path: root/web/webqtl/heatmap/heatmapPage_GN.py

# 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 htmlgen import HTMLgen2 as HT

from base.templatePage import templatePage
from base import webqtlConfig
from base.webqtlTrait import webqtlTrait
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 heatmapPage(templatePage):

        labelFont=pid.Font(ttf="tahoma",size=14,bold=0)

        topHeight = 0

        def __init__(self,fd):

                templatePage.__init__(self, fd)

                if not self.openMysql():
                        return
                if not fd.genotype:
                        fd.readGenotype()


                self.searchResult = fd.formdata.getvalue('searchResult')

                if not self.searchResult:
                        templatePage.__init__(self, fd)
                        heading = 'QTL Heatmap'
                        detail = ['You need to select at least two traits in order to generate correlation matrix.']
                        self.error(heading=heading,detail=detail)
                        return
                if type("1") == type(self.searchResult):
                        self.searchResult = string.split(self.searchResult,'\t')


                if self.searchResult:
                        if len(self.searchResult) > webqtlConfig.MAXCORR:
                                heading = 'QTL Heatmap'
                                detail = ['In order to display the QTL heat map properly, do not select more than %d traits for analysis.' % webqtlConfig.MAXCORR]
                                self.error(heading=heading,detail=detail)
                                return

                        traitList = []
                        traitDataList = []
                        for item in self.searchResult:
                                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
                                thisTrait.retrieveInfo()
                                thisTrait.retrieveData(fd.strainlist)
                                traitList.append(thisTrait)
                                traitDataList.append(thisTrait.exportData(fd.strainlist))
                else:
                        heading = 'QTL Heatmap'
                        detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
                        self.error(heading=heading,detail=detail)
                        return

                self.colorScheme = fd.formdata.getvalue('colorScheme')
                if not self.colorScheme:
                        self.colorScheme = '1'

                self.dict['title'] = 'QTL heatmap'

                NNN = len(traitList)

                if NNN == 0:
                        heading = "QTL Heatmap"
                        detail = ['No trait was selected for %s data set. No QTL heatmap was generated.' % fd.RISet]
                        self.error(heading=heading,detail=detail)
                        return
                elif NNN < 2:
                        templatePage.__init__(self, fd)
                        heading = 'QTL Heatmap'
                        detail = ['You need to select at least two traits in order to generate QTL heatmap.']
                        self.error(heading=heading,detail=detail)
                        return
                else:
                        #XZ: It's necessory to define canvas here
                        canvas = pid.PILCanvas(size=(80+NNN*20,880))

                        names = map(webqtlTrait.displayName, traitList)

                        self.targetDescriptionChecked = fd.formdata.getvalue('targetDescriptionCheck', '')

                        #XZ, 7/29/2009: create trait display and find max strWidth
                        strWidth = 0
                        for j in range(len(names)):
                                thisTrait = traitList[j]

                                if self.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.abbreviation:
                                            names[j] += ' [%s]' % (thisTrait.abbreviation)
                                        else:
                                            pass
                                    else:
                                        pass

                                i = canvas.stringWidth(names[j],font=self.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),fd.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)

                        self.clusterChecked = fd.formdata.getvalue('clusterCheck', '')


                        if not self.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+ self.topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))

                                self.drawTraitNameBottom(canvas,names,yoffset,neworder,strWidth)
                        else: #XZ: this part is to cluster traits
                                self.topHeight = 400
                                canvas = pid.PILCanvas(size=(80+NNN*20+240,80+ self.topHeight +5+5+strWidth+nLoci*cellHeight+80+20*cellHeight))

                                corArray = [([0] * (NNN))[:] for i in range(NNN)]

                                nnCorr = len(fd.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)
                                self.drawTraitNameTop(canvas,names,yoffset,neworder,strWidth)

                                #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, self.topHeight*3/4,font=self.labelFont,angle=90)

                                #draw Scale
                                scaleFont=pid.Font(ttf="tahoma",size=10,bold=0)
                                x = neworder[-1][0]
                                canvas.drawLine(x+5, self.topHeight+yoffset, x+5, yoffset, color=pid.black)
                                y = 0
                                while y <=2:
                                        canvas.drawLine(x+5, self.topHeight*y/2.0+yoffset, x+10, self.topHeight*y/2.0+yoffset)
                                        canvas.drawString('%2.1f' % (2-y), x+12, self.topHeight*y/2.0+yoffset, font=scaleFont)
                                        y += 0.5


                        chrname = 0
                        chrnameFont=pid.Font(ttf="tahoma",size=24,bold=0)
                        Ncol = 0

                        gifmap = HT.Map(name='traitMap')

                        nearestMarkers = self.getNearestMarker(traitList, fd.genotype)

                        # import cPickle
                        sessionfile = fd.formdata.getvalue("session")

                        if sessionfile:
                                fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
                                permData = cPickle.load(fp)
                                fp.close()
                        else:
                                permData = {}

                        #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 = self.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(fd.strainlist)):
                                        if tempVal[i] != None:
                                                _strains.append(fd.strainlist[i])
                                                _vals.append(tempVal[i])

                                qtlresult = fd.genotype.regression(strains = _strains, trait = _vals)

                                if sessionfile:
                                        LRSArray = permData[str(traitList[order[1]])]
                                else:
                                        LRSArray = fd.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 self.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 self.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 self.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,self.topHeight+40,startWidth+10,startHeight)
                                HREF = "javascript:showDatabase2('%s','%s','%s');" % (traitList[order[1]].db.name, traitList[order[1]].name, traitList[order[1]].cellid)
                                Areas = HT.Area(shape='rect',coords=COORDS,href=HREF, title='%s' % names[order[1]])
                                gifmap.areas.append(Areas)

                                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 = self.topHeight + 40+5+5+strWidth

                        if self.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 self.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 +' % fd.ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
                                canvas.drawString('%s +' % fd.mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)
                        elif self.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 +' % fd.ppolar,startSpect+120,startHeight+ 35,font=textFont,color=pid.red)
                                canvas.drawString('%s +' % fd.mpolar,startSpect+120,startHeight+ 15,font=textFont,color=pid.blue)


                        filename= webqtlUtil.genRandStr("Heatmap_")
                        canvas.save(webqtlConfig.IMGDIR+filename, format='png')
                        img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#traitMap')
                        imgUrl = 'Right-click or control-click on the link to download this graph as a <a href="/image/%s.png" class="normalsize" target="_blank">PNG file</a>' % filename

                        form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
                        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet,'searchResult':string.join(self.searchResult,'\t')}
                        if fd.incparentsf1:
                                hddn['incparentsf1']='ON'
                        for key in hddn.keys():
                                form.append(HT.Input(name=key, value=hddn[key], type='hidden'))

                        heatmap = HT.Input(type='button' ,name='mintmap',value='Redraw QTL Heatmap', onClick="databaseFunc(this.form,'heatmap');",Class="button")
                        spects = {'0':'Single Spectrum','1':'Grey + Blue + Red','2':'Blue + Red'}
                        schemeMenu = HT.Select(name='colorScheme')
                        schemeMenu.append(('Single Spectrum',0))
                        schemeMenu.append(('Grey + Blue + Red',1))
                        schemeMenu.append(('Blue + Red',2))
                        schemeMenu.selected.append(spects[self.colorScheme])

                        clusterCheck= HT.Input(type='checkbox', Class='checkbox', name='clusterCheck',checked=0)
                        targetDescriptionCheck = HT.Input(type='checkbox', Class='checkbox', name='targetDescriptionCheck',checked=0)

                        form.append(gifmap,schemeMenu, heatmap, HT.P(), clusterCheck, '  Cluster traits  ', targetDescriptionCheck, '  Add description', HT.P(),img2, HT.P(), imgUrl)

                        if not sessionfile:
                                filename = webqtlUtil.generate_session()
                                webqtlUtil.dump_session(permData, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
                                sessionfile=filename

                        form.append(HT.Input(name='session', value=sessionfile, type='hidden'))

                        heatmapHelp = HT.Input(type='button' ,name='heatmapHelpButton',value='Info', onClick="openNewWin('/heatmap.html');",Class="button")

                        heatmapHeading = HT.Paragraph('QTL Heatmap ', heatmapHelp, Class="title")

                        TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
                        TD_LR.append(heatmapHeading, HT.P(),HT.P(),HT.P(),HT.P(),HT.P(),form)

                        self.dict['body'] = str(TD_LR)

        #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):
                maxDistance = self.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)
                        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)
                        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)
                        d2 = self.draw(canvas,names,d[1],xoffset+d1[0],yoffset,neworder)
                        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):
                maxDistance = self.topHeight

                for oneOrder in neworder:
                        canvas.drawString(names[oneOrder[1]],oneOrder[0]-5,maxDistance+yoffset+5+strWidth-canvas.stringWidth(names[oneOrder[1]],font=self.labelFont),font=self.labelFont,color=pid.black,angle=270)

        def drawTraitNameTop (self,canvas,names,yoffset,neworder,strWidth):
                maxDistance = self.topHeight

                for oneOrder in neworder:
                        canvas.drawString(names[oneOrder[1]],oneOrder[0]-5,maxDistance+yoffset+5,font=self.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