diff options
Diffstat (limited to 'web/webqtl/genomeGraph/cmdGenomeScanPage.py')
| -rwxr-xr-x | web/webqtl/genomeGraph/cmdGenomeScanPage.py | 532 |
1 files changed, 532 insertions, 0 deletions
diff --git a/web/webqtl/genomeGraph/cmdGenomeScanPage.py b/web/webqtl/genomeGraph/cmdGenomeScanPage.py new file mode 100755 index 00000000..d880ce69 --- /dev/null +++ b/web/webqtl/genomeGraph/cmdGenomeScanPage.py @@ -0,0 +1,532 @@ +# 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 +import math + +from htmlgen import HTMLgen2 as HT + +from utility import svg +from base import webqtlConfig +from utility import Plot +from utility import webqtlUtil +from base.webqtlDataset import webqtlDataset +from base.templatePage import templatePage + + +######################################### +# Genome Scan PAGE +######################################### +class cmdGenomeScanPage(templatePage): + def __init__(self,fd): + templatePage.__init__(self,fd) + if not self.openMysql(): + return + self.database = fd.formdata.getvalue('database', '') + db = webqtlDataset(self.database, self.cursor) + + try: + self.openURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + \ + '?FormID=showDatabase&database=%s&incparentsf1=1&ProbeSetID=' % self.database + + if db.type != "ProbeSet" or not db.id: + raise DbNameError + + self.cursor.execute(""" + Select + InbredSet.Name + From + ProbeSetFreeze, ProbeFreeze, InbredSet + whERE + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND + ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeSetFreeze.Id = %d + """ % db.id) + thisRISet = self.cursor.fetchone()[0] + if thisRISet =='BXD300': + thisRISet = 'BXD' + + ################################################## + # exon data is too huge for GenoGraph, skip it # + ################################################## + self.cursor.execute('select count(*) from ProbeSetXRef where ProbeSetFreezeId=%d' % db.id) + amount = self.cursor.fetchall() + if amount: + amount = amount[0][0] + if amount>100000: + heading = "Whole Transcriptome Mapping" + detail = ["Whole Transcriptome Mapping is not available for this data set."] + self.error(heading=heading,detail=detail) + return + + self.cursor.execute(""" + Select + ProbeSet.Id, ProbeSet.Name, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus, ProbeSetXRef.pValue + From + ProbeSet, ProbeSetXRef + whERE + ProbeSetXRef.ProbeSetFreezeId = %d AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetXRef.Locus is not NULL + """ % db.id) + results = self.cursor.fetchall() + + if results: + self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet) + + import reaper + markerGMb = {} + genotype_1 = reaper.Dataset() + genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno')) + for chr in genotype_1: + chrlen = self.mouseChrLengthDict[chr.name] + + for locus in chr: + markerGMb[locus.name] = locus.Mb + chrlen + + try: + FDR = float(fd.formdata.getvalue("fdr", "")) + except: + FDR = 0.2 + self.grid = fd.formdata.getvalue("grid", "") + + NNN = len(results) + results = list(results) + results.sort(self.cmppValue) + + MbCoord = [] + MbCoord2 = [] + + for j in range(NNN, 0, -1): + if results[j-1][-1] <= (FDR*j)/NNN: + break + + if j > 0: + for i in range(j-1, -1, -1): + _Id, _probeset, _chr, _Mb, _marker, _pvalue = results[i] + try: + MbCoord.append([markerGMb[_marker], _Mb+self.mouseChrLengthDict[string.strip(_chr)], _probeset, _chr, _Mb, _marker, _pvalue]) + except: + pass + + filename=webqtlUtil.genRandStr("gScan_") + canvas = pid.PILCanvas(size=(1280,880)) + self.drawGraph(canvas, MbCoord, cLength=sum) + + canvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png') + + canvasSVG = self.drawSVG(MbCoord, cLength=sum, size=(1280,880)) + canvasSVG.toXml(os.path.join(webqtlConfig.IMGDIR, filename+'.svg')) #and write it to file + + img = HT.Embed(src='/image/'+filename+'.png', width=1280, height=880, border=0, alt='Genome Scan') + img2 = HT.Embed(src='/image/'+filename+'.svg', width=1280, height=880, border=0) + TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee') + + heading = HT.Paragraph('Whole Transcriptome Mapping') + heading.__setattr__("class","title") + intro = HT.Blockquote() + intro.append('The plot below is the Whole Transcriptome Mapping of Database ') + intro.append(HT.Href(text=db.fullname, url = webqtlConfig.INFOPAGEHREF % db.name ,target='_blank',Class="normalsize")) + intro.append(". %d from a total of %d ProbeSets were utilized to generate this graph." % (len(MbCoord), len(results))) + + mainfm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', \ + name=webqtlUtil.genRandStr("fm_"), submit=HT.Input(type='hidden')) + mainfm.append(HT.Input(name='database', value=self.database, type='hidden')) + mainfm.append(HT.Input(name='FormID', value='transciptMapping', type='hidden')) + + mainfm.append("<BLOCKQUOTE>") + mainfm.append("0 < FDR <= 1.0 ") + mainfm.append(HT.Input(name='fdr', value=FDR, type='text')) + + mainfm.append(HT.Input(name='submit', value='Redraw Graph', type='submit', Class='button')) + mainfm.append("</BLOCKQUOTE>") + mainfm.append(""" +<center> +<div id="gallery"> +<div class="on" title="img1"><span>Static</span></div> +<div class="off" title="img2"><span>Interactive</span></div> +</div> + +<div id="img1" class="show"> +""") + mainfm.append(img) + mainfm.append(""" +</div> + +<div id="img2" class="hide"> +""") + mainfm.append(img2) + mainfm.append(""" +</div> +</center> +""") + + TD_LR.append(heading, intro, HT.Paragraph(mainfm)) + + self.dict['title'] = 'Whole Transcriptome Mapping' + self.dict['body'] = TD_LR + else: + heading = "Whole Transcriptome Mapping" + detail = ["Database calculation is not finished."] + self.error(heading=heading,detail=detail) + return + except: + heading = "Whole Transcriptome Mapping" + detail = ["Whole Transcriptome Mapping only apply to Microarray database."] + self.error(heading=heading,detail=detail) + return + + def drawSVG(self, data, cLength = 2500, offset= (80, 160, 60, 60), size=(1280,880), + XLabel="Marker GMb", YLabel="Transcript GMb"): + entities = { + "colorText" : "fill:darkblue;", + "strokeText" : ";stroke:none;stroke-width:0;", + "allText" : "font-family:Helvetica;", + "titleText" : "font-size:22;font-weight:bold;", + "subtitleText" : "font-size:18;font-weight:bold;", + "headlineText" : "font-size:14;font-weight:bold;", + "normalText" : "font-size:12;", + "legendText" : "font-size:11;text-anchor:end;", + "valuesText" : "font-size:12;", + "boldValuesText" : "font-size:12;font-weight:bold;", + "smallText" : "font-size:10;", + "vText" : "writing-mode:tb-rl", + "rightText" : "text-anchor:end;", + "middleText" : "text-anchor:middle;", + "bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;", + "rectstyle" : "fill:lightblue;stroke:none;opacity:0.2;", + "fillUnbebaut" : "fill:#CCFFD4;stroke:none;", + "fillNodata" : "fill:#E7E7E7;stroke:black;stroke-width:2;stroke-antialiasing:true;", + "fillNodataLegend" : "fill:#E7E7E7;stroke:black;stroke-width:0.5;stroke-antialiasing:true;", + "grundzeitstyle" : "fill:none;stroke:#E00004;stroke-width:60;stroke-antialiasing:true;", + "bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;", + "mapAuthor" : "A. Neumann", + } + cWidth, cHeight = size + canvasSVG = svg.drawing(entities) #create a drawing + drawSpace=svg.svg((0, 0, cWidth, cHeight), cWidth, cHeight, xml__space="preserve", + zoomAndPan="disable", onload="initMap(evt);", + xmlns__a3="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/", + a3__scriptImplementation="Adobe") #create a svg drawingspace + canvasds=svg.description('Genome Graph') #define a description + drawSpace.addElement(canvasds) #add the description to the svg + + #need to be modified or deleted + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + plotWidth = cWidth - xLeftOffset - xRightOffset + plotHeight = cHeight - yTopOffset - yBottomOffset + drawSpace.addElement(svg.script("", language="javascript", xlink__href="/javascript/svg.js")) + + #add defs + defs = svg.defs() + symbol1= svg.symbol(id="magnifyer", overflow="visible", + style="fill:white;stroke:orange;stroke-width:2;") + symbol1.addElement(svg.line(0, 0, -8, 20)) + symbol1.addElement(svg.circle(0, 0, 8)) + symbol1.addElement(svg.line(-4, 0, 4, 0, style="stroke:orange;stroke-width:2;")) + defs.addElement(symbol1) + symbol2= svg.symbol(id="magnifyerZoomIn",overflow="visible") + symbol2.addElement(svg.use(link="#magnifyer", id="zoomIn")) + symbol2.addElement(svg.line(0, -4, 0, 4, style="stroke:orange;stroke-width:2;")) + defs.addElement(symbol2) + drawSpace.addElement(defs) + + symbol3= svg.symbol(id="msgbox", overflow="visible", + style="fill:white;stroke:orange;stroke-width:1;opacity:0.8;") + symbol3.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10)) + symbol3.addElement(svg.line(21, -40, 58, -40, style="stroke:white;")) + symbol3.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]])) + symbol3.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;")) + symbol3.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;")) + symbol3.addElement(svg.text(-60, -90, "LRS ", style="&colorText; &allText; &subtitleText; &strokeText;")) + symbol3.addElement(svg.text(-60, -55, "P value ", style="&colorText; &allText; &subtitleText; &strokeText;")) + defs.addElement(symbol3) + + g = svg.group("title") + g.addElement(svg.text(cWidth-40, 30, "Genome Graph", style="&colorText; &allText; &titleText; &rightText;")) + g.addElement(svg.text(cWidth-40, 50, "Whole Transcriptome Mapping", style="&colorText; &allText; &subtitleText; &rightText;")) + drawSpace.addElement(g) + + #draw Main display area border + mainSquare = cHeight-60 + cordZOOM = 10 + drawSpace.addElement(svg.rect(8, 8, mainSquare+4, mainSquare+4,'none',"orange",0.5, rx="5", ry="5")) + drawSpace.addElement(svg.text(10+mainSquare/2, 40+mainSquare,'Marker GMb', + style="&colorText; &allText; &titleText; &middleText;", id="XLabel")) + drawSpace.addElement(svg.text(mainSquare + 80, 10+mainSquare/2,'Transcript GMb', + style="&colorText; &allText; &titleText; &middleText; &vText;", id="YLabel")) + + #draw overview display area + drawSpace.addElement(svg.rect(cWidth-40-260, 60, 260, 260,'none',"orange",0.5, rx="5", ry="5")) + drawSpaceThumb= svg.svg(id="overviewPlot",x=cWidth-40-260,y="60",width="260", + height="260",viewBox=(0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM)) + g = svg.group(style="&bezgrenzstyle;") + g.addElement(svg.use("#grid")) + drawSpaceThumb.addElement(g) + drawSpaceThumb.addElement(svg.rect(id="overviewRect",style="&rectstyle;", + x="0",y="0",width=mainSquare*cordZOOM,height=mainSquare*cordZOOM, + onmouseover="statusChange('click and drag rectangle to change extent');", + onmousedown="beginPan(evt);", onmousemove="doPan(evt);", + onmouseup="endPan();", onmouseout="endPan();")) + drawSpace.addElement(drawSpaceThumb) + + #draw navigator + g = svg.group(id="navigatorElements") + g.addElement(svg.use("#magnifyerZoomIn", id="zoomIn", transform="translate(%d,350)" % (cWidth-40-130-20), + onmouseover="magnify(evt,1.3,'in');", onmouseout="magnify(evt,1,'in');", onclick="zoomIt('in');")) + g.addElement(svg.use("#magnifyer", id="zoomOut", transform="translate(%d,350)" % (cWidth-40-130+20), + onmouseover="magnify(evt,1.3,'out');",onmouseout="magnify(evt,1,'out');", onclick="zoomIt('out');")) + + drawSpace.addElement(g) + + g = svg.group(id="statusBar") + g.addElement(svg.text(cWidth-40-260, 360, "ZOOM: 100%", style="fill:orange; font-size:14;", id="zoomValueObj")) + g.addElement(svg.text(cWidth-40-260, 380, "Status:", style="&colorText; &allText; &smallText;")) + g.addElement(svg.text(cWidth-40-260, 395, "Loading Plot", style="&colorText; &allText; &smallText;", id="statusText")) + drawSpace.addElement(g) + + #draw main display area + drawSpaceMain= svg.svg((0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM), mainSquare, mainSquare, + id="mainPlot",x="10",y="10") + mPlotWidth = mPlotHeight = 0.8*mainSquare*cordZOOM + + drawSpaceMain.addElement(svg.rect(mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1, mPlotWidth, mPlotHeight,style="fill:white", + onmousemove="showChr(evt);", onmouseover="showChr(evt);", onmouseout="showNoChr(evt);")) + #draw grid + g = svg.group("grid", style="stroke:lightblue;stroke-width:3", + transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1)) + + if 1: #self.grid == "on": + js = [] + for key in self.mouseChrLengthDict.keys(): + length = self.mouseChrLengthDict[key] + js.append(mPlotWidth*length/cLength) + if length != 0: + yCoord = mPlotHeight*(1.0-length/cLength) + l = svg.line(0,yCoord ,mPlotWidth, yCoord) + g.addElement(l) + xCoord = mPlotWidth*length/cLength + l = svg.line(xCoord, 0 ,xCoord, mPlotHeight) + g.addElement(l) + js.sort() + drawSpace.addElement(svg.script("",language="javascript", cdata="var openURL=\"%s\";\nvar chrLength=%s;\n" % (self.openURL, js))) + + g.addElement(svg.rect(0, 0, mPlotWidth, mPlotHeight,'none','black',10)) + drawSpaceMain.addElement(g) + + #draw Scale + g = svg.group("scale", style="stroke:black;stroke-width:0", + transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1)) + i = 100 + scaleFontSize = 11*cordZOOM + while i < cLength: + yCoord = mPlotHeight - mPlotHeight*i/cLength + l = svg.line(0,yCoord ,-5*cordZOOM, yCoord) + g.addElement(l) + t = svg.text(-40*cordZOOM, yCoord +5*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag Y + g.addElement(t) + xCoord = mPlotWidth*i/cLength + l = svg.line(xCoord, mPlotHeight, xCoord, mPlotHeight+5*cordZOOM) + g.addElement(l) + if i%200 == 0: + t = svg.text(xCoord, mPlotHeight+10*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag X + g.addElement(t) + i += 100 + + drawSpaceMain.addElement(g) + #draw Points + finecolors = Plot.colorSpectrumSVG(12) + finecolors.reverse() + g = preColor = "" + for item in data: + _probeset, _chr, _Mb, _marker, _pvalue = item[2:] + try: + _idx = int((-math.log10(_pvalue))*12/6.0) # add module name + _color = finecolors[_idx] + except: + _color = finecolors[-1] + if _color != preColor: + preColor = _color + if g: + drawSpaceMain.addElement(g) + g = svg.group("points", style="stroke:%s;stroke-width:5" % _color, + transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1), + onmouseover="mvMsgBox(evt);", onmouseout="hdMsgBox();", onmousedown="openPage(evt);") + else: + pass + px = mPlotWidth*item[0]/cLength + py = mPlotHeight*(1.0-item[1]/cLength) + l = svg.line("%2.1f" % (px-3*cordZOOM), "%2.1f" % py, "%2.1f" % (px+3*cordZOOM), "%2.1f" % py, ps=_probeset, mk=_marker) + g.addElement(l) + + drawSpaceMain.addElement(g) + + """ + #draw spectrum + i = 0 + j = 0 + middleoffsetX = 40 + labelFont=pid.Font(ttf="tahoma",size=12,bold=0) + for dcolor in finecolors: + drawSpace.drawLine(xLeftOffset+ plotWidth + middleoffsetX -15 , plotHeight + yTopOffset - i, \ + xLeftOffset+ plotWidth + middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor) + if i % 50 == 0: + drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \ + xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black) + drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont) + j += 1 + i += 1 + drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1, \ + xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black) + drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont) + labelFont=pid.Font(ttf="tahoma",size=14,bold=1) + drawSpace.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90) + + labelFont=pid.Font(ttf="verdana",size=18,bold=0) + drawSpace.drawString(XLabel, xLeftOffset + (plotWidth -drawSpace.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont) + drawSpace.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -drawSpace.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90) + """ + drawSpace.addElement(drawSpaceMain) + + g= svg.group(id="dispBox", overflow="visible", + style="fill:white;stroke:orange;stroke-width:1;opacity:0.85;", + transform="translate(%d,650)" % (cWidth-40-300), visibility="hidden") + g.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10)) + g.addElement(svg.line(21, -40, 58, -40, style="stroke:white;")) + g.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]])) + g.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_probeset")) + g.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_marker")) + + drawSpace.addElement(g) + + canvasSVG.setSVG(drawSpace) #set the svg of the drawing to the svg + return canvasSVG + + + def drawGraph(self, canvas, data, cLength = 2500, offset= (80, 160, 60, 60), XLabel="QTL location (GMb)", YLabel="Gene location (GMb)"): + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset + plotHeight = canvas.size[1] - yTopOffset - yBottomOffset + + #draw Frame + canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset) + + #draw Scale + i = 100 + scaleFont=pid.Font(ttf="cour",size=11,bold=1) + while i < cLength: + yCoord = plotHeight + yTopOffset - plotHeight*i/cLength + canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset-5, yCoord) + canvas.drawString("%d"% i, xLeftOffset -40, yCoord +5,font=scaleFont) + xCoord = xLeftOffset + plotWidth*i/cLength + canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, plotHeight + yTopOffset+5) + canvas.drawString("%d"% i, xCoord -10, plotHeight + yTopOffset+15,font=scaleFont) + i += 100 + + #draw Points + finecolors = Plot.colorSpectrum(300) + finecolors.reverse() + for item in data: + _pvalue = item[-1] + try: + _idx = int((-math.log10(_pvalue))*300/6.0) # XZ, 09/11/2008: add module name + _color = finecolors[_idx] + except: + _color = finecolors[-1] + + canvas.drawCross(xLeftOffset + plotWidth*item[0]/cLength, plotHeight + yTopOffset - plotHeight*item[1]/cLength, color=_color,size=3) + + #draw grid / always draw grid + if 1: #self.grid == "on": + for key in self.mouseChrLengthDict.keys(): + length = self.mouseChrLengthDict[key] + if length != 0: + yCoord = plotHeight + yTopOffset - plotHeight*length/cLength + canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset+plotWidth, yCoord, color=pid.lightgrey) + xCoord = xLeftOffset + plotWidth*length/cLength + canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, yTopOffset, color=pid.lightgrey) + + #draw spectrum + i = 0 + j = 0 + middleoffsetX = 40 + labelFont=pid.Font(ttf="tahoma",size=12,bold=0) + 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: + canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \ + xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black) + canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont) + j += 1 + i += 1 + canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1, \ + xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black) + canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont) + labelFont=pid.Font(ttf="tahoma",size=14,bold=1) + canvas.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90) + + labelFont=pid.Font(ttf="verdana",size=18,bold=0) + canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont) + canvas.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90) + return + + def readMouseGenome(self, RISet): + ldict = {} + lengths = [] + sum = 0 + ##################################### + # Retrieve Chr Length Information + ##################################### + self.cursor.execute(""" + Select + Chr_Length.Name, Length from Chr_Length, InbredSet + where + Chr_Length.SpeciesId = InbredSet.SpeciesId AND + InbredSet.Name = '%s' + Order by + OrderId + """ % RISet) + lengths = self.cursor.fetchall() + ldict[lengths[0][0]] = 0 + prev = lengths[0][1]/1000000.0 + sum += lengths[0][1]/1000000.0 + for item in lengths[1:]: + ldict[item[0]] = prev + prev += item[1]/1000000.0 + sum += item[1]/1000000.0 + return ldict, sum + + def cmppValue(self, A,B): + if A[-1] < B[-1]: + return -1 + elif A[-1] == B[-1]: + return 0 + else: + return 1 + |