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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/networkGraph/networkGraphUtils.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
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+# 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
+