diff options
Diffstat (limited to 'web/webqtl/heatmap')
| -rwxr-xr-x | web/webqtl/heatmap/Heatmap.py | 437 | ||||
| -rwxr-xr-x | web/webqtl/heatmap/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/heatmap/heatmapPage.py | 116 | ||||
| -rwxr-xr-x | web/webqtl/heatmap/heatmapPage_GN.py | 522 | ||||
| -rwxr-xr-x | web/webqtl/heatmap/slink.py | 141 |
5 files changed, 0 insertions, 1216 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 diff --git a/web/webqtl/heatmap/__init__.py b/web/webqtl/heatmap/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/heatmap/__init__.py +++ /dev/null diff --git a/web/webqtl/heatmap/heatmapPage.py b/web/webqtl/heatmap/heatmapPage.py deleted file mode 100755 index b407b0c8..00000000 --- a/web/webqtl/heatmap/heatmapPage.py +++ /dev/null @@ -1,116 +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 -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from base import webqtlConfig -from heatmap.Heatmap import Heatmap - - -# 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): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - if not fd.genotype: - fd.readGenotype() - - searchResult = fd.formdata.getvalue('searchResult') - if not searchResult: - 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 - if type("1") == type(searchResult): - searchResult = string.split(searchResult,'\t') - if searchResult: - if len(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 - 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.dict['title'] = 'QTL heatmap' - NNN = len(searchResult) - 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: - 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: - colorScheme = fd.formdata.getvalue('colorScheme') - if not colorScheme: - colorScheme = '1' - heatmapObject = Heatmap(fd=fd, searchResult=searchResult, colorScheme=colorScheme, userPrivilege=self.privilege, userName=self.userName) - filename, areas, sessionfile = heatmapObject.getResult() - gifmap = HT.Map(name='traitMap') - for area in areas: - Areas = HT.Area(shape='rect', coords=area[0], href=area[1], title=area[2]) - gifmap.areas.append(Areas) - 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(searchResult,'\t')} - if fd.incparentsf1: - hddn['incparentsf1']='ON' - for key in hddn.keys(): - form.append(HT.Input(name=key, value=hddn[key], type='hidden')) - heatmapButton = 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[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, heatmapButton, HT.P(), clusterCheck, ' Cluster traits ', targetDescriptionCheck, ' Add description', HT.P(),img2, HT.P(), imgUrl) - 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) diff --git a/web/webqtl/heatmap/heatmapPage_GN.py b/web/webqtl/heatmap/heatmapPage_GN.py deleted file mode 100755 index abc5d8aa..00000000 --- a/web/webqtl/heatmap/heatmapPage_GN.py +++ /dev/null @@ -1,522 +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 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 - - - - diff --git a/web/webqtl/heatmap/slink.py b/web/webqtl/heatmap/slink.py deleted file mode 100755 index 3de41de4..00000000 --- a/web/webqtl/heatmap/slink.py +++ /dev/null @@ -1,141 +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 - -#--Only imported by correlationPage.py. -# -#Functions: -#slink(lists) -- the only function called outside of this file. -#nearest(lists,i,j) -- some sort of recursive function. -#printarray(array,n) -- prints n elements of the given array -#this is a myseterious piece of code in GN that Kev Adler and Rob Williams do not understand. -#but is used in some way by the Traits Correlation function -#Kev and Rob suspect that the d2 matrix below is unused -#We do not understand the signifance of "d" but Kev suspects it is unimportant -#These comments by Kev and Rob: May 23, 2008 - -d = [[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]] -d2 = [[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]] - -def nearest(lists,i,j): - if type(i) == type(1) and type(j) == type(1): - return lists[i][j] - elif type(i) == type(1): - dist = 1e10 - for itemj in j[:-1]: - d = nearest(lists,i,itemj) - if dist > d: - dist = d - elif type(j) == type(1): - dist = 1e10 - for itemi in i[:-1]: - d = nearest(lists,itemi,j) - if dist > d: - dist = d - else: - dist = 1e10 - for itemi in i[:-1]: - for itemj in j[:-1]: - d = nearest(lists,itemi,itemj) - if dist > d: - dist = d - return dist - -def printarray(array,n): - print "\n" - for i in range(n): - print array[i][:n] - print "\n" - -def slink(lists): - try: - if type(lists) != type([]) and type(lists) != type(()): - raise 'FormatError' - else: - size = len(lists) - for item in lists: - if type(item) != type([]) and type(item) != type(()): - raise 'FormatError' - else: - if len(item) != size: - raise 'LengthError' - for i in range(size): - if lists[i][i] != 0: - raise 'ValueError' - for j in range(0,i): - if lists[i][j] < 0: - raise 'ValueError' - if lists[i][j] != lists[j][i]: - raise 'MirrorError' - except 'FormatError': - print "the format of the list is incorrect!" - return [] - except 'LengthError': - print "the list is not a square list!" - return [] - except 'MirrorError': - print "the list is not symmetric!" - return [] - except 'ValueError': - print "the distance is negative value!" - return [] - except: - print "Unknown Error" - return [] - listindex = range(size) - listindexcopy = range(size) - listscopy = [] - for i in range(size): - listscopy.append(lists[i][:]) - initSize = size - candidate = [] - while initSize >2: - mindist = 1e10 - for i in range(initSize): - for j in range(i+1,initSize): - if listscopy[i][j] < mindist: - mindist = listscopy[i][j] - candidate=[[i,j]] - elif listscopy[i][j] == mindist: - mindist = listscopy[i][j] - candidate.append([i,j]) - else: - pass - newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist) - listindexcopy.pop(candidate[0][1]) - listindexcopy[candidate[0][0]] = newmem - - initSize -= 1 - for i in range(initSize): - for j in range(i+1,initSize): - listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j]) - listscopy[j][i] = listscopy[i][j] - #print listindexcopy - #printarray(listscopy,initSize) - listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1])) - return listindexcopy - - - |