size=2))
#the second UTR region
@@ -1194,18 +1317,23 @@ class DisplayMappingResults(object):
utrEndPix = xLeftOffset + plotWidth
if (utrStartPix > xLeftOffset + plotWidth):
utrStartPix = xLeftOffset + plotWidth
- #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
if strand == "-":
labelText = "5'"
else:
labelText = "3'"
- canvas.drawString(labelText, utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
+ im_drawer.text(
+ text=labelText,
+ xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT),
+ font=ImageFont.truetype(font=ARIAL_FILE, size=2))
#draw the genes as rectangles
else:
- canvas.drawRect(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
+ im_drawer.rectangle(
+ xy=((geneStartPix, geneYLocation),
+ (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom))),
+ outline= outlineColor, fill = fillColor)
COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
# NL: 06-02-2011 Rob required to display NCBI info in a new window
@@ -1354,12 +1482,22 @@ class DisplayMappingResults(object):
else:
mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
- 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))
+ im_drawer.line(
+ xy=((drawStart,
+ geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ (drawEnd,
+ geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom)),
+ fill= mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
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)
+ im_drawer.rectangle(
+ xy=((geneStartPix,
+ geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ (geneEndPix,
+ geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom)),
+ outline=outlineColor, fill=fillColor)
COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
@@ -1372,11 +1510,21 @@ class DisplayMappingResults(object):
if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0):
drawEnd = xLeftOffset + plotWidth - 6
mylineColor = self.HAPLOTYPE_RECOMBINATION
- canvas.drawLine(plotRight, 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))
+ im_drawer.line(
+ xy=((plotRight,
+ geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ (drawEnd,
+ geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom)),
+ fill= mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
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=BLACK, angle=-90)
+ im_drawer.text(
+ text="%s" % (_chr[j].name),
+ xy=(geneStartPix,
+ geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom),
+ font=ImageFont.truetype(font=VERDANA_FILE, size=12),
+ fill=BLACK, angle=-90)
oldgeneEndPix = geneEndPix;
oldgeno = _chr[j].genotype
@@ -1405,12 +1553,23 @@ 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=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)
+ im_drawer.text(
+ text="%s" % (samplelist[j]),
+ xy=((xLeftOffset + plotWidth + 10),
+ geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ font=ImageFont.truetype(font=VERDANA_FILE, size=12),
+ fill=BLACK)
+ im_drawer.text(
+ text="%2.2f" % (expr),
+ xy=((xLeftOffset + plotWidth + 60),
+ geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ font=ImageFont.truetype(font=VERDANA_FILE, size=12),
+ fill=BLACK)
## END HaplotypeAnalyst
def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1:
return
@@ -1426,7 +1585,7 @@ class DisplayMappingResults(object):
# but it makes the HTML huge, and takes forever to render the page in the first place)
# Draw the bands that you can click on to go to UCSC / Ensembl
MAX_CLICKABLE_REGION_DIVISIONS = 100
- clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
+ clickableRegionLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=9)
pixelStep = max(5, int(float(plotWidth)/MAX_CLICKABLE_REGION_DIVISIONS))
# pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome.
@@ -1463,8 +1622,14 @@ class DisplayMappingResults(object):
WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
- canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
- canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+ im_drawer.rectangle(
+ xy=((xBrowse1, paddingTop),
+ (xBrowse2, (paddingTop + self.BAND_HEIGHT))),
+ outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
+ fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
+ im_drawer.line(
+ xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+ fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))
@@ -1474,8 +1639,14 @@ class DisplayMappingResults(object):
PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
- canvas.drawRect(xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_PHENOGEN_REGION_COLOR, fillColor=self.CLICKABLE_PHENOGEN_REGION_COLOR)
- canvas.drawLine(xBrowse1, phenogenPaddingTop, xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
+ im_drawer.rectangle(
+ xy=((xBrowse1, phenogenPaddingTop),
+ (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))),
+ outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
+ fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
+ im_drawer.line(
+ xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
+ fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
@@ -1484,8 +1655,15 @@ class DisplayMappingResults(object):
UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
- canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
- canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
+ im_drawer.rectangle(
+ xy=((xBrowse1, ucscPaddingTop),
+ (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))),
+ outline=self.CLICKABLE_UCSC_REGION_COLOR,
+ fill=self.CLICKABLE_UCSC_REGION_COLOR)
+ im_drawer.line(
+ xy=((xBrowse1, ucscPaddingTop),
+ (xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT))),
+ fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
@@ -1494,32 +1672,59 @@ class DisplayMappingResults(object):
ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
- canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
- canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
+ im_drawer.rectangle(
+ xy=((xBrowse1, ensemblPaddingTop),
+ (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))),
+ outline=self.CLICKABLE_ENSEMBL_REGION_COLOR,
+ fill=self.CLICKABLE_ENSEMBL_REGION_COLOR)
+ im_drawer.line(
+ xy=((xBrowse1, ensemblPaddingTop),
+ (xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT))),
+ fill=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
# end for
- canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
+ im_drawer.text(
+ text="Click to view the corresponding section of the genome in an 8x expanded WebQTL map",
+ xy=((xLeftOffset + 10), paddingTop + self.BAND_HEIGHT/2),
+ font=clickableRegionLabelFont,
+ fill=self.CLICKABLE_WEBQTL_TEXT_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- canvas.drawString("Click to view the corresponding section of the genome in PhenoGen", (xLeftOffset + 10), phenogenPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_PHENOGEN_TEXT_COLOR)
- canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
- canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
+ im_drawer.text(
+ text="Click to view the corresponding section of the genome in PhenoGen",
+ xy=((xLeftOffset + 10), phenogenPaddingTop + self.BAND_HEIGHT/2),
+ font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR)
+ im_drawer.text(
+ text="Click to view the corresponding section of the genome in the UCSC Genome Browser",
+ xy=((xLeftOffset + 10), ucscPaddingTop + self.BAND_HEIGHT/2),
+ font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR)
+ im_drawer.text(
+ text="Click to view the corresponding section of the genome in the Ensembl Genome Browser",
+ xy=((xLeftOffset+10), ensemblPaddingTop + self.BAND_HEIGHT/2),
+ font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
#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 - 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=GRAY)
+ chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26*zoom)
+ traitFont = ImageFont.truetype(font=VERDANA_FILE, size=14)
+ chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize(
+ "Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0]
+ im_drawer.text(
+ text="Chr %s" % self.ChrList[self.selectedChr][0],
+ xy=(chrX, ensemblPaddingTop-5), font=chrFont, fill=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=GRAY)
+ chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26*zoom)
+ traitFont = ImageFont.truetype(font=VERDANA_FILE, size=14)
+ chrX = xLeftOffset + (plotWidth - im_drawer.textsize(
+ "Chr %s" % currentChromosome, font=chrFont)[0])/2
+ im_drawer.text(
+ text="Chr %s" % currentChromosome, xy=(chrX, 32), font=chrFont,
+ fill=GRAY)
# end of drawBrowserClickableRegions
pass
def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
@@ -1535,7 +1740,7 @@ class DisplayMappingResults(object):
X_AXIS_THICKNESS = 1*zoom
# ======= Alex: Draw the X-axis labels (megabase location)
- MBLabelFont = pid.Font(ttf="verdana", size=15*zoom, bold=0)
+ MBLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=15*zoom)
xMajorTickHeight = 10 * zoom # How high the tick extends below the axis
xMinorTickHeight = 5*zoom
xAxisTickMarkColor = BLACK
@@ -1544,7 +1749,7 @@ class DisplayMappingResults(object):
spacingFromLabelToAxis = 5
if self.plotScale == 'physic':
- strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
+ strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height
###Physical single chromosome view
if self.selectedChr > -1:
XScale = Plot.detScale(startMb, endMb)
@@ -1565,13 +1770,21 @@ class DisplayMappingResults(object):
continue
Xc = xLeftOffset + plotXScale*(_Mb - startMb)
if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
- canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
+ im_drawer.line(xy=((Xc,yZero),
+ (Xc,yZero+xMajorTickHeight)),
+ fill=xAxisTickMarkColor,
+ width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
- strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
+ strWidth, strHeight = im_drawer.textsize(labelStr, font=MBLabelFont)
drawStringXc = (Xc - (strWidth / 2.0))
- canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
+ im_drawer.text(xy=(drawStringXc, strYLoc),
+ text=labelStr, font=MBLabelFont,
+ fill=xAxisLabelColor)
else:
- canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
+ im_drawer.line(xy=((Xc,yZero),
+ (Xc,yZero+xMinorTickHeight)),
+ fill=xAxisTickMarkColor,
+ width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
###Physical genome wide view
else:
@@ -1586,17 +1799,27 @@ 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=BLACK, width=1*zoom)
+ im_drawer.line(
+ xy=((startPosX+tickdists*plotXScale, yZero),
+ (startPosX+tickdists*plotXScale, yZero + 7)),
+ fill=BLACK, width=1*zoom)
if j % 2 == 0:
- canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=BLACK, font=MBLabelFont, angle=270)
+ im_drawer.text(
+ xy=(startPosX+tickdists*plotXScale, yZero+10*zoom),
+ text=str(tickdists), fill=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=BLACK)
+ megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
+ im_drawer.text(
+ text="Megabases",
+ xy=(
+ xLeftOffset+(plotWidth-im_drawer.textsize(
+ "Megabases",font=megabaseLabelFont)[0])/2,
+ strYLoc+MBLabelFont.font.height+10*(zoom%2)+ 10),
+ font=megabaseLabelFont, fill=BLACK)
pass
else:
- strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont) + 8
+ strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height + 8
ChrAInfo = []
preLpos = -1
distinctCount = 0.0
@@ -1659,18 +1882,26 @@ class DisplayMappingResults(object):
else:
Zorder = 0
if differ:
- canvas.drawLine(startPosX+Lpos,yZero,xLeftOffset+offsetA,\
- yZero+25, color=lineColor)
- canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\
- yZero+40+Zorder*(LRectWidth+3),color=lineColor)
+ im_drawer.line(
+ xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\
+ yZero+25)),
+ fill=lineColor)
+ im_drawer.line(
+ xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\
+ yZero+40+Zorder*(LRectWidth+3))),
+ fill=lineColor)
rectColor = ORANGE
else:
- canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\
- xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor)
+ im_drawer.line(
+ xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\
+ xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))),
+ fill=lineColor)
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)
+ im_drawer.rectangle(
+ xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)),
+ (xLeftOffset+offsetA-LRectHeight,
+ yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
+ outline=rectColor,fill=rectColor,width = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
@@ -1679,17 +1910,25 @@ class DisplayMappingResults(object):
gifmap.areas.append(Areas)
##piddle bug
if j == 0:
- canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
+ im_drawer.line(
+ xy=((startPosX,yZero),(startPosX,yZero+40)),
+ fill=lineColor)
startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
- 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=BLACK)
+ centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=18*zoom*1.5)
+ im_drawer.text(
+ text="Centimorgans",
+ xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
+ "Megabases", font=centimorganLabelFont)[0])/2,
+ strYLoc + MBLabelFont.font.height+ 10*(zoom%2) + 10),
+ font=centimorganLabelFont, fill=BLACK)
- canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
+ im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)),
+ fill=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):
+ im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
@@ -1787,29 +2026,40 @@ class DisplayMappingResults(object):
else:
all_int = False
break
-
- if all_int:
- max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 40
- else:
- max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30
+ # TODO(PIL): Convert from PIL
+ # if all_int:
+ # max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 40
+ # else:
+ # max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30
#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=BLACK, angle=90)
+ LRSScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
+ LRSLODFont=ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
+ yZero = yTopOffset + plotHeight
+
+ im_drawer.text(
+ text=self.LRS_LOD,
+ xy=(xLeftOffset - im_drawer.textsize("999.99", font=LRSScaleFont)[0] - 15*(zoom-1),
+ yZero - 150 - 300*(zoom - 1)),
+ font=LRSLODFont, fill=BLACK, angle=90)
for item in LRSAxisList:
if LRS_LOD_Max == 0.0:
LRS_LOD_Max = 0.000001
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)
+ im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)),
+ fill=self.LRS_COLOR, width=1*zoom)
if all_int:
scaleStr = "%d" % item
else:
scaleStr = "%2.1f" % item
#Draw the LRS/LOD Y axis label
- canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)
+ im_drawer.text(
+ text=scaleStr,
+ xy=(xLeftOffset-4-im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5,
+ yLRS+3),
+ font=LRSScaleFont, fill=self.LRS_COLOR)
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max
@@ -1824,10 +2074,19 @@ class DisplayMappingResults(object):
#ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist):
rightEdge = int(start_pos_x + chr_length_dist*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
- canvas.drawLine(start_pos_x+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
- width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
- canvas.drawLine(start_pos_x+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
- width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
+ im_drawer.line(
+ xy=((start_pos_x+self.SUGGESTIVE_WIDTH/1.5, suggestiveY),
+ (rightEdge, suggestiveY)),
+ fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH*zoom
+ #,clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
+ )
+ im_drawer.line(
+ xy=((start_pos_x+self.SUGGESTIVE_WIDTH/1.5, significantY),
+ (rightEdge, significantY)),
+ fill=self.SIGNIFICANT_COLOR,
+ width=self.SIGNIFICANT_WIDTH*zoom
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
+ )
sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY-2, rightEdge + 2*zoom, significantY+2)
if self.LRS_LOD == 'LRS':
@@ -1868,7 +2127,7 @@ class DisplayMappingResults(object):
AdditiveCoordXY = []
DominanceCoordXY = []
- symbolFont = pid.Font(ttf="fnt_bs", size=5,bold=0) #ZS: For Manhattan Plot
+ symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) #ZS: For Manhattan Plot
previous_chr = 1
previous_chr_as_int = 0
@@ -1880,7 +2139,12 @@ class DisplayMappingResults(object):
thisLRSColor = self.colorCollection[0]
if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
if self.manhattan_plot != True:
- canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.polygon(
+ xy=LRSCoordXY,
+ outline=thisLRSColor
+ # , closed=0, edgeWidth=lrsEdgeWidth,
+ # clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
if not self.multipleInterval and self.additiveChecked:
plusColor = self.ADDITIVE_COLOR_POSITIVE
@@ -1895,22 +2159,58 @@ class DisplayMappingResults(object):
else:
Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
if Yc0 < yZero:
- canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xcm, yZero)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
+ im_drawer.line(
+ xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero-(Yc0-yZero)),
+ (Xcm, yZero)),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
+ im_drawer.line(
+ xy=((Xcm, yZero), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
elif (Yc0-yZero)*(Yc-yZero) > 0:
if Yc < yZero:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xc, Yc)),
+ fill=plusColor,
+ width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)),
+ (Xc, yZero - (Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
minYc = min(Yc-yZero, Yc0-yZero)
if minYc < 0:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)),
+ (Xc, yZero - (Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
LRSCoordXY = []
AdditiveCoordXY = []
@@ -1979,15 +2279,12 @@ class DisplayMappingResults(object):
point_color = RED
else:
point_color = BLUE
-
- final_x_pos = Xc-canvas.stringWidth("5",font=symbolFont)/2+1
- if final_x_pos > (xLeftOffset + plotWidth):
- continue
- #break ZS: This is temporary until issue with sorting for GEMMA is fixed
- elif final_x_pos < xLeftOffset:
- continue
- else:
- canvas.drawString("5", final_x_pos,Yc+2,color=point_color, font=symbolFont)
+ im_drawer.text(
+ text="5",
+ xy=(
+ Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1,
+ Yc+2),
+ fill=point_color, font=symbolFont)
else:
LRSCoordXY.append((Xc, Yc))
@@ -2000,7 +2297,11 @@ class DisplayMappingResults(object):
m += 1
if self.manhattan_plot != True:
- canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.polygon(
+ xy=LRSCoordXY,
+ outline=thisLRSColor
+ #, closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
if not self.multipleInterval and self.additiveChecked:
plusColor = self.ADDITIVE_COLOR_POSITIVE
@@ -2015,22 +2316,57 @@ class DisplayMappingResults(object):
else:
Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
if Yc0 < yZero:
- canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xcm, yZero)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
+ im_drawer.line(
+ xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)),
+ (Xcm, yZero)),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
+ im_drawer.line(
+ xy=((Xcm, yZero), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
elif (Yc0-yZero)*(Yc-yZero) > 0:
if Yc < yZero:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor,
+ width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0,yZero-(Yc0-yZero)),
+ (Xc,yZero-(Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
minYc = min(Yc-yZero, Yc0-yZero)
if minYc < 0:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)),
+ (Xc, yZero - (Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
plusColor = self.DOMINANCE_COLOR_POSITIVE
@@ -2045,27 +2381,61 @@ class DisplayMappingResults(object):
else:
Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
if Yc0 < yZero:
- canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xcm, yZero)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
+ im_drawer.line(
+ xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)), (Xcm, yZero)),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
+ im_drawer.line(
+ xy=((Xcm, yZero), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
elif (Yc0-yZero)*(Yc-yZero) > 0:
if Yc < yZero:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)),
+ (Xc, yZero - (Yc-yZero))),
+ fill=minusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
minYc = min(Yc-yZero, Yc0-yZero)
if minYc < 0:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, Yc0), (Xc, Yc)),
+ fill=plusColor, width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ im_drawer.line(
+ xy=((Xc0, yZero - (Yc0-yZero)),
+ (Xc, yZero - (Yc-yZero))), fill=minusColor,
+ width=lineWidth
+ #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ )
###draw additive scale
if not self.multipleInterval and self.additiveChecked:
- additiveScaleFont=pid.Font(ttf="verdana",size=16*zoom,bold=0)
+ additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom)
additiveScale = Plot.detScaleOld(0,additiveMax)
additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
@@ -2074,13 +2444,24 @@ class DisplayMappingResults(object):
additiveAxisList.append(additiveScale[1])
for item in additiveAxisList:
additiveY = yZero - item*addPlotScale
- canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
+ im_drawer.line(
+ xy=((xLeftOffset + plotWidth,additiveY),
+ (xLeftOffset+4+ plotWidth,additiveY)),
+ fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
scaleStr = "%2.3f" % item
- canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE)
+ im_drawer.text(
+ text=scaleStr,
+ xy=(xLeftOffset + plotWidth +6,additiveY+5),
+ font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE)
- canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
+ im_drawer.line(
+ xy=((xLeftOffset+plotWidth,additiveY),
+ (xLeftOffset+plotWidth,yZero)),
+ fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
- canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset + 30*(zoom - 1), color=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis
+ im_drawer.line(
+ xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30*(zoom - 1))),
+ fill=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis
def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None):
@@ -2088,6 +2469,7 @@ class DisplayMappingResults(object):
##multiple Chromosome view
##single Chromosome Physical
##single Chromosome Genetic
+ im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
@@ -2114,8 +2496,10 @@ class DisplayMappingResults(object):
else:
theBackColor = self.GRAPH_BACK_LIGHT_COLOR
i += 1
- canvas.drawRect(startPix, yTopOffset, min(startPix+spacingAmt, xLeftOffset+plotWidth), \
- yBottom, edgeColor=theBackColor, fillColor=theBackColor)
+ im_drawer.rectangle(
+ [(startPix, yTopOffset),
+ (min(startPix+spacingAmt, xLeftOffset+plotWidth), yBottom)],
+ outline=theBackColor, fill=theBackColor)
drawRegionDistance = self.ChrLengthDistList[self.ChrList[self.selectedChr][1]]
self.ChrLengthDistList = [drawRegionDistance]
@@ -2132,7 +2516,7 @@ class DisplayMappingResults(object):
chrFontZoom = 2
else:
chrFontZoom = 1
- chrLabelFont=pid.Font(ttf="verdana",size=24*chrFontZoom,bold=0)
+ chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom)
for i, _chr in enumerate(self.genotype):
if (i % 2 == 0):
@@ -2141,14 +2525,18 @@ class DisplayMappingResults(object):
theBackColor = self.GRAPH_BACK_LIGHT_COLOR
#draw the shaded boxes and the sig/sug thick lines
- canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \
- yBottom, edgeColor=GAINSBORO,fillColor=theBackColor)
+ im_drawer.rectangle(
+ ((startPosX, yTopOffset),
+ (startPosX + self.ChrLengthDistList[i]*plotXScale, yBottom)),
+ outline=GAINSBORO,
+ fill=theBackColor)
- chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont)
+ chrNameWidth, chrNameHeight = im_drawer.textsize(_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=BLACK)
+ im_drawer.text(xy=(chrStartPix, yTopOffset + 20),
+ text=_chr.name, font=chrLabelFont, fill=BLACK)
COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
#add by NL 09-03-2010
@@ -2164,7 +2552,7 @@ class DisplayMappingResults(object):
#########################################
# Permutation Graph
#########################################
- myCanvas = pid.PILCanvas(size=(500,300))
+ myCanvas = Image.new("RGBA", size=(500, 300))
if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS":
perm_output = [value*4.61 for value in self.perm_output]
elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD":
@@ -2174,7 +2562,8 @@ class DisplayMappingResults(object):
filename= webqtlUtil.genRandStr("Reg_")
Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test')
- myCanvas.save(GENERATED_IMAGE_DIR+filename, format='gif')
+ myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR+filename),
+ format='gif')
return filename
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 15:38:25 +0000