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Diffstat (limited to 'web/webqtl/networkGraph/networkGraphPage.py')
| -rwxr-xr-x | web/webqtl/networkGraph/networkGraphPage.py | 335 |
1 files changed, 335 insertions, 0 deletions
diff --git a/web/webqtl/networkGraph/networkGraphPage.py b/web/webqtl/networkGraph/networkGraphPage.py new file mode 100755 index 00000000..fb4021f0 --- /dev/null +++ b/web/webqtl/networkGraph/networkGraphPage.py @@ -0,0 +1,335 @@ +# 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 NL 2010/02/11 + +#!/usr/bin/python +# networkGraph.py +# Author: Stephen Pitts +# 6/2/2004 +# +# a script to take a matrix of data from a WebQTL job and generate a +# graph using the neato package from GraphViz +# +# See graphviz for documentation of the parameters +# + + +#from mod_python import apache, util, Cookie +#import cgi +import tempfile +import os +import time +import sys +import cgitb +import string + +from htmlgen import HTMLgen2 as HT + +from base.templatePage import templatePage +import networkGraphUtils +from base import webqtlConfig +from utility import webqtlUtil +from base.webqtlTrait import webqtlTrait +import compareCorrelates.trait as smpTrait +from GraphPage import GraphPage +from networkGraphPageBody import networkGraphPageBody +from correlationMatrix.tissueCorrelationMatrix import tissueCorrelationMatrix + +cgitb.enable() + + +class networkGraphPage(templatePage): + + 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'] + + |