diff options
Diffstat (limited to 'web/webqtl/networkGraph')
| -rwxr-xr-x | web/webqtl/networkGraph/GraphPage.py | 46 | ||||
| -rwxr-xr-x | web/webqtl/networkGraph/ProcessedPoint.py | 49 | ||||
| -rwxr-xr-x | web/webqtl/networkGraph/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/networkGraph/nGraphException.py | 33 | ||||
| -rwxr-xr-x | web/webqtl/networkGraph/networkGraphPage.py | 335 | ||||
| -rw-r--r-- | web/webqtl/networkGraph/networkGraphPageBody.py | 697 | ||||
| -rw-r--r-- | web/webqtl/networkGraph/networkGraphUtils.py | 750 |
7 files changed, 0 insertions, 1910 deletions
diff --git a/web/webqtl/networkGraph/GraphPage.py b/web/webqtl/networkGraph/GraphPage.py deleted file mode 100755 index b0d4063d..00000000 --- a/web/webqtl/networkGraph/GraphPage.py +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -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 deleted file mode 100755 index 6eb855e3..00000000 --- a/web/webqtl/networkGraph/ProcessedPoint.py +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -# 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 deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/networkGraph/__init__.py +++ /dev/null diff --git a/web/webqtl/networkGraph/nGraphException.py b/web/webqtl/networkGraph/nGraphException.py deleted file mode 100755 index d492fca9..00000000 --- a/web/webqtl/networkGraph/nGraphException.py +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -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 deleted file mode 100755 index fb4021f0..00000000 --- a/web/webqtl/networkGraph/networkGraphPage.py +++ /dev/null @@ -1,335 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by 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 deleted file mode 100644 index 22b49ccd..00000000 --- a/web/webqtl/networkGraph/networkGraphPageBody.py +++ /dev/null @@ -1,697 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -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> - - - - <input type="submit" name="mintmap" value=" Redraw " class="button" onClick="return sortSearchResults(this.form);" /> - - - <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'> - <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'> </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&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> -       - <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 deleted file mode 100644 index fd0e7484..00000000 --- a/web/webqtl/networkGraph/networkGraphUtils.py +++ /dev/null @@ -1,750 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -# 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 - |