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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
import string
import piddle as pid
import os
from htmlgen import HTMLgen2 as HT
import direct
from utility import Plot
from base.templatePage import templatePage
from utility import webqtlUtil
from base import webqtlConfig
#########################################
# PairPlotPage
#########################################
class PairPlotPage(templatePage):
def __init__(self, fd):
LRSFullThresh = 30
LRSInteractThresh = 25
maxPlotSize = 1000
mainfmName = webqtlUtil.genRandStr("fm_")
templatePage.__init__(self, fd)
self.dict['title'] = 'Pair-Scan Plot'
if not self.openMysql():
return
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
vals = fd.formdata.getvalue('idata')
vals = map(float,string.split(vals,','))
strains = fd.formdata.getvalue('istrain')
strains = string.split(strains,',')
Chr_A = int(fd.formdata.getvalue('Chr_A'))
Chr_B = int(fd.formdata.getvalue('Chr_B'))
if len(vals) > webqtlConfig.KMININFORMATIVE:
d = direct.exhaust(webqtlConfig.GENODIR, vals, strains, fd.RISet, Chr_A, Chr_B)#XZ, 08/14/2008: add module name webqtlConfig
chrsInfo = d[2]
longerChrLen = max(chrsInfo[Chr_A][0], chrsInfo[Chr_B][0])
shorterChrlen = min(chrsInfo[Chr_A][0], chrsInfo[Chr_B][0])
plotHeight = int(chrsInfo[Chr_B][0]*maxPlotSize/longerChrLen)
plotWidth = int(chrsInfo[Chr_A][0]*maxPlotSize/longerChrLen)
xLeftOffset = 200
xRightOffset = 40
yTopOffset = 40
yBottomOffset = 200
colorAreaWidth = 120
canvasHeight = plotHeight + yTopOffset + yBottomOffset
canvasWidth = plotWidth + xLeftOffset + xRightOffset + colorAreaWidth
canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
plotScale = plotHeight/chrsInfo[Chr_B][0]
rectInfo = d[1]
finecolors = Plot.colorSpectrum(250)
finecolors.reverse()
#draw LRS Full
for item in rectInfo:
LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
if Chr_A > Chr_B:
colorIndex = int(LRSFull *250 /LRSFullThresh)
else:
colorIndex = int(LRSInteract *250 /LRSInteractThresh)
if colorIndex >= 250:
colorIndex = 249
elif colorIndex < 0:
colorIndex = 0
dcolor = finecolors[colorIndex]
if chra != chrb or (abs(chrbe - chrae) > 10 and abs(chrbs - chras) > 10):
canvas.drawRect(xLeftOffset+chras*plotScale,yTopOffset+plotHeight- \
chrbs*plotScale,xLeftOffset+chrae*plotScale,yTopOffset+plotHeight- \
chrbe*plotScale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
elif chrbs >= chras:
canvas.drawPolygon([(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbs*plotScale),\
(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbe*plotScale),\
(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbe*plotScale)],\
edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
else:
canvas.drawPolygon([(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbs*plotScale),\
(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbs*plotScale), \
(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbe*plotScale)], \
edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
labelFont=pid.Font(ttf="verdana",size=24,bold=0)
chrName = "chromosome %s" % chrsInfo[Chr_A][1]
canvas.drawString(chrName,xLeftOffset + (plotWidth - canvas.stringWidth(chrName,font=labelFont))/2,\
yTopOffset+plotHeight+ 170,font=labelFont)
chrName = "chromosome %s" % chrsInfo[Chr_B][1]
canvas.drawString(chrName, 30, yTopOffset +(canvas.stringWidth(chrName,font=labelFont) + plotHeight)/2,\
font=labelFont, angle = 90)
if Chr_A == Chr_B:
infoStr = "minimum distance = 10 cM"
infoStrWidth = canvas.stringWidth(infoStr,font=labelFont)
canvas.drawString(infoStr, xLeftOffset + (plotWidth-infoStrWidth*0.707)/2, yTopOffset + \
(plotHeight+infoStrWidth*0.707)/2,font=labelFont, angle = 45, color=pid.red)
labelFont=pid.Font(ttf="verdana",size=12,bold=0)
gifmap = HT.Map(name='markerMap')
lineColor = pid.lightblue
#draw ChrA Loci
ChrAInfo = d[3]
preLpos = -1
i = 0
for item in ChrAInfo:
Lname,Lpos = item
if Lpos != preLpos:
i += 1
preLpos = Lpos
stepA = float(plotWidth)/i
offsetA = -stepA
LRectWidth = 10
LRectHeight = 3
i = 0
preLpos = -1
for item in ChrAInfo:
Lname,Lpos = item
if Lpos != preLpos:
offsetA += stepA
differ = 1
else:
differ = 0
preLpos = Lpos
Lpos *= plotScale
Zorder = i % 5
"""
LStrWidth = canvas.stringWidth(Lname,font=labelFont)
canvas.drawString(Lname,xLeftOffset+offsetA+4,yTopOffset+plotHeight+140,\
font=labelFont,color=pid.blue,angle=90)
canvas.drawLine(xLeftOffset+Lpos,yTopOffset+plotHeight,xLeftOffset+offsetA,\
yTopOffset+plotHeight+25,color=lineColor)
canvas.drawLine(xLeftOffset+offsetA,yTopOffset+plotHeight+25,xLeftOffset+offsetA,\
yTopOffset+plotHeight+140-LStrWidth,color=lineColor)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA+4,yTopOffset+plotHeight+140,\
xLeftOffset+offsetA-6,yTopOffset+plotHeight+140-LStrWidth)
"""
if differ:
canvas.drawLine(xLeftOffset+Lpos,yTopOffset+plotHeight,xLeftOffset+offsetA,\
yTopOffset+plotHeight+25,color=lineColor)
canvas.drawLine(xLeftOffset+offsetA,yTopOffset+plotHeight+25,xLeftOffset+offsetA,\
yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),color=lineColor)
rectColor = pid.orange
else:
canvas.drawLine(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)-3,\
xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),color=lineColor)
rectColor = pid.deeppink
canvas.drawRect(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA-LRectHeight,yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)+LRectWidth,\
edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA-LRectHeight,yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)+LRectWidth)
HREF="javascript:showTrait('%s','%s');" % (mainfmName, Lname)
Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
gifmap.areas.append(Areas)
i += 1
#print (i , offsetA, Lname, Lpos, preLpos)
#print "<BR>"
#draw ChrB Loci
ChrBInfo = d[4]
preLpos = -1
i = 0
for item in ChrBInfo:
Lname,Lpos = item
if Lpos != preLpos:
i += 1
preLpos = Lpos
stepB = float(plotHeight)/i
offsetB = -stepB
LRectWidth = 10
LRectHeight = 3
i = 0
preLpos = -1
for item in ChrBInfo:
Lname,Lpos = item
if Lpos != preLpos:
offsetB += stepB
differ = 1
else:
differ = 0
preLpos = Lpos
Lpos *= plotScale
Zorder = i % 5
Lname,Lpos = item
Lpos *= plotScale
"""
LStrWidth = canvas.stringWidth(Lname,font=labelFont)
canvas.drawString(Lname, 45,yTopOffset+plotHeight-offsetB+4,font=labelFont,color=pid.blue)
canvas.drawLine(45+LStrWidth,yTopOffset+plotHeight-offsetB,xLeftOffset-25,\
yTopOffset+plotHeight-offsetB,color=lineColor)
canvas.drawLine(xLeftOffset-25,yTopOffset+plotHeight-offsetB,xLeftOffset,\
yTopOffset+plotHeight-Lpos,color=lineColor)
COORDS = "%d,%d,%d,%d" %(45,yTopOffset+plotHeight-offsetB+4,45+LStrWidth,\
yTopOffset+plotHeight-offsetB-6)
"""
if differ:
canvas.drawLine(xLeftOffset,yTopOffset+plotHeight-Lpos, xLeftOffset-25,\
yTopOffset+plotHeight-offsetB,color=lineColor)
canvas.drawLine(xLeftOffset -25, yTopOffset+plotHeight-offsetB, \
xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB, color=lineColor)
rectColor = pid.orange
else:
canvas.drawLine(xLeftOffset -80 -Zorder*(LRectWidth+3)+3, yTopOffset+plotHeight-offsetB, \
xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB, color=lineColor)
rectColor = pid.deeppink
HREF = "javascript:showTrait('%s','%s');" % (mainfmName, Lname)
canvas.drawRect(xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB,\
xLeftOffset-80 -Zorder*(LRectWidth+3)-LRectWidth,yTopOffset+plotHeight-offsetB +LRectHeight,\
edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB,\
xLeftOffset-80 -Zorder*(LRectWidth+3)-LRectWidth,yTopOffset+plotHeight-offsetB +LRectHeight)
Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
gifmap.areas.append(Areas)
i += 1
canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight,edgeColor=pid.black)
#draw spectrum
i = 0
labelFont=pid.Font(ttf="tahoma",size=14,bold=0)
middleoffsetX = 80
for dcolor in finecolors:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 , plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
if i % 50 == 0:
if Chr_A >= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSFullThresh*i/250.0),xLeftOffset+ plotWidth +middleoffsetX+22,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
if Chr_A <= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX-20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSInteractThresh*i/250.0),xLeftOffset+plotWidth+middleoffsetX-40,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
i += 1
#draw spectrum label
labelFont2=pid.Font(ttf="verdana",size=20,bold=0)
if i % 50 == 0:
i -= 1
if Chr_A >= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSFullThresh*(i+1)/250.0),xLeftOffset+ plotWidth +middleoffsetX+22,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
canvas.drawString('LRS Full',xLeftOffset+ plotWidth +middleoffsetX+50,plotHeight + yTopOffset, \
font = labelFont2,color=pid.dimgray,angle=90)
if Chr_A <= Chr_B:
canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX-20,plotHeight + yTopOffset - i, color=pid.black)
canvas.drawString('%d' % int(LRSInteractThresh*(i+1)/250.0),xLeftOffset+ plotWidth+middleoffsetX-40,\
plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
canvas.drawString('LRS Interaction',xLeftOffset+ plotWidth +middleoffsetX-50,\
plotHeight + yTopOffset, font = labelFont2,color=pid.dimgray,angle=90)
filename= webqtlUtil.genRandStr("Pair_")
canvas.save(webqtlConfig.IMGDIR+filename, format='png')
img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#markerMap')
main_title = HT.Paragraph("Pair-Scan Results: Chromosome Pair")
main_title.__setattr__("class","title")
form = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', \
name=mainfmName, submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet, 'incparentsf1':'on'}
if fd.incparentsf1:
hddn['incparentsf1']='ON'
for key in hddn.keys():
form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
form.append(img2,gifmap)
TD_LR.append(main_title, HT.Center(form), HT.P())
else:
heading = "Direct Plot"
detail = ['Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted.'\
% (webqtlConfig.KMININFORMATIVE, fd.RISet)]
self.error(heading=heading,detail=detail)
return
self.dict['body'] = str(TD_LR)
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