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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
from htmlgen import HTMLgen2 as HT
from utility import Plot
from base.templatePage import templatePage
from utility import webqtlUtil
from base import webqtlConfig
#########################################
# Category Graph Page
#########################################
class CategoryGraphPage(templatePage):
def __init__(self, fd):
LRSFullThresh = 30
LRSInteractThresh = 25
maxPlotSize = 800
mainfmName = webqtlUtil.genRandStr("fm_")
templatePage.__init__(self, fd)
if not fd.genotype:
fd.readData()
##Remove F1 and Parents
fd.genotype = fd.genotype_1
plotType = fd.formdata.getvalue('plotType')
self.dict['title'] = '%s Plot' % plotType
main_title = HT.Paragraph("%s Plot" % plotType)
main_title.__setattr__("class","title")
interval1 = fd.formdata.getvalue('interval1')
interval2 = fd.formdata.getvalue('interval2')
flanka1, flanka2, chram = string.split(interval1)
flankb1, flankb2, chrbm = string.split(interval2)
traitValues = string.split(fd.formdata.getvalue('traitValues'), ',')
traitValues = map(webqtlUtil.StringAsFloat, traitValues)
traitStrains = string.split(fd.formdata.getvalue('traitStrains'), ',')
flankaGeno = []
flankbGeno = []
for chr in fd.genotype:
for locus in chr:
if locus.name in (flanka1, flankb1):
if locus.name == flanka1:
flankaGeno = locus.genotype[:]
else:
flankbGeno = locus.genotype[:]
if flankaGeno and flankbGeno:
break
flankaDict = {}
flankbDict = {}
for i in range(len(fd.genotype.prgy)):
flankaDict[fd.genotype.prgy[i]] = flankaGeno[i]
flankbDict[fd.genotype.prgy[i]] = flankbGeno[i]
BB = []
BD = []
DB = []
DD = []
iValues = []
for i in range(len(traitValues)):
if traitValues[i] != None:
iValues.append(traitValues[i])
thisstrain = traitStrains[i]
try:
a1 = flankaDict[thisstrain]
b1 = flankbDict[thisstrain]
except:
continue
if a1 == -1.0:
if b1 == -1.0:
BB.append((thisstrain, traitValues[i]))
elif b1 == 1.0:
BD.append((thisstrain, traitValues[i]))
elif a1 == 1.0:
if b1 == -1.0:
DB.append((thisstrain, traitValues[i]))
elif b1 == 1.0:
DD.append((thisstrain, traitValues[i]))
else:
pass
#print BB, BD, DB, DD, max(iValues), min(iValues)
plotHeight = 400
plotWidth = 600
xLeftOffset = 60
xRightOffset = 40
yTopOffset = 40
yBottomOffset = 60
canvasHeight = plotHeight + yTopOffset + yBottomOffset
canvasWidth = plotWidth + xLeftOffset + xRightOffset
canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
XXX = [('Mat/Mat', BB), ('Mat/Pat', BD), ('Pat/Mat', DB), ('Pat/Pat', DD)]
XLabel = "Interval 1 / Interval 2"
if plotType == "Box":
Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel = XLabel)
else:
#Could be a separate function, but seems no other uses
max_Y = max(iValues)
min_Y = min(iValues)
scaleY = Plot.detScale(min_Y, max_Y)
Yll = scaleY[0]
Yur = scaleY[1]
nStep = scaleY[2]
stepY = (Yur - Yll)/nStep
stepYPixel = plotHeight/(nStep)
canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
##draw Y Scale
YYY = Yll
YCoord = plotHeight + yTopOffset
scaleFont=pid.Font(ttf="cour",size=11,bold=1)
for i in range(nStep+1):
strY = Plot.cformat(d=YYY, rank=0)
YCoord = max(YCoord, yTopOffset)
canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont)
YYY += stepY
YCoord -= stepYPixel
##draw X Scale
stepX = plotWidth/len(XXX)
XCoord = xLeftOffset + 0.5*stepX
YCoord = plotHeight + yTopOffset
scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
for item in XXX:
itemname, itemvalue = item
canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,YCoord +20,font=labelFont)
itemvalue.sort(webqtlUtil.cmpOrder2)
j = 0
for item2 in itemvalue:
tstrain, tvalue = item2
canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
if j % 2 == 0:
canvas.drawString(tstrain, XCoord+5, plotHeight + yTopOffset - \
(tvalue-Yll)*plotHeight/(Yur - Yll) +5, font=scaleFont, color=pid.blue)
else:
canvas.drawString(tstrain, XCoord-canvas.stringWidth(tstrain,font=scaleFont)-5, \
plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll) +5, font=scaleFont, color=pid.blue)
j += 1
XCoord += stepX
labelFont=pid.Font(ttf="verdana",size=18,bold=0)
canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, YCoord +40, font=labelFont)
canvas.drawString("Value",xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth("Value",font=labelFont))/2.0, font=labelFont, angle =90)
filename= webqtlUtil.genRandStr("Cate_")
canvas.save(webqtlConfig.IMGDIR+filename, format='gif')
img=HT.Image('/image/'+filename+'.gif',border=0)
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign='top')
TD_LR.append(main_title, HT.Center(img))#, traitValues , len(traitValues), traitStrains, len(traitStrains), len(fd.genotype.prgy))
#TD_LR.append(main_title, HT.BR(), flanka1, flanka2, chram, HT.BR(), flankb1, flankb2, chrbm)
self.dict['body'] = str(TD_LR)
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