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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/networkGraph
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/networkGraph')
-rwxr-xr-xweb/webqtl/networkGraph/GraphPage.py46
-rwxr-xr-xweb/webqtl/networkGraph/ProcessedPoint.py49
-rwxr-xr-xweb/webqtl/networkGraph/__init__.py0
-rwxr-xr-xweb/webqtl/networkGraph/nGraphException.py33
-rwxr-xr-xweb/webqtl/networkGraph/networkGraphPage.py335
-rw-r--r--web/webqtl/networkGraph/networkGraphPageBody.py697
-rw-r--r--web/webqtl/networkGraph/networkGraphUtils.py750
7 files changed, 1910 insertions, 0 deletions
diff --git a/web/webqtl/networkGraph/GraphPage.py b/web/webqtl/networkGraph/GraphPage.py
new file mode 100755
index 00000000..b0d4063d
--- /dev/null
+++ b/web/webqtl/networkGraph/GraphPage.py
@@ -0,0 +1,46 @@
+# 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
+
+class GraphPage:
+
+ def __init__(self, imagefile, mapfile):
+ # open and read the image map file
+ try:
+ mapData = open(mapfile).read()
+ except:
+ mapData = "<p><b>Unable to load image map with trait links</b></p>"
+
+ self.content = '''%s
+ <img border="0" alt="the graph" src="%s" usemap="#webqtlGraph" />
+ ''' % (mapData, imagefile)
+
+ def writeToFile(self, filename):
+ """
+ Output the contents of this HTML page to a file
+ """
+ handle = open(filename, "w")
+ handle.write(self.content)
+ handle.close()
diff --git a/web/webqtl/networkGraph/ProcessedPoint.py b/web/webqtl/networkGraph/ProcessedPoint.py
new file mode 100755
index 00000000..6eb855e3
--- /dev/null
+++ b/web/webqtl/networkGraph/ProcessedPoint.py
@@ -0,0 +1,49 @@
+# 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
+
+# ProcessedPoint: to store information about the relationship between
+# two particular traits
+# ProcessedPoint represents the calculations made by the program
+
+class ProcessedPoint:
+
+ def __init__(self, i, j):
+ self.i = i
+ self.j = j
+
+ def __eq__(self, other):
+ # print "ProcessedPoint: comparing %s and %s" % (self, other)
+ return (self.i == other.i and
+ self.j == other.j and
+ self.value == other.value and
+ self.color == other.color)
+
+ def __str__(self):
+ return "(%s,%s,%s,%s,%s)" % (self.i,
+ self.j,
+ self.value,
+ self.length,
+ self.color)
diff --git a/web/webqtl/networkGraph/__init__.py b/web/webqtl/networkGraph/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/networkGraph/__init__.py
diff --git a/web/webqtl/networkGraph/nGraphException.py b/web/webqtl/networkGraph/nGraphException.py
new file mode 100755
index 00000000..d492fca9
--- /dev/null
+++ b/web/webqtl/networkGraph/nGraphException.py
@@ -0,0 +1,33 @@
+# 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
+
+class nGraphException(Exception):
+ def __init__(self, message):
+ self.message = message
+
+ def __str__(self):
+ return "Network Graph Exception: %s" % self.message
+
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']
+
+
diff --git a/web/webqtl/networkGraph/networkGraphPageBody.py b/web/webqtl/networkGraph/networkGraphPageBody.py
new file mode 100644
index 00000000..22b49ccd
--- /dev/null
+++ b/web/webqtl/networkGraph/networkGraphPageBody.py
@@ -0,0 +1,697 @@
+# 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
+
+from base.templatePage import templatePage
+import networkGraphUtils
+from base import webqtlConfig
+
+
+# our output representation is fairly complicated
+# because we use an iframe to represent the image and the image has
+# an associated image map, our output is actually three files
+# 1) a networkGraphPage instance -- the URL we pass to the user
+# 2) a GraphPage with the image map and the graph -- this page has to be
+# there to pass the imagemap data to the browser
+# 3) a PNG graph file itself
+
+class networkGraphPageBody(templatePage):
+ """
+ Using the templatePage class, we build an HTML shell for the graph
+ that displays the parameters used to generate it and allows the
+ user to redraw the graph with different parameters.
+
+ The way templatePage works, we build the page in pieces in the __init__
+ method and later on use the inherited write method to render the page.
+ """
+
+ def __init__(self, fd, matrix, traits, imageHtmlName, imageName, pdfName, nodes,
+ edges, rawEdges, totalTime, p, graphcode, graphName, optimalNode):
+
+ templatePage.__init__(self, fd)
+
+ if p["printIslands"] == 0:
+ island = "Only nodes with edges"
+ else:
+ island = "All nodes"
+
+ body = """ <td><P class='title'>Network Graph</P>
+ <Blockquote><p>The %s nodes in the
+ graph below show the selected traits. %s are displayed. The
+ %s edges between the nodes, filtered from the %s total edges and
+ drawn as %s, show <b>%s</b> correlation
+ coefficients greater than %s or less than -%s. The graph\'s
+ canvas is %s by %s cm, and the node
+ labels are drawn with a %s point font, and the edge
+ labels are drawn with a %s point font. Right-click or control-click
+ on the graph to save it to disk for further manipulation. See
+ below for the trait key, and graph options.</p>
+ """ % (nodes, island, edges, rawEdges,
+ p["splineName"], p["correlationName"],
+ p["kValue"],
+ p["kValue"],
+ p["width"],
+ p["height"],
+ p["nfontsize"],
+ p["cfontsize"])
+
+ #Generate a list of symbols for the central node selection drop-down menu
+
+ symbolList = networkGraphUtils.generateSymbolList(traits)
+
+ #Some of these hidden variables (CellID, CellID2, ProbesetID2, etc) exist
+ #to be used by the javascript functions called when a user clicks on an edge or node
+
+ formParams = '''
+
+ <form name="showDatabase" action="%s%s" METHOD="POST" enctype="multipart/form-data">
+
+ <input type="hidden" name="filename" value="%s" />
+ <input type="hidden" name="exportFilename" value="%s" />
+ <input type="hidden" name="progress" value="1" />
+ <input type="hidden" name="database" value="_" />
+ <input type="hidden" name="database2" value="_" />
+ <input type="hidden" name="ProbeSetID" value="_" />
+ <input type="hidden" name="ProbeSetID2" value="_" />
+ <input type="hidden" name="CellID" value="_" />
+ <input type="hidden" name="CellID2" value="_" />
+ <input type="hidden" name="tune" value="no" />
+ <input type="hidden" name="ShowLine" value="ON">
+ <input type="hidden" name="ShowStrains" value="ON">
+ <input type="hidden" name="FormID" value="showDatabase" />
+ <input type="hidden" name="RISet" value="%s" />
+ <input type="hidden" name="incparentsf1" value="ON" />
+ <input type="hidden" name="session" value="%s" />
+ <input type="hidden" name="searchResult" id="searchResult" value="%s" />
+ <input type="hidden" name="symbolList" id="symbolList" value="%s" />
+ <input type="hidden" name="optimalNode" id="optimalNode" value="%s" />
+ <input type="hidden" name="rankOrder" id="rankOrder" value="_" />
+ <input type="hidden" name="X_geneID" id="X_geneID" value="_" />
+ <input type="hidden" name="Y_geneID" id="Y_geneID" value="_" />
+ <input type="hidden" name="X_geneSymbol" id="X_geneSymbol" value="_" />
+ <input type="hidden" name="Y_geneSymbol" id="Y_geneSymbol" value="_" />
+ <input type="hidden" name="TissueProbeSetFreezeId" id="TissueProbeSetFreezeId" value="1" />
+ ''' % (webqtlConfig.CGIDIR,
+ webqtlConfig.SCRIPTFILE,
+ p["filename"],
+ graphName,
+ p["riset"],
+ p["session"],
+ p["searchResult"],
+ symbolList,
+ optimalNode)
+
+ body += formParams
+
+ #Adds the html generated by graphviz that displays the graph itself
+ body += graphcode
+
+ #Initializes all form values
+
+ selected = ["","","",""]
+ selected[p["whichValue"]] = "CHECKED"
+
+ selected3 = ["",""]
+ if p["splines"] == "yes":
+ selected3[0] = "CHECKED"
+ else:
+ selected3[1] = "CHECKED"
+
+ selected5 = ["",""]
+ if p["nodeshape"] == "yes":
+ selected5[0] = "CHECKED"
+ else:
+ selected5[1] = "CHECKED"
+
+ selected7 = ["",""]
+ if p["nodelabel"] == "yes":
+ selected7[0] = "CHECKED"
+ else:
+ selected7[1] = "CHECKED"
+
+ selected6 = ["",""]
+ if p["dispcorr"] == "yes":
+ selected6[0] = "CHECKED"
+ else:
+ selected6[1] = "CHECKED"
+
+ selected4 = ["", ""]
+ selected4[p["printIslands"]] = "CHECKED"
+
+ selectedExportFormat = ["",""]
+ if p["exportFormat"] == "xgmml":
+ selectedExportFormat[0] = "selected='selected'"
+ elif p["exportFormat"] == "plain":
+ selectedExportFormat[1] = "selected='selected'"
+
+ selectedTraitType = ["",""]
+ if p["traitType"] == "symbol":
+ selectedTraitType[0] = "selected='selected'"
+ elif p["traitType"] == "name":
+ selectedTraitType[1] = "selected='selected'"
+
+ selectedgType = ["","","","",""]
+ if p["gType"] == "none":
+ selectedgType[0] = "selected='selected'"
+ elif p["gType"] == "neato":
+ selectedgType[1] = "selected='selected'"
+ elif p["gType"] == "fdp":
+ selectedgType[2] = "selected='selected'"
+ elif p["gType"] == "circular":
+ selectedgType[3] = "selected='selected'"
+ elif p["gType"] == "radial":
+ selectedgType[4] = "selected='selected'"
+
+
+ selectedLock = ["",""]
+ if p["lock"] == "no":
+ selectedLock[0] = "selected='selected'"
+ elif p["lock"] == "yes":
+ selectedLock[1] = "selected='selected'"
+
+ # line 1~6
+
+ selectedL1style = ["","","","",""]
+ if p["L1style"] == "":
+ selectedL1style[0] = "selected='selected'"
+ elif p["L1style"] == "bold":
+ selectedL1style[1] = "selected='selected'"
+ elif p["L1style"] == "dotted":
+ selectedL1style[2] = "selected='selected'"
+ elif p["L1style"] == "dashed":
+ selectedL1style[3] = "selected='selected'"
+ else:
+ selectedL1style[4] = "selected='selected'"
+
+ selectedL2style = ["","","","",""]
+ if p["L2style"] == "":
+ selectedL2style[0] = "selected='selected'"
+ elif p["L2style"] == "bold":
+ selectedL2style[1] = "selected='selected'"
+ elif p["L2style"] == "dotted":
+ selectedL2style[2] = "selected='selected'"
+ elif p["L2style"] == "dashed":
+ selectedL2style[3] = "selected='selected'"
+ else:
+ selectedL2style[4] = "selected='selected'"
+
+ selectedL3style = ["","","","",""]
+ if p["L3style"] == "":
+ selectedL3style[0] = "selected='selected'"
+ elif p["L3style"] == "bold":
+ selectedL3style[1] = "selected='selected'"
+ elif p["L3style"] == "dotted":
+ selectedL3style[2] = "selected='selected'"
+ elif p["L3style"] == "dashed":
+ selectedL3style[3] = "selected='selected'"
+ else:
+ selectedL3style[4] = "selected='selected'"
+
+ selectedL4style = ["","","","",""]
+ if p["L4style"] == "":
+ selectedL4style[0] = "selected='selected'"
+ elif p["L4style"] == "bold":
+ selectedL4style[1] = "selected='selected'"
+ elif p["L4style"] == "dotted":
+ selectedL4style[2] = "selected='selected'"
+ elif p["L4style"] == "dashed":
+ selectedL4style[3] = "selected='selected'"
+ else:
+ selectedL4style[4] = "selected='selected'"
+
+ selectedL5style = ["","","","",""]
+ if p["L5style"] == "":
+ selectedL5style[0] = "selected='selected'"
+ elif p["L5style"] == "bold":
+ selectedL5style[1] = "selected='selected'"
+ elif p["L5style"] == "dotted":
+ selectedL5style[2] = "selected='selected'"
+ elif p["L5style"] == "dashed":
+ selectedL5style[3] = "selected='selected'"
+ else:
+ selectedL5style[4] = "selected='selected'"
+
+ selectedL6style = ["","","","",""]
+ if p["L6style"] == "":
+ selectedL6style[0] = "selected='selected'"
+ elif p["L6style"] == "bold":
+ selectedL6style[1] = "selected='selected'"
+ elif p["L6style"] == "dotted":
+ selectedL6style[2] = "selected='selected'"
+ elif p["L6style"] == "dashed":
+ selectedL6style[3] = "selected='selected'"
+ else:
+ selectedL6style[4] = "selected='selected'"
+
+ nfontSelected = ["", "", ""]
+ if p["nfont"] == "arial":
+ nfontSelected[0] = "selected='selected'"
+ elif p["nfont"] == "verdana":
+ nfontSelected[1] = "selected='selected'"
+ elif p["nfont"] == "times":
+ nfontSelected[2] = "selected='selected'"
+
+ cfontSelected = ["", "", ""]
+ if p["cfont"] == "arial":
+ cfontSelected[0] = "selected='selected'"
+ elif p["cfont"] == "verdana":
+ cfontSelected[1] = "selected='selected'"
+ elif p["cfont"] == "times":
+ cfontSelected[2] = "selected='selected'"
+
+ #Writes the form part of the body
+
+ body += ''' <br><br>
+ <TABLE cellspacing=0 Cellpadding=0>
+ <TR>
+ <TD class="doubleBorder">
+
+ <Table Cellpadding=3>
+
+ <tr><td align="left">
+ <dd>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+ <input type="submit" name="mintmap" value=" Redraw " class="button" onClick="return sortSearchResults(this.form);" />
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+ <input TYPE="Button" class="button" value=" Info " onclick="javascript:window.open('/networkGraphInfo.html', '_blank');">
+ </dd>
+ </td></tr>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+ <tr>
+ <tr align='left' valign='top'>
+ <td align='left'>
+ &nbsp;<select align='left' name='gType' id='gType' onchange='addTraitSelection();'>
+ <option value='none' %s>Select Graph Method</option>
+ <option value='neato' %s>Spring Model Layout (energy reduction)</option>
+ <option value='fdp' %s>Spring Model Layout (force reduction)</option>
+ <option value='circular' %s>Circular Layout</option>
+ <option value='radial' %s>Radial Layout</option>
+ </select>
+ <div align="left" id='nodeSelect'> </div>
+ </td>
+ </tr>
+ </tr>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <tr><td align='center' colspan='2'>
+
+ <table width='100%%'>
+
+ <tr align='left'>
+ <td>Lock Graph Structure</td>
+ <td align='left'><select name='lock' id='lock' onChange="changeThreshold();">
+ <option value='no' %s>No</option>
+ <option value='yes' %s>Yes</option>
+ </select></td>
+ </tr>
+ <tr><td align='left' colspan='2' nowrap='nowrap'>
+ Locking the graph structure allows the user to hold the position of<br>
+ all nodes and the length of all edges constant, letting him/her easily<br>
+ compare between different correlation types. Changing the value to "yes"<br>
+ requires the line threshold to be set to 0 in order to lock the structure.<br>
+ </td></tr>
+ </td>
+ </tr>
+
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <tr><td align='center' colspan='2'>
+
+ <table width='100%%'>
+
+ <tr align='center'>
+ <td>Line Type 1:</td>
+ <td>-1</td>
+ <td>to</td>
+ <td>-0.7</td>
+ <td><Input type=radio name=colorS value="cL1" checked></TD>
+ <td bgcolor="%s" ID="cL1" width=20></td>
+ <td><select name='L1style'>
+ <option value='' %s>normal</option>
+ <option value='bold' %s>bold</option>
+ <option value='dotted' %s>dotted</option>
+ <option value='dashed' %s>dashed</option>
+ <option value='invis' %s>invisible</option>
+ </select></td>
+ </tr>
+
+ <tr align='center'>
+ <td>Line Type 2:</td>
+ <td>-0.7</td>
+ <td>to</td>
+ <td>-0.5</td>
+ <td><Input type=radio name=colorS value="cL2"></TD>
+ <Td bgcolor="%s" ID="cL2" width=20></td>
+ <td><select name='L2style'>
+ <option value='' %s>normal</option>
+ <option value='bold' %s>bold</option>
+ <option value='dotted' %s>dotted</option>
+ <option value='dashed' %s>dashed</option>
+ <option value='invis' %s>invisible</option>
+ </select></td>
+ </tr>
+
+ <tr align='center'>
+ <td>Line Type 3:</td>
+ <td>-0.5</td>
+ <td>to</td>
+ <td>0</td>
+ <td><Input type=radio name=colorS value="cL3"></TD>
+ <Td bgcolor="%s" ID="cL3" width=20></td>
+ <td><select name='L3style'>
+ <option value='' %s>normal</option>
+ <option value='bold' %s>bold</option>
+ <option value='dotted' %s>dotted</option>
+ <option value='dashed' %s>dashed</option>
+ <option value='invis' %s>invisible</option>
+ </select></td>
+ </tr>
+
+ <tr align='center'>
+ <td>Line Type 4:</td>
+ <td>0</td>
+ <td>to</td>
+ <td>0.5</td>
+ <td><Input type=radio name=colorS value="cL4"></TD>
+ <Td bgcolor="%s" ID="cL4" width=20></td>
+ <td><select name='L4style'>
+ <option value='' %s>normal</option>
+ <option value='bold' %s>bold</option>
+ <option value='dotted' %s>dotted</option>
+ <option value='dashed' %s>dashed</option>
+ <option value='invis' %s>invisible</option>
+ </select></td>
+ </tr>
+
+ <tr align='center'>
+ <td>Line Type 5:</td>
+ <td>0.5</td>
+ <td>to</td>
+ <td>0.7</td>
+ <td><Input type=radio name=colorS value="cL5"></TD>
+ <Td bgcolor="%s" ID="cL5" width=20></td>
+ <td><select name='L5style'>
+ <option value='' %s>normal</option>
+ <option value='bold' %s>bold</option>
+ <option value='dotted' %s>dotted</option>
+ <option value='dashed' %s>dashed</option>
+ <option value='invis' %s>invisible</option>
+ </select></td>
+ </tr>
+
+ <tr align='center'>
+ <td>Line Type 6:</td>
+ <td>0.7</td>
+ <td>to</td>
+ <td>1</td>
+ <td><Input type=radio name=colorS value="cL6"></TD>
+ <Td bgcolor="%s" ID="cL6" width=20></td>
+ <td><select name='L6style'>
+ <option value='' %s>normal</option>
+ <option value='bold' %s>bold</option>
+ <option value='dotted' %s>dotted</option>
+ <option value='dashed' %s>dashed</option>
+ <option value='invis' %s>invisible</option>
+ </select></td>
+ </tr>
+
+ </table>
+ </td>
+ </tr>
+
+ <tr><td align='center' colspan='2' nowrap='nowrap'>To change colors, select Line Type then select Color below.</td></tr>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <tr>
+ <TD align="right">Correlation Type:</TD>
+ <TD>
+ <table border='0' cellspacing='0' cellpadding='0' width='100%%'>
+ <tr>
+ <td><Input type="radio" name="whichValue" value="0" %s>Pearson</td>
+ <td><Input type="radio" name="whichValue" value="1" %s>Spearman</td>
+ <td rowspan=2 align="center"><input TYPE="Button" class="button" value="Info" onclick="javascript:window.open('/correlationAnnotation.html', '_blank');"></td>
+ </tr>
+ <tr>
+ <td><Input type="radio" name="whichValue" value="2" %s>Literature</td>
+ <td><Input type="radio" name="whichValue" value="3" %s>Tissue</td>
+ </tr>
+ </table>
+ </TD>
+ </TR>
+
+ <TR>
+ <TD align="right" NOWRAP>Line Threshold:</TD>
+ <TD NOWRAP>Absolute values greater than <input size="5" name="kValue" id="kValue" value="%s"></TD>
+ </TR>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <TR>
+ <TD align="right">Draw Nodes :</TD>
+ <TD NOWRAP>
+ <Input type="radio" name="printIslands" value="1" %s>all
+ <Input type="radio" name="printIslands" value="0" %s>connected only
+ </TD>
+ </TR>
+
+ <TR>
+ <TD align="right">Node Shape:</TD>
+ <TD>
+ <Input type="radio" name="nodeshape" value="yes" %s>rectangle
+ <Input type="radio" name="nodeshape" value="no" %s>ellipse
+ </TD>
+ </TR>
+
+ <TR>
+ <TD align="right">Node Label:</TD>
+ <TD>
+ <Input type="radio" name="nodelabel" value="yes" %s>trait name<br>
+ <Input type="radio" name="nodelabel" value="no" %s>gene symbol / marker name
+ </TD>
+ </TR>
+
+ <tr>
+ <td align="right">Node Font:</td>
+ <TD>
+ <select name='nfont'>
+ <option value='Arial' %s>Arial</option>
+ <option value='Verdana' %s>Verdana</option>
+ <option value='Times' %s>Times</option>
+ </select>
+ </TD>
+ </TR>
+
+ <tr>
+ <td align="right">Node Font Size:</td>
+ <TD><input size="5" name="nfontsize" value="%s"> point</TD>
+ </TR>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <TR>
+ <TD align="right">Draw Lines:</TD>
+ <TD>
+ <Input type="radio" name="splines" value="yes" %s>curved
+ <Input type="radio" name="splines" value="no" %s>straight
+ </TD>
+ </TR>
+
+ <TR>
+ <TD align="right">Display Correlations:</TD>
+ <TD>
+ <Input type="radio" name="dispcorr" value="no" %s>no
+ <Input type="radio" name="dispcorr" value="yes" %s>yes
+ </TD>
+ </tr>
+
+ <tr>
+ <td align="right">Line Font:</td>
+ <TD>
+ <select name='cfont'>
+ <option value='Arial' %s>Arial</option>
+ <option value='Verdana' %s>Verdana</option>
+ <option value='Times' %s>Times</option>
+ </select>
+ </TD>
+ </TR>
+
+ <TR>
+ <TD align="right" nowrap="nowrap">Line Font Size:</TD>
+ <TD><input size="5" name="cfontsize" value="%s"> point</TD>
+ </TR>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <TR><TD colspan = 2>
+
+ <Input type=hidden name=cPubName value="%s">
+ <Input type=hidden name=cMicName value="%s">
+ <Input type=hidden name=cGenName value="%s">
+
+ <Input type=hidden name=cPubColor value="%s">
+ <Input type=hidden name=cMicColor value="%s">
+ <Input type=hidden name=cGenColor value="%s">
+
+ <Input type=hidden name=cL1Name value="%s">
+ <Input type=hidden name=cL2Name value="%s">
+ <Input type=hidden name=cL3Name value="%s">
+ <Input type=hidden name=cL4Name value="%s">
+ <Input type=hidden name=cL5Name value="%s">
+ <Input type=hidden name=cL6Name value="%s">
+
+ <Input type=hidden name=cL1Color value="%s">
+ <Input type=hidden name=cL2Color value="%s">
+ <Input type=hidden name=cL3Color value="%s">
+ <Input type=hidden name=cL4Color value="%s">
+ <Input type=hidden name=cL5Color value="%s">
+ <Input type=hidden name=cL6Color value="%s">
+
+ <Input type=hidden id=initThreshold value="0.5">
+
+ <Table CellSpacing = 3>
+ <tr>
+ <TD><Input type=radio name=colorS value="cPub"> Publish </TD>
+ <Td bgcolor="%s" ID="cPub" width=20 height=10></td>
+ <TD><Input type=radio name=colorS value="cMic"> Microarray </TD>
+ <Td bgcolor="%s" ID="cMic" width=20 height=10></td>
+ <TD><Input type=radio name=colorS value="cGen"> Genotype </TD>
+ <Td bgcolor="%s" ID="cGen" width=20 height=10></td>
+ </tr>
+ </table>
+
+ </td></tr>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <tr>
+ <td colspan='2' align='center'>
+ <img NAME="colorPanel" src="/images/colorPanel.png" alt="colorPanel" onClick="clickHandler(event, this);">
+ </TD>
+ </TR>
+
+ <tr><td align='center' colspan='2'><hr size='1'></td></tr>
+
+ <tr><td align='center' colspan='2'><input type="submit" name="mintmap" value=" Redraw Graph " class="button" onClick="return sortSearchResults(this.form);"/></td></tr>
+
+ </TABLE>
+ </form></TD>
+ <SCRIPT type="text/javascript" SRC="/javascript/networkGraph.js"></SCRIPT>
+ ''' % (selectedgType[0], selectedgType[1], selectedgType[2], selectedgType[3], selectedgType[4],
+ selectedLock[0], selectedLock[1],
+ p["cL1Color"],
+ selectedL1style[0], selectedL1style[1], selectedL1style[2], selectedL1style[3], selectedL1style[4],
+ p["cL2Color"],
+ selectedL2style[0], selectedL2style[1], selectedL2style[2], selectedL2style[3], selectedL2style[4],
+ p["cL3Color"],
+ selectedL3style[0], selectedL3style[1], selectedL3style[2], selectedL3style[3], selectedL3style[4],
+ p["cL4Color"],
+ selectedL4style[0], selectedL4style[1], selectedL4style[2], selectedL4style[3], selectedL4style[4],
+ p["cL5Color"],
+ selectedL5style[0], selectedL5style[1], selectedL5style[2], selectedL5style[3], selectedL5style[4],
+ p["cL6Color"],
+ selectedL6style[0], selectedL6style[1], selectedL6style[2], selectedL6style[3], selectedL6style[4],
+ selected[0], selected[1], selected[2], selected[3],
+ p["kValue"],
+ selected4[1], selected4[0],
+ selected5[0], selected5[1],
+ selected7[0], selected7[1],
+ nfontSelected[0], nfontSelected[1], nfontSelected[2],
+ p["nfontsize"],
+ selected3[0], selected3[1],
+ selected6[1], selected6[0],
+ cfontSelected[0], cfontSelected[1], cfontSelected[2],
+ p["cfontsize"],
+ p["cPubName"], p["cMicName"], p["cGenName"],
+ p["cPubColor"], p["cMicColor"], p["cGenColor"],
+ p["cL1Name"], p["cL2Name"], p["cL3Name"], p["cL4Name"], p["cL5Name"], p["cL6Name"],
+ p["cL1Color"], p["cL2Color"], p["cL3Color"], p["cL4Color"], p["cL5Color"], p["cL6Color"],
+ p["cPubColor"], p["cMicColor"], p["cGenColor"])
+
+ #updated by NL 09-03-2010 function changeFormat() has been moved to webqtl.js and be changed to changeFormat(graphName)
+ #Javascript that selects the correct graph export file given what the user selects
+ #from the two drop-down menus
+
+ body += ''' <td width='10'>&nbsp;</td>
+ <TD valign="top"><p>Right-click or control-click on the following
+ links to download this graph as a <a href="%s" class="normalsize" target="_blank">GIF file</a> or
+ a <a href="%s" class="normalsize" target="_blank">PDF file</a>.</p> ''' % (imageName, pdfName)
+
+ body += ''' <p>Initial edge lengths were computed by applying an r-to-Z transform to the correlation coefficents
+ and then inverting the results. The graph drawing algorithm
+ found a configuration that minimizes the total stretching of the edges.</p> '''
+
+ body += ''' <p>This graph took %s seconds to generate with the <a href="http://www.research.att.com/sw/tools/graphviz/" class="normalsize" target="_blank">
+ GraphViz</a> visualization toolkit from <a href="http://www.research.att.com" class="normalsize" target="_blank">AT&amp;T Research</a>.</p>''' % (round(totalTime, 2))
+
+ #Form to export graph file as either XGMML (standardized graphing format) or a
+ #plain text file with trait names/symbols and correlations
+
+ body += '''
+ <form name="graphExport">
+ <p>Export Graph File:</p>
+ <p><select name='exportFormat' id='exportFormat' onchange='changeFormat("%s")'>
+ <option value='plain' %s>Plain Text Format</option>
+ <option value='xgmml' %s>XGMML Format</option>
+ </select>
+ &nbsp&nbsp&nbsp&nbsp&nbsp
+ <select name='traitType' id='traitType' onchange='changeFormat("%s")'>
+ <option value='symbol' %s>Trait Symbol</option>
+ <option value='name' %s>Full Trait Name</option>
+ </select></p>
+
+ <p>
+ <input type="button" class="button" name="exportGraphFile" value=" Export Graph File "/>
+ </p>
+ </form>
+ ''' % (graphName, selectedExportFormat[0], selectedExportFormat[1],
+ graphName, selectedTraitType[0], selectedTraitType[1])
+
+ body += '''</Blockquote></td>
+ </TR></TABLE>
+ <form method="get" action="http://www.google.com/search">
+ <input type="text" name="q" size="31" maxlength="255" value="" />
+ <input type="submit" value="Google Search" />
+ <input type="radio" name="sitesearch" value="" /> The Web
+ <input type="radio" name="sitesearch" value="genenetwork.org" checked /> GeneNetwork <br />
+ </form>
+ '''
+
+
+ self.dict["body"] = body
+
+ def writeToFile(self, filename):
+ """
+ Output the contents of this HTML page to a file.
+ """
+ handle = open(filename, "w")
+ handle.write(str(self))
+ handle.close()
diff --git a/web/webqtl/networkGraph/networkGraphUtils.py b/web/webqtl/networkGraph/networkGraphUtils.py
new file mode 100644
index 00000000..fd0e7484
--- /dev/null
+++ b/web/webqtl/networkGraph/networkGraphUtils.py
@@ -0,0 +1,750 @@
+# 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
+
+# graphviz:
+# a library for sending trait data to the graphviz utilities to get
+# graphed
+
+# ParamDict: a dictionary of strings that map to strings where the keys are
+# valid parameters and the values are validated versions of those parameters
+#
+# The list below also works for visualize.py; different parameters apply to different
+# functions in the pipeline. See visualize.py for more details.
+#
+# parameters:
+# filename: an input file with comma-delimited data to visualize
+# kValue:
+# how to filter the edges; edges with correlation coefficents in
+# [-k, k] are not drawn
+# whichValue: which of the two correlation coefficents are used;
+# 0 means the top half (pearson) and
+# 1 means the bottom half (spearman)
+# width: the width of the graph in inches
+# height: the height of the graph in inches
+# --scale: an amount to multiply the length factors by to space out the nodes
+# spline: whether to use splines instead of straight lines to draw graphs
+# tune: whether to automatically pick intelligent default values for
+# kValue and spline based on the number of edges in the input data
+# whichVersion: whether to display the graph zoomed or fullscreen
+# 0 means zoom
+# 1 means fullscreen
+# printIslands: whether to display nodes with no visible edges
+#
+
+# DataMatrix: a one-dimensional array of DataPoints in sorted order by i first
+
+
+
+import copy
+import os
+#import os.path
+import math
+import string
+
+from base import webqtlConfig
+from utility import webqtlUtil
+#import trait
+from nGraphException import nGraphException
+from ProcessedPoint import ProcessedPoint
+
+
+# processDataMatrix: DataMatrix -> ParamDict -> void
+# this is the second part after filterDataMatrix
+# To process the set of points in a DataMatrix as follows
+# 1) choose an appropriate color for the data point
+# 2) filter those between k values
+# 3) to use an r-to-Z transform to spread out the correlation
+# values from [-1,1] to (-inf, inf)
+# 4) to invert the values so that higher correlations result in
+# shorter edges
+#
+# Note: this function modifies the matrix in-place. My functional
+# programming instincts tell me that this is a bad idea.
+def processDataMatrix(matrix, p):
+ for pt2 in matrix:
+ # filter using k
+ if (-p["kValue"] <= pt2.value) and (pt2.value <= p["kValue"]):
+ pt2.value = 0.00
+
+ # Lei Yan
+ # 05/28/2009
+ # fix color
+
+ # pick a color
+ if pt2.value >= 0.7:
+ pt2.color = p["cL6Name"]
+ pt2.style = p["L6style"]
+ elif pt2.value >= 0.5:
+ pt2.color = p["cL5Name"]
+ pt2.style = p["L5style"]
+ elif pt2.value >= 0.0:
+ pt2.color = p["cL4Name"]
+ pt2.style = p["L4style"]
+ elif pt2.value >= -0.5:
+ pt2.color = p["cL3Name"]
+ pt2.style = p["L3style"]
+ elif pt2.value >= -0.7:
+ pt2.color = p["cL2Name"]
+ pt2.style = p["L2style"]
+ else:
+ pt2.color = p["cL1Name"]
+ pt2.style = p["L1style"]
+
+ # r to Z transform to generate the length
+ # 0 gets transformed to infinity, which we can't
+ # represent here, and 1 gets transformed to 0
+ if p["lock"] == "no":
+ if -0.01 < pt2.value and pt2.value < 0.01:
+ pt2.length = 1000
+ elif pt2.value > 0.99 or pt2.value < -0.99:
+ pt2.length = 0
+ else:
+ pt2.length = pt2.value
+ pt2.length = 0.5 * math.log((1 + pt2.length)/(1 - pt2.length))
+
+ # invert so higher correlations mean closer edges
+ #pt2.length = abs(p["scale"] * 1/pt2.length)
+ pt2.length = abs(1/pt2.length)
+ else:
+ pt2.length = 2
+
+
+# tuneParamDict: ParamDict -> Int -> Int -> ParamDict
+# to adjust the parameter dictionary for a first-time run
+# so that the graphing doesn't take so long, especially since
+# small parameter changes can make a big performance difference
+# note: you can pass this function an empty dictionary and
+# get back a good set of default parameters for your
+# particular graph
+def tuneParamDict(p, nodes, edges):
+ newp = copy.deepcopy(p)
+
+ if nodes > 50:
+ newp["splines"] = "no"
+ else:
+ newp["splines"] = "yes"
+
+ if edges > 1000:
+ newp["printIslands"] = 0
+ else:
+ newp["printIslands"] = 1
+
+ if edges > 1000:
+ newp["kValue"] = 0.8
+ elif edges > 500:
+ newp["kValue"] = 0.7
+ elif edges > 250:
+ newp["kValue"] = 0.6
+
+ if nodes > 50:
+ # there's no magic here; this formula
+ # just seems to work
+ dim = 3*math.sqrt(nodes)
+ newp["width"] = round(dim,2)
+ newp["height"] = round(dim,2)
+
+ # the two values below shouldn't change
+ # newp["scale"] = round(dim/10.0,2)
+ # newp["fontsize"] = round(14*newp["scale"],0)
+
+ else:
+ newp["width"] = 40.0
+ newp["height"] = 40.0
+
+ return newp
+
+# fixLabel : string -> string
+def fixLabel(lbl):
+ """
+ To split a label with newlines so it looks a bit better
+ Note: we send the graphing program literal '\n' strings and
+ it converts these into newlines
+ """
+ lblparts = lbl.split(" ")
+ newlbl = ""
+ i = 0
+ for part in lblparts:
+ if 10*(i+1) < len(newlbl):
+ i += 1
+ newlbl = newlbl + r"\n" + part
+ else:
+ newlbl = newlbl + " " + part
+ return newlbl
+ #return "\N"
+
+def writeGraphFile(matrix, traits, filename, p):
+ """
+ Expresses the same information as the neato file, only in
+ eXtensible Graph Markup and Modeling Language (XGMML) so the user can develop his/her
+ own graph in a program such as Cytoscape
+ """
+ inputFile1 = open(filename + "_xgmml_symbol.txt", "w")
+ inputFile2 = open(filename + "_xgmml_name.txt", "w")
+ inputFile3 = open(filename + "_plain_symbol.txt", "w")
+ inputFile4 = open(filename + "_plain_name.txt", "w")
+
+ inputFile1.write("<graph directed=\"1\" label=\"Network Graph\">\n")
+ inputFile2.write("<graph directed=\"1\" label=\"Network Graph\">\n")
+
+ #Write out nodes
+ traitEdges = []
+ for i in range(0, len(traits)):
+ traitEdges.append(0)
+
+ for i in range(0, len(traits)):
+
+ labelName = traits[i].symbol
+ inputFile1.write("\t<node id=\"%s\" label=\"%s\"></node>\n" % (i, labelName))
+
+ for i in range(0, len(traits)):
+
+ labelName = traits[i].name
+ inputFile2.write("\t<node id=\"%s\" label=\"%s\"></node>\n" % (i, labelName))
+
+ #Write out edges
+ for point in matrix:
+
+ traitEdges[point.i] = 1
+ traitEdges[point.j] = 1
+ if p["edges"] == "complex":
+ _traitValue = "%.3f" % point.value
+ inputFile1.write("\t<edge source=\"%s\" target=\"%s\" label=\"%s\"></edge>\n"
+ % (point.i,
+ point.j,
+ _traitValue))
+ inputFile2.write("\t<edge source=\"%s\" target=\"%s\" label=\"%s\"></edge>\n"
+ % (point.i,
+ point.j,
+ _traitValue))
+
+ inputFile1.write("</graph>")
+ inputFile2.write("</graph>")
+
+ for edge in matrix:
+ inputFile3.write("%s\t%s\t%s\n" % (traits[edge.i].symbol, edge.value, traits[edge.j].symbol))
+
+
+ for edge in matrix:
+ inputFile4.write("%s\t%s\t%s\n" % (traits[edge.i].name, edge.value, traits[edge.j].name))
+
+ inputFile1.close()
+ inputFile2.close()
+ inputFile3.close()
+ inputFile4.close()
+
+ return (os.path.split(filename))[1]
+
+# writeNeatoFile : DataMatrix -> arrayof Traits -> String -> ParamDict -> String
+def writeNeatoFile(matrix, traits, filename, GeneIdArray, p):
+ """
+ Given input data, to write a valid input file for neato, optionally
+ writing entries for nodes that have no edges.
+
+ NOTE: There is a big difference between removing an edge and zeroing
+ its value. Because writeNeatoFile is edge-driven, zeroing an edge's value
+ will still result in its node being written.
+ """
+ inputFile = open(filename, "w")
+
+ """
+ This file (inputFile_pdf) is rotated 90 degrees. This is because of a bug in graphviz
+ that causes pdf output onto a non-landscape layout to often be cut off at the edge
+ of the page. This second filename (which is just the first + "_pdf" is then read
+ in the "visualizePage" class in networkGraph.py and used to generate the postscript
+ file that is converted to pdf.
+ """
+ inputFile_pdf = open(filename + "_pdf", "w")
+
+
+ if p["splines"] == "yes":
+ splines = "true"
+ else:
+ splines = "false"
+
+ # header
+ inputFile.write('''graph webqtlGraph {
+ overlap="false";
+ start="regular";
+ splines="%s";
+ ratio="auto";
+ fontpath = "%s";
+ node [fontname="%s", fontsize=%s, shape="%s"];
+ edge [fontname="%s", fontsize=%s];
+ ''' % (splines, webqtlConfig.PIDDLE_FONT_PATH,
+ p["nfont"], p["nfontsize"], p["nodeshapeType"],
+ p["cfont"], p["cfontsize"]))
+
+ inputFile_pdf.write('''graph webqtlGraph {
+ overlap="false";
+ start="regular";
+ splines="%s";
+ rotate="90";
+ center="true";
+ size="11,8.5";
+ margin="0";
+ ratio="fill";
+ fontpath = "%s";
+ node [fontname="%s", fontsize=%s, shape="%s"];
+ edge [fontname="%s", fontsize=%s];
+ ''' % (splines, webqtlConfig.PIDDLE_FONT_PATH,
+ p["nfont"], p["nfontsize"], p["nodeshapeType"],
+ p["cfont"], p["cfontsize"]))
+
+ # traitEdges stores whether a particular trait has edges
+ traitEdges = []
+ for i in range(0, len(traits)):
+ traitEdges.append(0)
+
+ if p["dispcorr"] == "yes":
+ _dispCorr = 1
+ else:
+ _dispCorr = 0
+ # print edges first while keeping track of nodes
+ for point in matrix:
+ if point.value != 0:
+ traitEdges[point.i] = 1
+ traitEdges[point.j] = 1
+ if p["edges"] == "complex":
+ if _dispCorr:
+ _traitValue = "%.3f" % point.value
+ else:
+ _traitValue = ""
+ if p["correlationName"] == "Pearson":
+ inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showCorrelationPlot2(db=\'%s\',ProbeSetID=\'%s\',CellID=\'\',db2=\'%s\',ProbeSetID2=\'%s\',CellID2=\'\',rank=\'%s\');\", edgetooltip="%s"];\n'
+ % (point.i,
+ point.j,
+ point.length,
+ point.length,
+ _traitValue,
+ point.color,
+ point.style,
+ str(traits[point.i].datasetName()),
+ str(traits[point.i].nameNoDB()),
+ str(traits[point.j].datasetName()),
+ str(traits[point.j].nameNoDB()),
+ "0",
+ "Pearson Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
+ elif p["correlationName"] == "Spearman":
+ inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showCorrelationPlot2(db=\'%s\',ProbeSetID=\'%s\',CellID=\'\',db2=\'%s\',ProbeSetID2=\'%s\',CellID2=\'\',rank=\'%s\');\", edgetooltip="%s"];\n'
+ % (point.i,
+ point.j,
+ point.length,
+ point.length,
+ _traitValue,
+ point.color,
+ point.style,
+ str(traits[point.j].datasetName()),
+ str(traits[point.j].nameNoDB()),
+ str(traits[point.i].datasetName()),
+ str(traits[point.i].nameNoDB()),
+ "1",
+ "Spearman Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
+ elif p["correlationName"] == "Tissue":
+ inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showTissueCorrPlot(fmName=\'showDatabase\', X_geneSymbol=\'%s\', Y_geneSymbol=\'%s\', rank=\'0\');\", edgetooltip="%s"];\n'
+ % (point.i,
+ point.j,
+ point.length,
+ point.length,
+ _traitValue,
+ point.color,
+ point.style,
+ str(traits[point.i].symbol),
+ str(traits[point.j].symbol),
+ "Tissue Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
+ else:
+ inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showCorrelationPlot2(db=\'%s\',ProbeSetID=\'%s\',CellID=\'\',db2=\'%s\',ProbeSetID2=\'%s\',CellID2=\'\',rank=\'%s\');\", edgetooltip="%s"];\n'
+ % (point.i,
+ point.j,
+ point.length,
+ point.length,
+ _traitValue,
+ point.color,
+ point.style,
+ str(traits[point.i].datasetName()),
+ str(traits[point.i].nameNoDB()),
+ str(traits[point.j].datasetName()),
+ str(traits[point.j].nameNoDB()),
+ "0",
+ "Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
+ inputFile_pdf.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgetooltip="%s"];\n'
+ % (point.i,
+ point.j,
+ point.length,
+ point.length,
+ _traitValue,
+ point.color,
+ point.style,
+ "Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
+
+ else:
+ inputFile.write('%s -- %s [color="%s", style="%s"];\n'
+ % (point.i,
+ point.j,
+ point.color,
+ point.style))
+ inputFile_pdf.write('%s -- %s [color="%s", style="%s"];\n'
+ % (point.i,
+ point.j,
+ point.color,
+ point.style))
+
+ # now print nodes
+ # the target attribute below is undocumented; I found it by looking
+ # in the neato code
+ for i in range(0, len(traits)):
+ if traitEdges[i] == 1 or p["printIslands"] == 1:
+ _tname = str(traits[i])
+ if _tname.find("Publish") > 0:
+ plotColor = p["cPubName"]
+ elif _tname.find("Geno") > 0:
+ plotColor = p["cGenName"]
+ else:
+ plotColor = p["cMicName"]
+ if p['nodelabel'] == 'yes':
+ labelName = _tname
+ else:
+ labelName = traits[i].symbol
+
+ inputFile.write('%s [label="%s", href="javascript:showDatabase2(\'%s\',\'%s\',\'\');", color="%s", style = "filled"];\n'
+ % (i, labelName, traits[i].datasetName(), traits[i].nameNoDB(), plotColor))# traits[i].color
+ inputFile_pdf.write('%s [label="%s", href="javascript:showDatabase2(\'%s\',\'%s\',\'\');", color="%s", style = "filled"];\n'
+ % (i, labelName, traits[i].datasetName(), traits[i].nameNoDB(), plotColor))# traits[i].color
+
+ # footer
+ inputFile.write("}\n")
+ inputFile_pdf.write("]\n")
+ inputFile.close()
+ inputFile_pdf.close()
+
+ # return only the filename portion, omitting the directory
+ return (os.path.split(filename))[1]
+
+# runNeato : string -> string -> string
+def runNeato(filename, extension, format, gType):
+ """
+ to run neato on the dataset in the given filename and produce an image file
+ in the given format whose name we will return. Right now we assume
+ that format is a valid neato output (see graphviz docs) and a valid extension
+ for the source datafile. For example,
+ runNeato('input1', 'png') will produce a file called 'input1.png'
+ by invoking 'neato input1 -Tpng -o input1.png'
+ """
+ # trim extension off of filename before adding output extension
+ if filename.find(".") > 0:
+ filenameBase = filename[:filename.find(".")]
+ else:
+ filenameBase = filename
+
+ imageFilename = filenameBase + "." + extension
+
+ #choose which algorithm to run depended upon parameter gType
+ #neato: energy based algorithm
+ #circular: nodes given circular structure determined by which nodes are most closely correlated
+ #radial: first node listed (when you search) is center of the graph, all other nodes are in a circular structure around it
+ #fdp: force based algorithm
+
+ if gType == "none":
+ # to keep the output of neato from going to stdout, we open a pipe
+ # and then wait for it to terminate
+
+ if format in ('gif', 'cmapx', 'ps'):
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ else:
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ if neatoExit == 0:
+ return imageFilename
+
+ return imageFilename
+
+
+ elif gType == "neato":
+ # to keep the output of neato from going to stdout, we open a pipe
+ # and then wait for it to terminate
+ if format in ('gif', 'cmapx', 'ps'):
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ else:
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ if neatoExit == 0:
+ return imageFilename
+
+ return imageFilename
+
+ elif gType == "circular":
+
+ if format in ('gif', 'cmapx', 'ps'):
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/circo", "/usr/local/bin/circo", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ else:
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/circo", "/usr/local/bin/circo", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ if neatoExit == 0:
+ return imageFilename
+
+ return imageFilename
+
+ elif gType == "radial":
+
+ if format in ('gif', 'cmapx', 'ps'):
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/twopi", "/usr/local/bin/twopi", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ else:
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/twopi", "/usr/local/bin/twopi", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ if neatoExit == 0:
+ return imageFilename
+
+ return imageFilename
+
+ elif gType == "fdp":
+
+ if format in ('gif', 'cmapx', 'ps'):
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/fdp", "/usr/local/bin/fdp", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ else:
+ neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/fdp", "/usr/local/bin/fdp", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
+
+ if neatoExit == 0:
+ return imageFilename
+
+ return imageFilename
+
+
+ return imageFilename
+# runPsToPdf: string -> int -> intstring
+# to run Ps2Pdf to convert the given input postscript file to an 8.5 by 11
+# pdf file The width and height should be specified in inches. We assume
+# that the PS files output by GraphViz are 72 dpi.
+def runPsToPdf(psfile, width, height):
+ # we add 1 for padding b/c sometimes a small part of the graph gets
+ # cut off
+ newwidth = int((width + 1) * 720)
+ newheight = int((height + 1) * 720)
+
+ # replace the ps extension with a pdf one
+ pdffile = psfile[:-2] + "pdf"
+
+ os.spawnlp(os.P_WAIT, "ps2pdf",
+ "-g%sx%s" % (newwidth, newheight),
+ webqtlConfig.IMGDIR + psfile, webqtlConfig.IMGDIR + pdffile)
+
+ return pdffile
+
+# buildParamDict: void -> ParamDict
+# to process and validate CGI arguments,
+# looking up human-readable names where necessary
+# see the comment at the top of the file for valid cgi parameters
+def buildParamDict(fs, sessionfile):
+ params = {}
+
+ params["inputFile"] = fs.formdata.getvalue("inputFile", "")
+ params["progress"] = fs.formdata.getvalue("progress", "1")
+ params["filename"] = fs.formdata.getvalue("filename", "")
+ params["session"] = sessionfile
+
+ if type("1") != type(fs.formdata.getvalue("searchResult")):
+ params["searchResult"] = string.join(fs.formdata.getvalue("searchResult"),'\t')
+ else:
+ params["searchResult"] = fs.formdata.getvalue("searchResult")
+
+ params["riset"] = fs.formdata.getvalue("RISet", "")
+ #if params["filename"] == "":
+ # raise nGraphException("Required parameter filename missing")
+
+ #parameter determining whether export button returns an xgmml graph file or plain text file
+ params["exportFormat"] = fs.formdata.getvalue("exportFormat", "xgmml")
+
+ #parameter determining whether or not traits in the graph file are listed by their symbol or name
+ params["traitType"] = fs.formdata.getvalue("traitType", "symbol")
+
+ #parameter saying whether or not graph structure should be locked when you redraw the graph
+ params["lock"] = fs.formdata.getvalue("lock", "no")
+
+ #parameter saying what algorithm should be used to draw the graph
+ params["gType"] = fs.formdata.getvalue("gType", "none")
+
+ params["kValue"] = webqtlUtil.safeFloat(fs.formdata.getvalue("kValue", "0.5"), 0.5)
+ params["whichValue"] = webqtlUtil.safeInt(fs.formdata.getvalue("whichValue","0"),0)
+
+ # 1 inch = 2.54 cm
+ # 1 cm = 0.3937 inch
+
+ params["width"] = webqtlUtil.safeFloat(fs.formdata.getvalue("width", "40.0"), 40.0)
+ params["height"] = webqtlUtil.safeFloat(fs.formdata.getvalue("height", "40.0"), 40.0)
+
+ yesno = ["yes", "no"]
+
+ params["tune"] = webqtlUtil.safeString(fs.formdata.getvalue("tune", "yes"), yesno, "yes")
+
+ params["printIslands"] = webqtlUtil.safeInt(fs.formdata.getvalue("printIslands", "1"),1)
+ params["nodeshape"] = webqtlUtil.safeString(fs.formdata.getvalue("nodeshape","yes"), yesno, "yes")
+ params["nodelabel"] = webqtlUtil.safeString(fs.formdata.getvalue("nodelabel","no"), yesno, "no")
+ params["nfont"] = fs.formdata.getvalue("nfont","Arial")
+ params["nfontsize"] = webqtlUtil.safeFloat(fs.formdata.getvalue("nfontsize", "10.0"), 10.0)
+
+ params["splines"] = webqtlUtil.safeString(fs.formdata.getvalue("splines","yes"), yesno, "yes")
+ params["dispcorr"] = webqtlUtil.safeString(fs.formdata.getvalue("dispcorr","no"), yesno, "no")
+ params["cfont"] = fs.formdata.getvalue("cfont","Arial")
+ params["cfontsize"] = webqtlUtil.safeFloat(fs.formdata.getvalue("cfontsize", "10.0"), 10.0)
+
+ params["cPubName"] = fs.formdata.getvalue("cPubName","palegreen")
+ params["cMicName"] = fs.formdata.getvalue("cMicName","lightblue")
+ params["cGenName"] = fs.formdata.getvalue("cGenName","lightcoral")
+
+ params["cPubColor"] = fs.formdata.getvalue("cPubColor","98fb98")
+ params["cMicColor"] = fs.formdata.getvalue("cMicColor","add8e6")
+ params["cGenColor"] = fs.formdata.getvalue("cGenColor","f08080")
+
+ params["cL1Name"] = fs.formdata.getvalue("cL1Name","blue")
+ params["cL2Name"] = fs.formdata.getvalue("cL2Name","green")
+ params["cL3Name"] = fs.formdata.getvalue("cL3Name","black")
+ params["cL4Name"] = fs.formdata.getvalue("cL4Name","pink")
+ params["cL5Name"] = fs.formdata.getvalue("cL5Name","orange")
+ params["cL6Name"] = fs.formdata.getvalue("cL6Name","red")
+
+ params["cL1Color"] = fs.formdata.getvalue("cL1Color","0000ff")
+ params["cL2Color"] = fs.formdata.getvalue("cL2Color","00ff00")
+ params["cL3Color"] = fs.formdata.getvalue("cL3Color","000000")
+ params["cL4Color"] = fs.formdata.getvalue("cL4Color","ffc0cb")
+ params["cL5Color"] = fs.formdata.getvalue("cL5Color","ffa500")
+ params["cL6Color"] = fs.formdata.getvalue("cL6Color","ff0000")
+
+ params["L1style"] = fs.formdata.getvalue("L1style","bold")
+ params["L2style"] = fs.formdata.getvalue("L2style","")
+ params["L3style"] = fs.formdata.getvalue("L3style","dashed")
+ params["L4style"] = fs.formdata.getvalue("L4style","dashed")
+ params["L5style"] = fs.formdata.getvalue("L5style","")
+ params["L6style"] = fs.formdata.getvalue("L6style","bold")
+
+ if params["splines"] == "yes":
+ params["splineName"] = "curves"
+ else:
+ params["splineName"] = "lines"
+
+ if params["nodeshape"] == "yes":
+ params["nodeshapeType"] = "box"
+ else:
+ params["nodeshapeType"] = "ellipse"
+
+ if params["whichValue"] == 0:
+ params["correlationName"] = "Pearson"
+ elif params["whichValue"] == 1:
+ params["correlationName"] = "Spearman"
+ elif params["whichValue"] == 2:
+ params["correlationName"] = "Literature"
+ else:
+ params["correlationName"] = "Tissue"
+
+ # see graphviz::writeNeatoFile to find out what this done
+ params["edges"] = "complex"
+
+ return params
+
+def optimalRadialNode(matrix):
+ """
+ Automatically determines the node with the most/strongest correlations with
+ other nodes. If the user selects "radial" for Graph Type and then "Auto" for the
+ central node then this node is used as the central node. The algorithm is simply a sum of
+ each node's correlations that fall above the threshold set by the user.
+ """
+
+ optMatrix = [0]*(len(matrix)+1)
+
+ for pt in matrix:
+ if abs(pt.value) > 0.5:
+ optMatrix[pt.i] += abs(pt.value)
+ optMatrix[pt.j] += abs(pt.value)
+
+ optPoint = 0
+ optCorrTotal = 0
+
+ j = 0
+
+ for point in optMatrix:
+ if (float(point) > float(optCorrTotal)):
+ optPoint = j
+ optCorrTotal = point
+ j += 1
+
+
+ return optPoint
+
+# filterDataMatrix : DataMatrix -> ParamDict -> DataMatrix
+def filterDataMatrix(matrix, p):
+ """
+ To convert a set of input RawPoints to a set of
+ ProcessedPoints and to choose the appropriate
+ correlation coefficent.
+ """
+ newmatrix = []
+ for pt in matrix:
+ pt2 = ProcessedPoint(pt.i, pt.j) # XZ, 09/11/2008: add module name
+
+ # pick right value
+ if p["whichValue"] == 0:
+ pt2.value = pt.pearson
+ elif p["whichValue"] == 1:
+ pt2.value = pt.spearman
+ elif p["whichValue"] == 2:
+ pt2.value = pt.literature
+ elif p["whichValue"] == 3:
+ pt2.value = pt.tissue
+ else:
+ raise nGraphException("whichValue should be either 0, 1, 2 or 3")
+
+ try:
+ pt2.value = float(pt2.value)
+ except:
+ pt2.value = 0.00
+
+ newmatrix.append(pt2)
+
+
+
+ return newmatrix
+
+def generateSymbolList(traits):
+ """
+ Generates a list of trait symbols to be displayed in the central node
+ selection drop-down menu when plotting a radial graph
+ """
+
+ traitList = traits
+
+ symbolList = [None]*len(traitList)
+
+ i=0
+ for trait in traitList:
+ symbolList[i] = str(trait.symbol)
+ i = i+1
+
+ symbolListString = "\t".join(symbolList)
+
+ return symbolListString
+