From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001
From: root
Date: Tue, 8 May 2012 18:39:56 -0500
Subject: Add all the source codes into the github.
---
web/webqtl/networkGraph/networkGraphPage.py | 335 ++++++++++++++++++++++++++++
1 file changed, 335 insertions(+)
create mode 100755 web/webqtl/networkGraph/networkGraphPage.py
(limited to 'web/webqtl/networkGraph/networkGraphPage.py')
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"] = '
'
+ #self.dict["js1"] += ''
+
+ #Set body of current templatePage to body of the templatePage networkGraphPage
+ self.dict['body'] = page1.dict['body']
+
+
--
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