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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31
+ − 32 """
+ − 33 Plot the data from the data files
+ − 34 """
+ − 35
+ − 36 import os, re, math
+ − 37 from optparse import OptionParser
+ − 38 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 39 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 40 from SMART.Java.Python.misc.Progress import Progress
+ − 41 from commons.core.utils.FileUtils import FileUtils
+ − 42
+ − 43 class Plot(object):
+ − 44
+ − 45 def __init__(self, verbosity):
+ − 46 self.verbosity = verbosity
+ − 47 self.keep = False
+ − 48
+ − 49 def keepTmpFiles(self, boolean):
+ − 50 self.keep = boolean
+ − 51
+ − 52 def setShape(self, shape):
+ − 53 self.shape = shape
+ − 54
+ − 55 def setInputFileName(self, fileName, format):
+ − 56 self.parser = TranscriptContainer(fileName, format, self.verbosity)
+ − 57
+ − 58 def setXData(self, tag, default):
+ − 59 self.x = tag
+ − 60 self.xDefault = default
+ − 61
+ − 62 def setYData(self, tag, default):
+ − 63 self.y = tag
+ − 64 self.yDefault = default
+ − 65
+ − 66 def setZData(self, tag, default):
+ − 67 self.z = tag
+ − 68 self.zDefault = default
+ − 69
+ − 70 def setNbBars(self, nbBars):
+ − 71 self.nbBars = nbBars
+ − 72
+ − 73 def setOutputFileName(self, fileName):
+ − 74 self.outputFileName = fileName
+ − 75
+ − 76 def setRegression(self, regression):
+ − 77 self.regression = regression
+ − 78
+ − 79 def setLog(self, log):
+ − 80 self.log = log
+ − 81
+ − 82 def createPlotter(self):
+ − 83 self.plotter = RPlotter(self.outputFileName, self.verbosity, self.keep)
+ − 84 if self.shape == "barplot":
+ − 85 self.plotter.setBarplot(True)
+ − 86 elif self.shape == "line":
+ − 87 pass
+ − 88 elif self.shape == "points":
+ − 89 self.plotter.setPoints(True)
+ − 90 elif self.shape == "heatPoints":
+ − 91 self.plotter.setHeatPoints(True)
+ − 92 else:
+ − 93 raise Exception("Do not understand shape '%s'\n" % (self.shape))
+ − 94
+ − 95 self.plotter.setLog(self.log)
+ − 96 self.plotter.setRegression(self.regression)
+ − 97
+ − 98 def getValues(self, transcript):
+ − 99 x = transcript.getTagValue(self.x)
+ − 100 y = None
+ − 101 z = None
+ − 102 if self.y != None:
+ − 103 y = transcript.getTagValue(self.y)
+ − 104 if self.z != None:
+ − 105 z = transcript.getTagValue(self.z)
+ − 106 if x == None:
+ − 107 if self.xDefault != None:
+ − 108 x = self.xDefault
+ − 109 else:
+ − 110 raise Exception("Error! Transcript %s do not have the x-tag %s\n" % (transcript, self.x))
+ − 111 if self.y != None:
+ − 112 if y == None:
+ − 113 if self.yDefault != None:
+ − 114 y = self.yDefault
+ − 115 else:
+ − 116 raise Exception("Error! Transcript %s do not have the y-tag %s\n" % (transcript, self.y))
+ − 117 if self.z != None:
+ − 118 if z == None:
+ − 119 if self.zDefault != None:
+ − 120 z = self.zDefault
+ − 121 else:
+ − 122 raise Exception("Error! Transcript %s do not have the z-tag %s\n" % (transcript, self.z))
+ − 123 x = float(x)
+ − 124 if self.y != None:
+ − 125 y = float(y)
+ − 126 if self.z != None:
+ − 127 z = float(z)
+ − 128 return (x, y, z)
+ − 129
+ − 130 def correctPointsToBarplot(self, line):
+ − 131 minValue = int(math.floor(min(line.keys())))
+ − 132 maxValue = int(math.ceil(max(line.keys())))
+ − 133 step = (maxValue - minValue) / self.nbBars
+ − 134 values = dict([i * step + minValue, 0] for i in range(0, self.nbBars))
+ − 135 top = (self.nbBars - 1) * step + minValue
+ − 136 for key, value in line.iteritems():
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+ − 137 newKey = min(top, int(math.floor((key - minValue) / float(maxValue - minValue) * self.nbBars)) * step + minValue)
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+ − 138 values[newKey] += value
+ − 139 return values
+ − 140
+ − 141 def parseFile(self):
+ − 142 line = {}
+ − 143 heatLine = {}
+ − 144
+ − 145 cpt = 1
+ − 146 for transcript in self.parser.getIterator():
+ − 147 x, y, z = self.getValues(transcript)
+ − 148 name = transcript.name
+ − 149 if name == "unnamed transcript":
+ − 150 name = "transcript %d" % (cpt)
+ − 151 cpt += 1
+ − 152 if self.shape in ("points", "heatPoints"):
+ − 153 line[name] = (x, y)
+ − 154 if self.shape == "heatPoints":
+ − 155 heatLine[name] = z
+ − 156 if self.shape == "line":
+ − 157 line[x] = y
+ − 158 if self.shape == "barplot":
+ − 159 line[x] = line.get(x, 0) + 1
+ − 160 if self.shape == "barplot":
+ − 161 line = self.correctPointsToBarplot(line)
+ − 162 self.plotter.setXLabel(self.x)
+ − 163 if self.y != None:
+ − 164 self.plotter.setYLabel(self.y)
+ − 165 else:
+ − 166 self.plotter.setYLabel("Count")
+ − 167 self.plotter.addLine(line)
+ − 168 if self.shape == "heatPoints":
+ − 169 self.plotter.addHeatLine(heatLine)
+ − 170 self.plotter.plot()
+ − 171
+ − 172 def close(self):
+ − 173 if self.regression:
+ − 174 print self.plotter.getCorrelationData()
+ − 175 if self.shape == "points":
+ − 176 rho = self.plotter.getSpearmanRho()
+ − 177 if rho == None:
+ − 178 print "Cannot compute Spearman rho."
+ − 179 else:
+ − 180 print "Spearman rho: %f" % (rho)
+ − 181
+ − 182 def run(self):
+ − 183 self.createPlotter()
+ − 184 self.parseFile()
+ − 185 self.close()
+ − 186
+ − 187
+ − 188 if __name__ == "__main__":
+ − 189
+ − 190 # parse command line
+ − 191 description = "Plot v1.0.2: Plot some information from a list of transcripts. [Category: Visualization]"
+ − 192
+ − 193 parser = OptionParser(description = description)
+ − 194 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 195 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: transcript file format]")
+ − 196 parser.add_option("-x", "--x", dest="x", action="store", type="string", help="tag for the x value [format: string]")
+ − 197 parser.add_option("-y", "--y", dest="y", action="store", type="string", help="tag for the y value [format: string]")
+ − 198 parser.add_option("-z", "--z", dest="z", action="store", default=None, type="string", help="tag for the z value [format: string]")
+ − 199 parser.add_option("-X", "--xDefault", dest="xDefault", action="store", default=None, type="float", help="value for x when tag is not present [format: float]")
+ − 200 parser.add_option("-Y", "--yDefault", dest="yDefault", action="store", default=None, type="float", help="value for y when tag is not present [format: float]")
+ − 201 parser.add_option("-Z", "--zDefault", dest="zDefault", action="store", default=None, type="float", help="value for z when tag is not present [format: float]")
+ − 202 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file names [format: output file in PNG format]")
+ − 203 parser.add_option("-s", "--shape", dest="shape", action="store", default="barplot", type="string", help="shape of the plot [format: choice (barplot, line, points, heatPoints)]")
+ − 204 parser.add_option("-n", "--nbBars", dest="nbBars", action="store", default=2, type="int", help="number of bars in barplot [format: int]")
+ − 205 parser.add_option("-k", "--keep", dest="keep", action="store_true", default=False, help="keep temporary files [format: bool]")
+ − 206 parser.add_option("-r", "--regression", dest="regression", action="store_true", default=False, help="plot regression line (in 'points' format) [format: bool]")
+ − 207 parser.add_option("-l", "--log", dest="log", action="store", default="y", type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string]")
+ − 208 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 209 (options, args) = parser.parse_args()
+ − 210
+ − 211 plot = Plot(options.verbosity)
+ − 212 plot.setInputFileName(options.inputFileName, options.format)
+ − 213 plot.setOutputFileName(options.outputFileName)
+ − 214 plot.setXData(options.x, options.xDefault)
+ − 215 plot.setYData(options.y, options.yDefault)
+ − 216 plot.setZData(options.z, options.zDefault)
+ − 217 plot.setShape(options.shape)
+ − 218 plot.setNbBars(options.nbBars)
+ − 219 plot.setRegression(options.regression)
+ − 220 plot.setLog(options.log)
+ − 221 plot.keepTmpFiles(options.keep)
+ − 222 plot.run()
+ − 223
