def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
#read input fields
self.action = fd.formdata.getvalue("action", "").strip()
self.geneSymbols = fd.formdata.getvalue("geneSymbols","").strip()
self.tissueProbeSetFeezeId = fd.formdata.getvalue("tissueProbeSetFeezeId", "").strip()
self.recordReturnNum = fd.formdata.getvalue("recordReturnNum", "0").strip()
self.calculateMethod = fd.formdata.getvalue("calculateMethod", "0").strip()
TissueCorrMatrixObject = tissueCorrelationMatrix(tissueProbeSetFreezeId=self.tissueProbeSetFeezeId)
if not self.geneSymbols:
# default page
Heading = HT.Paragraph("Tissue Correlation", Class="title")
Intro = HT.Blockquote("This function computes correlations between transcript expression across different organs and tissues.")
Intro.append(HT.BR(),"Select a data set from the pull-down menu and then compute correlations.")
formName='searchTissueCorrelation'
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), target='_blank',enctype='multipart/form-data', name= formName, submit=HT.Input(type='hidden'))
form.append(HT.Input(type="hidden", name="FormID", value=""))
form.append(HT.Input(type="hidden", name="action", value="disp"))
# added by NL 10/12/2010, retreive dataSet info from TissueProbeSetFreeze to get all TissueProbeSetFreezeId, datasetName and FullName
tissProbeSetFreezeIds,dataSetNames,dataSetfullNames = TissueCorrMatrixObject.getTissueDataSet()
dataSetList=[]
for i in range(len(tissProbeSetFreezeIds)):
dataSetList.append((dataSetfullNames[i], tissProbeSetFreezeIds[i]))
dataSetMenu = HT.Select(dataSetList,name="tissueProbeSetFeezeId")
InfoFile =HT.Input(type="button", Class="button", value=" Info ", onClick="tissueDatasetInfo(this.form.tissueProbeSetFeezeId,%s);"%(dataSetNames))
form.append(HT.Strong(" "),dataSetMenu,InfoFile,HT.BR());
form.append(HT.BR(),HT.Strong(" Please enter only one gene symbol/ENTREZ gene Id per line."),HT.BR(),HT.Strong(" "),HT.Textarea(name="geneSymbols", rows=10, cols=50, text=""),HT.BR(),HT.BR())
# calculate method radio button
calculateMethodMenu =HT.Input(type="radio", name="calculateMethod", value="0", checked="checked")
calculateMethodMenu1 =HT.Input(type="radio", name="calculateMethod", value="1")
# record Return method dropdown menu
recordReturnMenu = HT.Select(name="recordReturnNum")
recordReturnMenu.append(('Top 100','0'))
recordReturnMenu.append(('Top 200','1'))
recordReturnMenu.append(('Top 500','2'))
recordReturnMenu.append(('Top 1000','3'))
recordReturnMenu.append(('Top 2000','4'))
recordReturnMenu.append(('All','5'))
# working for input symbol has only one;
form.append(HT.Strong(" "),HT.Span("Return:", Class="ffl fwb fs12"),HT.Strong(" "),recordReturnMenu,HT.BR());
form.append(HT.BR(),HT.Strong(" "),'Pearson',calculateMethodMenu," "*3,'Spearman Rank',calculateMethodMenu1,HT.BR(),HT.BR());
form.append(HT.Strong(" "),HT.Input(type="button", value=" Compute ", Class="button",onClick="selectFormIdForTissueCorr('%s');"%formName))
form.append(HT.Strong(" "),HT.Input(type="button", Class="button", value=" Make Default ", onClick = "makeTissueCorrDefault(this.form);"))
TD_LR = HT.TD(height=200,width="100%",bgcolor='#eeeeee',align="left")
TD_LR.append(Heading,Intro,form)
self.content_type = 'text/html'
self.dict['js1'] = '<SCRIPT SRC="/javascript/correlationMatrix.js"></SCRIPT><BR>'
# get tissueProbesetFreezeId from cookie
self.dict['js2'] = 'onload ="getTissueCorrDefault(\'searchTissueCorrelation\');"'
self.dict['body'] = str(TD_LR)
self.dict['title'] = "Tissue Correlation"
elif self.action == 'disp':
TissueCount =TissueCorrMatrixObject.getTissueCountofCurrentDataset()
# add by NL for first Note part in the tissue correlation page. 2010-12-23
note =""
dataSetName=""
datasetFullName=""
dataSetName, datasetFullName= TissueCorrMatrixObject.getFullnameofCurrentDataset()
noteURL = "../dbdoc/"+ dataSetName+".html"
noteText = " was used to compute expression correlation across %s samples of tissues and organs. ["%TissueCount
# dataset download
datasetURL = "../dbdoc/"+ dataSetName+".xls"
datasetDownload =HT.Href(text="Download experiment data",url=datasetURL,Class='fs13',target="_blank")
note = HT.Blockquote(HT.Href(text=datasetFullName,url=noteURL,Class='fs13',target="_blank"),noteText, datasetDownload,"]",HT.BR())
geneSymbolLst = [] # gene Symbol list
geneSymbolLst = TissueCorrMatrixObject.getGeneSymbolLst(self.geneSymbols)
symbolCount = len(geneSymbolLst)
# The input symbol limit is 100.
heading = "Tissue Correlation"
if symbolCount > 100:
detail = ['The Gene symbols you have input are more than 100. Please limit them to 100.']
self.error(heading=heading,detail=detail)
return
elif symbolCount==0:
detail = ['No Gene Symbol was input. No Tissue Correlation matrix generated.' ]
self.error(heading=heading,detail=detail)
return
else:
# search result page
# The input symbols should be no less than 1.
self.content_type = 'text/html'
if symbolCount == 1:
self.displaySingleSymbolResultPage(primaryGeneSymbol=geneSymbolLst[0],datasetFullName=datasetFullName,tProbeSetFreezeId=self.tissueProbeSetFeezeId, TissueCorrMatrixObject =TissueCorrMatrixObject,recordReturnNum=self.recordReturnNum,method=self.calculateMethod, note=note,TissueCount =TissueCount)
else:
self.displayMultiSymbolsResultPage(geneSymbolLst=geneSymbolLst, symbolCount=symbolCount, tProbeSetFreezeId=self.tissueProbeSetFeezeId,TissueCorrMatrixObject =TissueCorrMatrixObject,note=note,TissueCount =TissueCount)
else:
heading = "Tissue Correlation"
detail = ['There\'s something wrong with input gene symbol(s), or the value of parameter [action] is not right.' ]
self.error(heading=heading,detail=detail)
return
def __init__(self,fd,InputData=None):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if not fd.genotype:
fd.readGenotype()
self.searchResult = fd.formdata.getvalue('searchResult')
self.tissueProbeSetFeezeId = "1" #XZ, Jan 03, 2010: currently, this dataset is "UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)"
TissueCorrMatrixObject = tissueCorrelationMatrix(tissueProbeSetFreezeId=self.tissueProbeSetFeezeId)
if type("1") == type(self.searchResult):
self.searchResult = string.split(self.searchResult, '\t')
if (not self.searchResult or (len(self.searchResult) < 2)):
heading = 'Network Graph'
detail = ['You need to select at least two traits in order to generate Network Graph.']
self.error(heading=heading,detail=detail)
print 'Content-type: text/html\n'
self.write()
return
if self.searchResult:
if len(self.searchResult) > webqtlConfig.MAXCORR:
heading = 'Network Graph'
detail = ['In order to display Network Graph properly, Do not select more than %d traits for Network Graph.' % webqtlConfig.MAXCORR]
self.error(heading=heading,detail=detail)
print 'Content-type: text/html\n'
self.write()
return
else:
pass
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 = 'Network Graph'
detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
self.error(heading=heading,detail=detail)
print 'Content-type: text/html\n'
self.write()
return
NNN = len(traitList)
if NNN < 2:
templatePage.__init__(self, fd)
heading = 'Network Graph'
detail = ['You need to select at least two traits in order to generate a Network Graph']
print 'Content-type: text/html\n'
self.write()
return
else:
pearsonArray = [([0] * (NNN))[:] for i in range(NNN)]
spearmanArray = [([0] * (NNN))[:] for i in range(NNN)]
GeneIdArray = []
GeneSymbolList = [] #XZ, Jan 03, 2011: holds gene symbols for calculating tissue correlation
traitInfoArray = []
i = 0
nnCorr = len(fd.strainlist)
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)
pearsonArray[i][j] = corr
pearsonArray[j][i] = corr
elif j == i:
pearsonArray[i][j] = 1.0
spearmanArray[i][j] = 1.0
else:
corr,nOverlap = webqtlUtil.calCorrelationRank(traitDataList[i],traitDataList[j],nnCorr)
spearmanArray[i][j] = corr
spearmanArray[j][i] = corr
GeneId1 = None
tmpSymbol = None
if thisTrait.db.type == 'ProbeSet':
try:
GeneId1 = int(thisTrait.geneid)
except:
GeneId1 = 0
if thisTrait.symbol:
tmpSymbol = thisTrait.symbol.lower()
GeneIdArray.append(GeneId1)
GeneSymbolList.append(tmpSymbol)
_traits = []
_matrix = []
for i in range(NNN):
turl = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s&ProbeSetID=%s' % (traitList[i].db.name, traitList[i].name)
if traitList[i].cellid:
turl += "&CellID=%s" % traitList[i].cellid
if traitList[i].db.type == 'ProbeSet':
if traitList[i].symbol:
_symbol = traitList[i].symbol
else:
_symbol = 'unknown'
elif traitList[i].db.type == 'Publish':
_symbol = traitList[i].name
if traitList[i].confidential:
if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=traitList[i].authorized_users):
if traitList[i].post_publication_abbreviation:
_symbol = traitList[i].post_publication_abbreviation
else:
if traitList[i].pre_publication_abbreviation:
_symbol = traitList[i].pre_publication_abbreviation
else:
if traitList[i].post_publication_abbreviation:
_symbol = traitList[i].post_publication_abbreviation
#XZ, 05/26/2009: Xiaodong add code for Geno data
elif traitList[i].db.type == 'Geno':
_symbol = traitList[i].name
else:
_symbol = traitList[i].description
#####if this trait entered by user
if _symbol.__contains__('entered'):
_symbol = _symbol[:_symbol.index('entered')]
#####if this trait generaged by genenetwork
elif _symbol.__contains__('generated'):
_symbol = _symbol[_symbol.rindex(':')+1:]
newTrait = smpTrait.Trait(name=str(traitList[i]), href=turl, symbol=_symbol)
newTrait.color = "black"
_traits.append(newTrait)
for j in range(i+1, NNN):
dataPoint = smpTrait.RawPoint(i, j)
dataPoint.spearman = spearmanArray[i][j]
dataPoint.pearson = pearsonArray[i][j]
#XZ: get literature correlation info.
if GeneIdArray[i] and GeneIdArray[j]:
if GeneIdArray[i] == GeneIdArray[j]:
dataPoint.literature = 1
else:
self.cursor.execute("SELECT Value from LCorrRamin3 WHERE (GeneId1 = %d and GeneId2 = %d) or (GeneId1 = %d and GeneId2 = %d)" % (GeneIdArray[i], GeneIdArray[j], GeneIdArray[j], GeneIdArray[i]))
try:
dataPoint.literature = self.cursor.fetchone()[0]
except:
dataPoint.literature = 0
else:
dataPoint.literature = 0
#XZ: get tissue correlation info
if GeneSymbolList[i] and GeneSymbolList[j]:
dataPoint.tissue = 0
geneSymbolPair = []
geneSymbolPair.append(GeneSymbolList[i])
geneSymbolPair.append(GeneSymbolList[j])
corrArray,pvArray = TissueCorrMatrixObject.getCorrPvArrayForGeneSymbolPair(geneNameLst=geneSymbolPair)
if corrArray[1][0]:
dataPoint.tissue = corrArray[1][0]
else:
dataPoint.tissue = 0
_matrix.append(dataPoint)
OrigDir = os.getcwd()
sessionfile = fd.formdata.getvalue('session')
inputFilename = fd.formdata.getvalue('inputFile')
#If there is no sessionfile generate one and dump all matrix/trait values
if not sessionfile:
filename = webqtlUtil.generate_session()
webqtlUtil.dump_session([_matrix, _traits], os.path.join(webqtlConfig.TMPDIR, filename + '.session'))
sessionfile = filename
startTime = time.time()
#Build parameter dictionary used by networkGraphPage class using buildParamDict function
params = networkGraphUtils.buildParamDict(fd, sessionfile)
nodes = len(_traits)
rawEdges = len(_matrix)
if params["tune"] == "yes":
params = networkGraphUtils.tuneParamDict(params, nodes, rawEdges)
matrix = networkGraphUtils.filterDataMatrix(_matrix, params)
optimalNode = networkGraphUtils.optimalRadialNode(matrix)
if not inputFilename:
inputFilename = tempfile.mktemp()
inputFilename = webqtlConfig.IMGDIR + inputFilename.split("/")[2]
#writes out 4 graph files for exporting
graphFile = "/image/" + networkGraphUtils.writeGraphFile(matrix, _traits, inputFilename, params)
networkGraphUtils.processDataMatrix(matrix, params)
edges = 0
for edge in matrix:
if edge.value != 0:
edges +=1
for trait in _traits:
trait.name = networkGraphUtils.fixLabel(trait.name)
RootDir = webqtlConfig.IMGDIR
RootDirURL = "/image/"
#This code writes the datafile that the graphviz function runNeato uses to generate the
#"digraph" file that defines the graphs parameters
datafile = networkGraphUtils.writeNeatoFile(matrix=matrix, traits=_traits, filename=inputFilename, GeneIdArray=GeneIdArray, p=params)
#Generate graph in various file types
layoutfile = networkGraphUtils.runNeato(datafile, "dot", "dot", params["gType"]) # XZ, 09/11/2008: add module name
# ZS 03/04/2010 This second output file (layoutfile_pdf) is rotated by 90 degrees to prevent an issue with pdf output being cut off at the edges
layoutfile_pdf = networkGraphUtils.runNeato(datafile + "_pdf", "dot", "dot", params["gType"]) # ZS 03/04/2010
pngfile = networkGraphUtils.runNeato(layoutfile, "png", "png", params["gType"])
mapfile = networkGraphUtils.runNeato(layoutfile, "cmapx", "cmapx", params["gType"])# XZ, 09/11/2008: add module name
giffile = networkGraphUtils.runNeato(layoutfile, "gif", "gif", params["gType"])# XZ, 09/11/2008:add module name
psfile = networkGraphUtils.runNeato(layoutfile_pdf, "ps", "ps", params["gType"])# XZ, 09/11/2008: add module name
pdffile = networkGraphUtils.runPsToPdf(psfile, params["width"], params["height"])# XZ, 09/11/2008: add module name
#This generates text files in XGGML (standardized graphing language) and plain text
#so the user can create his/her own graphs in a program like Cytoscape
htmlfile1 = datafile + ".html"
htmlfile2 = datafile + ".graph.html"
os.chdir(OrigDir)
#This generates the graph in various image formats
giffile = RootDirURL + giffile
pngfile = RootDirURL + pngfile
pdffile = RootDirURL + pdffile
endTime = time.time()
totalTime = endTime - startTime
os.chdir(RootDir)
page2 = GraphPage(giffile, mapfile)
page2.writeToFile(htmlfile2)
#This generates the HTML for the body of the Network Graph page
page1 = networkGraphPageBody(fd, matrix, _traits, htmlfile2, giffile, pdffile, nodes, edges, rawEdges, totalTime, params, page2.content, graphFile, optimalNode)
#Adds the javascript colorSel to the body to allow line color selection
self.dict["js1"] = '<SCRIPT SRC="/javascript/colorSel.js"></SCRIPT><BR>'
#self.dict["js1"] += '<SCRIPT SRC="/javascript/networkGraph.js"></SCRIPT>'
#Set body of current templatePage to body of the templatePage networkGraphPage
self.dict['body'] = page1.dict['body']
