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comparison smart_toolShed/SMART/Java/Python/plot.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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():
137 newKey = min(top, int(math.floor((key - minValue) / float(maxValue - minValue) * self.nbBars)) * step + minValue)
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