Merge branch 'master' into lmm

1 files changed, 0 insertions, 437 deletions

diff --git a/web/webqtl/heatmap/Heatmap.py b/web/webqtl/heatmap/Heatmap.py
deleted file mode 100755
index c4543cee..00000000
--- a/web/webqtl/heatmap/Heatmap.py
+++ /dev/null
@@ -1,437 +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 os
-import string
-import piddle as pid
-import cPickle
-
-from base import webqtlConfig
-from base.webqtlTrait import webqtlTrait
-from dbFunction import webqtlDatabaseFunction
-from utility import webqtlUtil 
-from utility import Plot
-import slink
-
-
-# XZ, 09/09/2008: After adding several traits to collection, click "QTL Heatmap" button,
-# XZ, 09/09/2008: This class will generate what you see.
-#########################################
-#      QTL heatmap Page
-#########################################
-class Heatmap:
-
-        def __init__(self, fd=None, searchResult=None, colorScheme=None, userPrivilege=None, userName=None):
-                cursor = webqtlDatabaseFunction.getCursor()
-                if (not cursor):
-                        return
-                targetDescriptionChecked = fd.formdata.getvalue('targetDescriptionCheck', '')
-                clusterChecked = fd.formdata.getvalue('clusterCheck', '')
-                sessionfile = fd.formdata.getvalue("session")
-                genotype = fd.genotype
-                strainlist = fd.strainlist
-                ppolar = fd.ppolar
-                mpolar = fd.mpolar
-                traitList = []
-                traitDataList = []
-                for item in searchResult:
-                        thisTrait = webqtlTrait(fullname=item, cursor=cursor)
-                        thisTrait.retrieveInfo()
-                        thisTrait.retrieveData(fd.strainlist)
-                        traitList.append(thisTrait)
-                        traitDataList.append(thisTrait.exportData(fd.strainlist))
-                self.buildCanvas(colorScheme=colorScheme, targetDescriptionChecked=targetDescriptionChecked, clusterChecked=clusterChecked, sessionfile=sessionfile, genotype=genotype, strainlist=strainlist, ppolar=ppolar, mpolar=mpolar, traitList=traitList, traitDataList=traitDataList, userPrivilege=userPrivilege, userName=userName)
-
-       	def buildCanvas(self, colorScheme='', targetDescriptionChecked='', clusterChecked='', sessionfile='', genotype=None, strainlist=None, ppolar=None, mpolar=None, traitList=None, traitDataList=None, userPrivilege=None, userName=None):
-                labelFont = pid.Font(ttf="tahoma",size=14,bold=0)
-                topHeight = 0
-       	       	NNN = len(traitList)
-       	       	#XZ: It's necessory to define canvas here
-                canvas = pid.PILCanvas(size=(80+NNN*20,880))
-                names = map(webqtlTrait.displayName, traitList)
-                #XZ, 7/29/2009: create trait display and find max strWidth
-                strWidth = 0
-                for j in range(len(names)):
-                        thisTrait = traitList[j]
-                        if targetDescriptionChecked:
-                            if thisTrait.db.type == 'ProbeSet':
-                                if thisTrait.probe_target_description:
-                                        names[j] += ' [%s at Chr %s @ %2.3fMB, %s]' % (thisTrait.symbol, thisTrait.chr, thisTrait.mb, thisTrait.probe_target_description)
-                                else:
-                                        names[j] += ' [%s at Chr %s @ %2.3fMB]' % (thisTrait.symbol, thisTrait.chr, thisTrait.mb)
-                            elif thisTrait.db.type == 'Geno':
-                                names[j] += ' [Chr %s @ %2.3fMB]' % (thisTrait.chr, thisTrait.mb)
-                            elif thisTrait.db.type == 'Publish':
-                                if thisTrait.confidential:
-                                    if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=userPrivilege, userName=userName, authorized_users=thisTrait.authorized_users):
-                                        if thisTrait.post_publication_abbreviation:
-                                            names[j] += ' [%s]' % (thisTrait.post_publication_abbreviation)
-                                    else:
-                                        if thisTrait.pre_publication_abbreviation:
-                                            names[j] += ' [%s]' % (thisTrait.pre_publication_abbreviation)
-                                else:
-                                    if thisTrait.post_publication_abbreviation:
-                                        names[j] += ' [%s]' % (thisTrait.post_publication_abbreviation)
-                            else:
-                                pass
-
-                        i = canvas.stringWidth(names[j], font=labelFont)
-                        if i > strWidth:
-                                strWidth = i
-
-                width = NNN*20
-                xoffset = 40
-                yoffset = 40
-                cellHeight = 3
-                nLoci = reduce(lambda x,y: x+y, map(lambda x: len(x),genotype),0)
-
-                if nLoci > 2000:
-                        cellHeight = 1
-                elif nLoci > 1000:
-                        cellHeight = 2
-                elif nLoci < 200:
-                        cellHeight = 10
-                else:
-                        pass
-
-                pos = range(NNN)
-                neworder = []
-                BWs = Plot.BWSpectrum()
-                colors100 = Plot.colorSpectrum()
-                colors = Plot.colorSpectrum(130)
-                finecolors = Plot.colorSpectrum(250)
-                colors100.reverse()
-                colors.reverse()
-                finecolors.reverse()
-
-                scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
-				
-                if not clusterChecked: #XZ: this part is for original order
-                        for i in range(len(names)):
-                                neworder.append((xoffset+20*(i+1), i))
-
-                        canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))
-
-                        self.drawTraitNameBottom(canvas,names,yoffset,neworder,strWidth,topHeight,labelFont)
-                else: #XZ: this part is to cluster traits
-                        topHeight = 400
-                        canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))
-
-                        corArray = [([0] * (NNN))[:] for i in range(NNN)]
-
-                        nnCorr = len(strainlist)
-
-                        #XZ, 08/04/2009: I commented out pearsonArray, spearmanArray
-                        for i, thisTrait in enumerate(traitList):
-                            names1 = [thisTrait.db.name, thisTrait.name, thisTrait.cellid]
-                            for j, thisTrait2 in enumerate(traitList):
-                                    names2 = [thisTrait2.db.name, thisTrait2.name, thisTrait2.cellid]
-                                    if j < i:
-                                            corr,nOverlap = webqtlUtil.calCorrelation(traitDataList[i], traitDataList[j],nnCorr)
-                                            if (1-corr) < 0:
-                                                    distance = 0.0
-                                            else:
-                                                    distance = 1-corr
-                                            corArray[i][j] = distance
-                                            corArray[j][i] = distance
-                                    elif j == i:
-                                            corArray[i][j] = 0.0
-                                    else:
-                                            pass
-
-                        #XZ, 7/29/2009: The parameter d has info of cluster (group member and distance). The format of d is tricky. Print it out to see it's format.
-                        d = slink.slink(corArray)
-
-                        #XZ, 7/29/2009: Attention: The 'neworder' is changed by the 'draw' function
-                        #XZ, 7/30/2009: Only toppos[1][0] and top[1][1] are used later. Then what toppos[0] is used for? 
-                        toppos = self.draw(canvas,names,d,xoffset,yoffset,neworder,topHeight)
-                        self.drawTraitNameTop(canvas,names,yoffset,neworder,strWidth,topHeight,labelFont)
-
-                        #XZ, 7/29/2009: draw the top vertical line
-                        canvas.drawLine(toppos[1][0],toppos[1][1],toppos[1][0],yoffset)
-
-                        #XZ: draw string 'distance = 1-r'
-                        canvas.drawString('distance = 1-r',neworder[-1][0] + 50, topHeight*3/4,font=labelFont,angle=90)
-
-                        #draw Scale
-                        scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
-                        x = neworder[-1][0]
-                        canvas.drawLine(x+5, topHeight+yoffset, x+5, yoffset, color=pid.black)
-                        y = 0
-                        while y <=2:
-                                canvas.drawLine(x+5, topHeight*y/2.0+yoffset, x+10, topHeight*y/2.0+yoffset)
-                                canvas.drawString('%2.1f' % (2-y), x+12, topHeight*y/2.0+yoffset, font=scaleFont)
-                                y += 0.5
-
-
-                chrname = 0
-                chrnameFont=pid.Font(ttf="tahoma",size=24,bold=0)
-                Ncol = 0
-
-                nearestMarkers = self.getNearestMarker(traitList, genotype)
-
-                # import cPickle
-                if sessionfile:
-                        fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
-                        permData = cPickle.load(fp)
-                        fp.close()
-                else:
-                        permData = {}
-
-                areas = []
-				#XZ, 7/31/2009: This for loop is to generate the heatmap
-                #XZ: draw trait by trait instead of marker by marker
-                for order in neworder:
-                        #startHeight = 40+400+5+5+strWidth
-                        startHeight = topHeight + 40+5+5+strWidth
-                        startWidth = order[0]-5
-                        if Ncol and Ncol % 5 == 0:
-                                drawStartPixel = 8
-                        else:
-                                drawStartPixel = 9
-
-                        tempVal = traitDataList[order[1]]
-                        _vals = []
-                        _strains = [] 
-                        for i in range(len(strainlist)):
-                                if tempVal[i] != None:
-                                        _strains.append(strainlist[i])
-                                        _vals.append(tempVal[i])
-
-                        qtlresult = genotype.regression(strains = _strains, trait = _vals)
-
-                        if sessionfile:
-                                LRSArray = permData[str(traitList[order[1]])]
-                        else:
-                                LRSArray = genotype.permutation(strains = _strains, trait = _vals, nperm = 1000)
-                                permData[str(traitList[order[1]])] = LRSArray
-
-                        sugLRS = LRSArray[369]
-                        sigLRS = LRSArray[949]
-                        prechr = 0
-                        chrstart = 0
-                        nearest = nearestMarkers[order[1]]
-                        midpoint = []
-
-                        for item in qtlresult:
-                                if item.lrs > webqtlConfig.MAXLRS:
-                                        adjustlrs = webqtlConfig.MAXLRS
-                                else:
-                                        adjustlrs = item.lrs
-
-                                if item.locus.chr != prechr:
-                                        if prechr:
-                                                canvas.drawRect(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight+3,edgeColor=pid.white, edgeWidth=0, fillColor=pid.white)
-                                                startHeight+= 3
-                                                if not chrname:
-                                                        canvas.drawString(prechr,xoffset-20,(chrstart+startHeight)/2,font = chrnameFont,color=pid.dimgray)
-                                        prechr = item.locus.chr
-                                        chrstart = startHeight
-                                if colorScheme == '0':
-                                        if adjustlrs <= sugLRS:
-                                                colorIndex = int(65*adjustlrs/sugLRS)
-                                        else:
-                                                colorIndex = int(65 + 35*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
-                                        if colorIndex > 99:
-                                                colorIndex = 99
-                                        colorIndex = colors100[colorIndex]
-                                elif colorScheme == '1':
-                                        sugLRS = LRSArray[369]/2.0
-                                        if adjustlrs <= sugLRS:
-                                                colorIndex = BWs[20+int(50*adjustlrs/sugLRS)]
-                                        else:
-                                                if item.additive > 0:
-                                                        colorIndex = int(80 + 50*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
-                                                else:
-                                                        colorIndex = int(50 - 50*(adjustlrs-sugLRS)/(sigLRS-sugLRS))
-                                                if colorIndex > 129:
-                                                        colorIndex = 129
-                                                if colorIndex < 0:
-                                                        colorIndex = 0
-                                                colorIndex = colors[colorIndex]
-                                elif colorScheme == '2':
-                                        if item.additive > 0:
-                                                colorIndex = int(150 + 100*(adjustlrs/sigLRS))
-                                        else:
-                                                colorIndex = int(100 - 100*(adjustlrs/sigLRS))
-                                        if colorIndex > 249:
-                                                colorIndex = 249
-                                        if colorIndex < 0:
-                                                        colorIndex = 0
-                                        colorIndex = finecolors[colorIndex]
-                                else:
-                                        colorIndex = pid.white
-
-                                if startHeight > 1:
-                                        canvas.drawRect(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight+cellHeight,edgeColor=colorIndex, edgeWidth=0, fillColor=colorIndex)
-                                else:
-                                        canvas.drawLine(startWidth-drawStartPixel, startHeight, startWidth+10, startHeight, Color=colorIndex)
-
-                                if item.locus.name == nearest:
-                                        midpoint = [startWidth,startHeight-5]
-                                startHeight+=cellHeight
-
-                        #XZ, map link to trait name and band
-                        COORDS = "%d,%d,%d,%d" %(startWidth-drawStartPixel,topHeight+40,startWidth+10,startHeight)
-                        HREF = "javascript:showDatabase2('%s','%s','%s');" % (traitList[order[1]].db.name, traitList[order[1]].name, traitList[order[1]].cellid)
-                        area = (COORDS, HREF, '%s' % names[order[1]])
-                        areas.append(area)
-
-                        if midpoint:
-                                traitPixel = ((midpoint[0],midpoint[1]),(midpoint[0]-6,midpoint[1]+12),(midpoint[0]+6,midpoint[1]+12))
-                                canvas.drawPolygon(traitPixel,edgeColor=pid.black,fillColor=pid.orange,closed=1)
-
-                        if not chrname:
-                                canvas.drawString(prechr,xoffset-20,(chrstart+startHeight)/2,font = chrnameFont,color=pid.dimgray)
-                        chrname = 1
-                        Ncol += 1
-
-
-                #draw Spectrum
-                startSpect = neworder[-1][0] + 30
-                startHeight = topHeight + 40+5+5+strWidth
-
-                if colorScheme == '0':
-                        for i in range(100):
-                                canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=colors100[i])
-                        scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
-                        canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
-                        canvas.drawString('LRS = 0',startSpect,startHeight+55,font=scaleFont)
-                        canvas.drawLine(startSpect+64,startHeight+45,startSpect+64,startHeight+39,color=pid.black)
-                        canvas.drawString('Suggestive LRS',startSpect+64,startHeight+55,font=scaleFont)
-                        canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
-                        canvas.drawString('Significant LRS',startSpect+105,startHeight+40,font=scaleFont)
-                elif colorScheme == '1':
-                        for i in range(50):
-                                canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+40,color=BWs[20+i])
-                        for i in range(50,100):
-                                canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+20,color=colors[100-i])
-                                canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=colors[30+i])
-
-                        canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
-                        canvas.drawString('LRS = 0',startSpect,startHeight+60,font=scaleFont)
-                        canvas.drawLine(startSpect+50,startHeight+45,startSpect+50,startHeight+39,color=pid.black)
-                        canvas.drawString('0.5*Suggestive LRS',startSpect+50,startHeight+ 60,font=scaleFont)
-                        canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
-                        canvas.drawString('Significant LRS',startSpect+105,startHeight+50,font=scaleFont)
-                        textFont=pid.Font(ttf="verdana",size=18,bold=0)
-                        canvas.drawString('%s +' % ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
-                        canvas.drawString('%s +' % mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
-                elif colorScheme == '2':
-                        for i in range(100):
-                                canvas.drawLine(startSpect+i,startHeight,startSpect+i,startHeight+20,color=finecolors[100-i])
-                                canvas.drawLine(startSpect+i,startHeight+20,startSpect+i,startHeight+40,color=finecolors[150+i])
-
-                        canvas.drawLine(startSpect,startHeight+45,startSpect,startHeight+39,color=pid.black)
-                        canvas.drawString('LRS = 0',startSpect,startHeight+60,font=scaleFont)
-                        canvas.drawLine(startSpect+99,startHeight+45,startSpect+99,startHeight+39,color=pid.black)
-                        canvas.drawString('Significant LRS',startSpect+105,startHeight+50,font=scaleFont)
-                        textFont=pid.Font(ttf="verdana",size=18,bold=0)
-                        canvas.drawString('%s +' % ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
-                        canvas.drawString('%s +' % mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
-						
-                filename= webqtlUtil.genRandStr("Heatmap_")
-                canvas.save(webqtlConfig.IMGDIR+filename, format='png')
-                if not sessionfile:
-                        sessionfile = webqtlUtil.generate_session()
-                        webqtlUtil.dump_session(permData, os.path.join(webqtlConfig.TMPDIR, sessionfile +'.session'))
-                self.filename=filename
-                self.areas=areas
-                self.sessionfile=sessionfile
-        
-        def getResult(self):
-                return self.filename, self.areas, self.sessionfile
-
-        #XZ, 7/31/2009: This function put the order of traits into parameter neworder,
-        #XZ: return the position of the top vertical line of the hierarchical tree, draw the hierarchical tree.
-        def draw(self,canvas,names,d,xoffset,yoffset,neworder,topHeight):
-                maxDistance = topHeight
-                fontoffset = 4    #XZ, 7/31/2009: used only for drawing tree
-                if type(d[0]) == type(1) and type(d[1]) == type(1):
-                        neworder.append((xoffset+20,d[0]))
-                        neworder.append((xoffset+40,d[1]))
-                        height = d[2]*maxDistance/2
-                        canvas.drawLine(xoffset+20-fontoffset,maxDistance+yoffset,xoffset+20-fontoffset,maxDistance-height+yoffset)
-                        canvas.drawLine(xoffset+40-fontoffset,maxDistance+yoffset,xoffset+40-fontoffset,maxDistance-height+yoffset)
-                        canvas.drawLine(xoffset+40-fontoffset,maxDistance+yoffset-height,xoffset+20-fontoffset,maxDistance-height+yoffset)
-                        return (40,(xoffset+30-fontoffset,maxDistance-height+yoffset))
-                elif type(d[0]) == type(1):
-                        neworder.append((xoffset+20,d[0]))
-                        d2 = self.draw(canvas,names,d[1],xoffset+20,yoffset,neworder,topHeight)
-                        height = d[2]*maxDistance/2
-                        canvas.drawLine(xoffset+20-fontoffset,maxDistance+yoffset,xoffset+20-fontoffset,maxDistance-height+yoffset)
-                        canvas.drawLine(d2[1][0],d2[1][1],d2[1][0],maxDistance-height+yoffset)
-                        canvas.drawLine(d2[1][0],maxDistance-height+yoffset,xoffset+20-fontoffset,maxDistance-height+yoffset)
-                        return (20+d2[0],((d2[1][0]+xoffset+20-fontoffset)/2,maxDistance-height+yoffset))
-                elif type(d[1]) == type(1):
-                        d1 = self.draw(canvas,names,d[0],xoffset,yoffset,neworder,topHeight)
-                        neworder.append((xoffset+d1[0]+20,d[1]))
-                        height = d[2]*maxDistance/2
-                        canvas.drawLine(xoffset+d1[0]+20-fontoffset,maxDistance+yoffset,xoffset+d1[0]+20-fontoffset,maxDistance-height+yoffset)
-                        canvas.drawLine(d1[1][0],d1[1][1],d1[1][0],maxDistance-height+yoffset)
-                        canvas.drawLine(d1[1][0],maxDistance-height+yoffset,xoffset+d1[0]+20-fontoffset,maxDistance-height+yoffset)
-                        return (d1[0]+20,((d1[1][0]+xoffset+d1[0]+20-fontoffset)/2,maxDistance-height+yoffset))
-                else:
-                        d1 = self.draw(canvas,names,d[0],xoffset,yoffset,neworder,topHeight)
-                        d2 = self.draw(canvas,names,d[1],xoffset+d1[0],yoffset,neworder,topHeight)
-                        height = d[2]*maxDistance/2
-                        canvas.drawLine(d2[1][0],d2[1][1],d2[1][0],maxDistance-height+yoffset)
-                        canvas.drawLine(d1[1][0],d1[1][1],d1[1][0],maxDistance-height+yoffset)
-                        canvas.drawLine(d1[1][0],maxDistance-height+yoffset,d2[1][0],maxDistance-height+yoffset)
-                        return (d1[0]+d2[0],((d1[1][0]+d2[1][0])/2,maxDistance-height+yoffset))
-
-        #XZ, 7/31/2009: dras trait names
-        def drawTraitNameBottom (self,canvas,names,yoffset,neworder,strWidth,topHeight,labelFont):
-                maxDistance = topHeight
-                for oneOrder in neworder:
-                        canvas.drawString(names[oneOrder[1]],oneOrder[0]-5,maxDistance+yoffset+5+strWidth-canvas.stringWidth(names[oneOrder[1]],font=labelFont),font=labelFont,color=pid.black,angle=270)
-
-        def drawTraitNameTop (self,canvas,names,yoffset,neworder,strWidth,topHeight,labelFont):
-                maxDistance = topHeight
-                for oneOrder in neworder:
-                        canvas.drawString(names[oneOrder[1]],oneOrder[0]-5,maxDistance+yoffset+5,font=labelFont,color=pid.black,angle=270)
-
-
-        def getNearestMarker(self, traitList, genotype):
-                out = []
-                if not genotype.Mbmap:
-                        return [None]* len(traitList)
-                for item in traitList:
-                        try:
-                                nearest = None
-                                for _chr in genotype:
-                                        if _chr.name != item.chr:
-                                                continue
-                                        distance = 1e30
-                                        for _locus in _chr:
-                                                if abs(_locus.Mb-item.mb) < distance:
-                                                        distance = abs(_locus.Mb-item.mb)
-                                                        nearest = _locus.name
-                                out.append(nearest)
-                        except:
-                                out.append(None)
-
-                return out