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Diffstat (limited to 'web/webqtl/networkGraph/networkGraphUtils.py')
| -rw-r--r-- | web/webqtl/networkGraph/networkGraphUtils.py | 750 |
1 files changed, 0 insertions, 750 deletions
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 - |