6
+ − 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 Plot the data from the data files
+ − 33 """
+ − 34 import sys
+ − 35 import math
+ − 36 from optparse import OptionParser
+ − 37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 38 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 39
+ − 40
+ − 41 class PlotTranscriptList(object):
+ − 42
+ − 43 def __init__(self, verbosity = 0):
+ − 44 self.inputFileName = None
+ − 45 self.format = None
+ − 46 self.x = None
+ − 47 self.y = None
+ − 48 self.z = None
+ − 49 self.xDefault = None
+ − 50 self.yDefault = None
+ − 51 self.zDefault = None
+ − 52 self.xLabel = None
+ − 53 self.yLabel = None
+ − 54 self.shape = None
+ − 55 self.bucket = None
+ − 56 self.keep = None
+ − 57 self.log = None
+ − 58 self.verbosity = None
+ − 59
+ − 60
+ − 61 def setPlotter(self, outputFileName, keep, log, xLabel, yLabel):
+ − 62 self.plotter = RPlotter(outputFileName, self.verbosity, keep)
+ − 63 if self.shape != "barplot":
+ − 64 self.plotter.setLog(log)
+ − 65 self.plotter.setXLabel(xLabel)
+ − 66 self.plotter.setYLabel(yLabel)
+ − 67
+ − 68
+ − 69 def setShape(self, shape):
+ − 70 if self.shape == "line":
+ − 71 pass
+ − 72 elif shape == "barplot":
+ − 73 self.plotter.setBarplot(True)
+ − 74 elif shape == "points":
+ − 75 self.plotter.setPoints(True)
+ − 76 elif shape == "heatPoints":
+ − 77 self.plotter.setHeatPoints(True)
+ − 78 else:
+ − 79 sys.exit("Do not understand shape '%s'" % (shape))
+ − 80
+ − 81
+ − 82 def setInput(self, inputFileName, format):
+ − 83 self.parser = TranscriptContainer(inputFileName, format, self.verbosity)
+ − 84
+ − 85
+ − 86 def getValues(self, transcript):
+ − 87 x, y, z = None, None, None
+ − 88 x = transcript.getTagValue(self.x)
+ − 89 if self.y != None:
+ − 90 y = transcript.getTagValue(self.y)
+ − 91 if self.z != None:
+ − 92 z = transcript.getTagValue(self.z)
+ − 93 if x == None:
+ − 94 if self.xDefault != None:
+ − 95 x = self.xDefault
+ − 96 else:
+ − 97 sys.exit("Error! Transcript %s do not have the x-tag %s" % (transcript, self.x))
+ − 98 if y == None and self.shape != "line" and self.shape != "barplot":
+ − 99 if self.yDefault != None:
+ − 100 y = self.yDefault
+ − 101 else:
+ − 102 sys.exit("Error! Transcript %s do not have the y-tag %s" % (transcript, self.y))
+ − 103 if self.z != None:
+ − 104 if z == None:
+ − 105 if self.zDefault != None:
+ − 106 z = self.zDefault
+ − 107 else:
+ − 108 sys.exit("Error! Transcript %s do not have the z-tag %s" % (transcript, self.z))
+ − 109 x = float(x)
+ − 110 if self.y != None:
+ − 111 y = float(y)
+ − 112 if self.z != None:
+ − 113 z = float(z)
+ − 114 return (x, y, z)
+ − 115
+ − 116
+ − 117 def readFile(self):
+ − 118 cpt = 1
+ − 119 line = {}
+ − 120 heatLine = {}
+ − 121 for transcript in self.parser.getIterator():
+ − 122 x, y, z = self.getValues(transcript)
+ − 123
+ − 124 name = transcript.name
+ − 125 if name == "unnamed transcript":
+ − 126 name = "transcript %d" % (cpt)
+ − 127 cpt += 1
+ − 128 if self.shape == "points":
+ − 129 line[name] = (x, y)
+ − 130 elif self.shape == "heatPoints":
+ − 131 line[name] = (x, y)
+ − 132 heatLine[name] = z
+ − 133 elif self.shape == "line" or self.shape == "barplot":
+ − 134 if x not in line:
+ − 135 line[x] = 1
+ − 136 else:
+ − 137 line[x] += 1
+ − 138 else:
+ − 139 sys.exit("Do not understand shape '%s'" % (self.shape))
+ − 140 return line, heatLine
+ − 141
+ − 142
+ − 143 def putLineInBuckets(self, line):
+ − 144 tmpLine = line
+ − 145 line = {}
+ − 146 for key, value in tmpLine.iteritems():
+ − 147 line[int(key / float(self.bucket)) * self.bucket] = value
+ − 148 return line
+ − 149
+ − 150
+ − 151 def clusterInBarplot(self, line):
+ − 152 nbZeros = 0
+ − 153 minValue = min(line.keys())
+ − 154 maxValue = max(line.keys())
+ − 155 if self.log != "":
+ − 156 if minValue == 0:
+ − 157 minValue = 1000000000
+ − 158 for value in line:
+ − 159 if value < minValue:
+ − 160 if value == 0:
+ − 161 nbZeros += 1
+ − 162 else:
+ − 163 minValue = value
+ − 164 minValue = math.log(minValue)
+ − 165 maxValue = math.log(maxValue)
+ − 166 bucketSize = (maxValue - minValue) / self.bucket
+ − 167 tmpLine = line
+ − 168 line = {}
+ − 169 for i in range(int(self.bucket) + 1):
+ − 170 line[i * bucketSize + minValue] = 0
+ − 171 for key, value in tmpLine.iteritems():
+ − 172 if self.log != "" and key != 0:
+ − 173 key = math.log(key)
+ − 174 bucketKey = int((key - minValue) / bucketSize) * bucketSize + minValue
+ − 175 if self.log == "" or key != 0:
+ − 176 line[bucketKey] += value
+ − 177 # if self.log != "":
+ − 178 # tmpLine = line
+ − 179 # line = {}
+ − 180 # for key, value in tmpLine.iteritems():
+ − 181 # line[math.exp(key)] = value
+ − 182 print "%d zeros have been removed" % (nbZeros)
+ − 183 return line
+ − 184
+ − 185
+ − 186 def getSpearmanRho(self):
+ − 187 rho = self.plotter.getSpearmanRho()
+ − 188 if rho == None:
+ − 189 print "Cannot compute Spearman rho."
+ − 190 else:
+ − 191 print "Spearman rho: %f" % (rho)
+ − 192
+ − 193
+ − 194 def run(self):
+ − 195 line, heatLine = self.readFile()
+ − 196
+ − 197 if self.shape == "line" and self.bucket != None:
+ − 198 line = self.putLineInBuckets(line)
+ − 199 if self.shape == "barplot":
+ − 200 line = self.clusterInBarplot(line)
+ − 201
+ − 202 if self.shape == "points" or self.shape == "barplot" or self.shape == "line":
+ − 203 self.plotter.addLine(line)
+ − 204 elif self.shape == "heatPoints":
+ − 205 self.plotter.addLine(line)
+ − 206 self.plotter.addHeatLine(heatLine)
+ − 207 else:
+ − 208 sys.exit("Do not understand shape '%s'" % (self.shape))
+ − 209
+ − 210 self.plotter.plot()
+ − 211
+ − 212 if self.shape == "points" or self.shape == "heatPoints":
+ − 213 self.getSpearmanRho()
+ − 214
+ − 215
+ − 216
+ − 217 if __name__ == "__main__":
+ − 218
+ − 219 # parse command line
+ − 220 description = "Plot v1.0.2: Plot some information from a list of transcripts. [Category: Visualization]"
+ − 221
+ − 222 parser = OptionParser(description = description)
+ − 223 parser.add_option("-i", "--input",dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 224 parser.add_option("-f", "--format",dest="format", action="store",type="string", help="format of the input [compulsory] [format: transcript file format]")
+ − 225 parser.add_option("-x", "--x",dest="x",action="store", type="string", help="tag for the x value [format: string]")
+ − 226 parser.add_option("-y", "--y",dest="y",action="store", type="string", help="tag for the y value [format: string]")
+ − 227 parser.add_option("-z", "--z",dest="z", action="store", default=None,type="string", help="tag for the z value [format: string]")
+ − 228 parser.add_option("-X", "--xDefault",dest="xDefault",action="store", default=None,type="float",help="value for x when tag is not present [format: float]")
+ − 229 parser.add_option("-Y", "--yDefault",dest="yDefault",action="store",default=None,type="float",help="value for y when tag is not present [format: float]")
+ − 230 parser.add_option("-Z", "--zDefault",dest="zDefault", action="store",default=None,type="float",help="value for z when tag is not present [format: float]")
+ − 231 parser.add_option("-n", "--xLabel",dest="xLabel",action="store",default="",type="string", help="label on the x-axis [format: string] [default: ]")
+ − 232 parser.add_option("-m", "--yLabel",dest="yLabel",action="store",default="", type="string", help="label on the y-axis [format: string] [default: ]")
+ − 233 parser.add_option("-o", "--output",dest="outputFileName",action="store",type="string", help="output file names [format: output file in PNG format]")
+ − 234 parser.add_option("-s", "--shape",dest="shape",action="store", type="string", help="shape of the plot [format: choice (barplot, line, points, heatPoints)]")
+ − 235 parser.add_option("-b", "--bucket",dest="bucket",action="store",default=None,type="float",help="bucket size (for the line plot) [format: int] [default: 1]")
+ − 236 parser.add_option("-k", "--keep",dest="keep",action="store_true", default=False, help="keep temporary files [format: bool]")
+ − 237 parser.add_option("-l", "--log",dest="log",action="store",default="",type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string] [default: ]")
+ − 238 parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1, type="int",help="trace level [format: int]")
+ − 239 (options, args) = parser.parse_args()
+ − 240
+ − 241 plotTranscriptList = PlotTranscriptList(options.verbosity)
+ − 242 plotTranscriptList.x = options.x
+ − 243 plotTranscriptList.y = options.y
+ − 244 plotTranscriptList.z = options.z
+ − 245 plotTranscriptList.xDefault = options.xDefault
+ − 246 plotTranscriptList.yDefault = options.yDefault
+ − 247 plotTranscriptList.zDefault = options.zDefault
+ − 248 plotTranscriptList.shape = options.shape
+ − 249 plotTranscriptList.bucket = options.bucket
+ − 250 plotTranscriptList.log = options.log
+ − 251 plotTranscriptList.setPlotter(options.outputFileName, options.keep, options.log, options.xLabel, options.yLabel)
+ − 252 plotTranscriptList.setShape(options.shape)
+ − 253 plotTranscriptList.setInput(options.inputFileName, options.format)
+ − 254 plotTranscriptList.run()
+ − 255