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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/genomeGraph/cmdGenomeScanPage.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/genomeGraph/cmdGenomeScanPage.py')
-rwxr-xr-xweb/webqtl/genomeGraph/cmdGenomeScanPage.py532
1 files changed, 0 insertions, 532 deletions
diff --git a/web/webqtl/genomeGraph/cmdGenomeScanPage.py b/web/webqtl/genomeGraph/cmdGenomeScanPage.py
deleted file mode 100755
index d880ce69..00000000
--- a/web/webqtl/genomeGraph/cmdGenomeScanPage.py
+++ /dev/null
@@ -1,532 +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
-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
-