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Diffstat (limited to 'web/webqtl/pairScan/CategoryGraphPage.py')
| -rwxr-xr-x | web/webqtl/pairScan/CategoryGraphPage.py | 199 |
1 files changed, 0 insertions, 199 deletions
diff --git a/web/webqtl/pairScan/CategoryGraphPage.py b/web/webqtl/pairScan/CategoryGraphPage.py deleted file mode 100755 index 696c05ce..00000000 --- a/web/webqtl/pairScan/CategoryGraphPage.py +++ /dev/null @@ -1,199 +0,0 @@ -# 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) - - - |