annotate SMART/Java/Python/plot.py @ 62:8c42a6d7ffd4

Added simple test BED file.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
# 
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# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
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# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
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"""
Plot the data from the data files
"""

import os, re, math
from optparse import OptionParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.misc.RPlotter import RPlotter
from SMART.Java.Python.misc.Progress import Progress
from commons.core.utils.FileUtils import FileUtils

class Plot(object):

    def __init__(self, verbosity):
        self.verbosity = verbosity
        self.keep      = False

    def keepTmpFiles(self, boolean):
        self.keep = boolean

    def setShape(self, shape):
        self.shape = shape

    def setInputFileName(self, fileName, format):
        self.parser = TranscriptContainer(fileName, format, self.verbosity)

    def setXData(self, tag, default):
        self.x        = tag
        self.xDefault = default

    def setYData(self, tag, default):
        self.y        = tag
        self.yDefault = default

    def setZData(self, tag, default):
        self.z        = tag
        self.zDefault = default

    def setNbBars(self, nbBars):
        self.nbBars = nbBars

    def setOutputFileName(self, fileName):
        self.outputFileName = fileName

    def setRegression(self, regression):
        self.regression = regression

    def setLog(self, log):
        self.log = log

    def createPlotter(self):
        self.plotter = RPlotter(self.outputFileName, self.verbosity, self.keep)
        if self.shape == "barplot":
            self.plotter.setBarplot(True)
        elif self.shape == "line":
            pass
        elif self.shape == "points":
            self.plotter.setPoints(True)
        elif self.shape == "heatPoints":
            self.plotter.setHeatPoints(True)
        else:
            raise Exception("Do not understand shape '%s'\n" % (self.shape))
            
        self.plotter.setLog(self.log)
        self.plotter.setRegression(self.regression)

    def getValues(self, transcript):
        x = transcript.getTagValue(self.x)
        y = None
        z = None
        if self.y != None:
            y = transcript.getTagValue(self.y)
        if self.z != None:
            z = transcript.getTagValue(self.z)
        if x == None:
            if self.xDefault != None:
                x = self.xDefault
            else:
                raise Exception("Error! Transcript %s do not have the x-tag %s\n" % (transcript, self.x))
        if self.y != None:
            if y == None:
                if self.yDefault != None:
                    y = self.yDefault
                else:
                    raise Exception("Error! Transcript %s do not have the y-tag %s\n" % (transcript, self.y))
        if self.z != None:
            if z == None:
                if self.zDefault != None:
                    z = self.zDefault
                else:
                    raise Exception("Error! Transcript %s do not have the z-tag %s\n" % (transcript, self.z))
        x = float(x)
        if self.y != None:
            y = float(y)
        if self.z != None:
            z = float(z)
        return (x, y, z)

    def correctPointsToBarplot(self, line):
        minValue = int(math.floor(min(line.keys())))
        maxValue = int(math.ceil(max(line.keys())))
        step     = (maxValue - minValue) / self.nbBars
        values   = dict([i * step + minValue, 0] for i in range(0, self.nbBars))
        top      = (self.nbBars - 1) * step + minValue
        for key, value in line.iteritems():
            newKey = min(top, int(math.floor((key - minValue) / float(maxValue - minValue) * self.nbBars)) * step + minValue)
            values[newKey] += value
        return values

    def parseFile(self):
        line     = {}
        heatLine = {}

        cpt = 1
        for transcript in self.parser.getIterator():
            x, y, z = self.getValues(transcript)
            name = transcript.name
            if name == "unnamed transcript":
                name = "transcript %d" % (cpt)
                cpt += 1
            if self.shape in ("points", "heatPoints"):
                line[name] = (x, y)
            if self.shape == "heatPoints":
                heatLine[name] = z
            if self.shape == "line":
                line[x] = y
            if self.shape == "barplot":
                line[x] = line.get(x, 0) + 1
        if self.shape == "barplot":
            line = self.correctPointsToBarplot(line)
        self.plotter.setXLabel(self.x)
        if self.y != None:
            self.plotter.setYLabel(self.y)
        else:
            self.plotter.setYLabel("Count")
        self.plotter.addLine(line)
        if self.shape == "heatPoints":
            self.plotter.addHeatLine(heatLine)
        self.plotter.plot()

    def close(self):
        if self.regression:
            print self.plotter.getCorrelationData()
        if self.shape == "points":
            rho = self.plotter.getSpearmanRho()
            if rho == None:
                print "Cannot compute Spearman rho."
            else:
                print "Spearman rho: %f" % (rho)    

    def run(self):
        self.createPlotter()
        self.parseFile() 
        self.close()


if __name__ == "__main__":
    
    # parse command line
    description = "Plot v1.0.2: Plot some information from a list of transcripts. [Category: Visualization]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",      dest="inputFileName",  action="store",                      type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format",     dest="format",         action="store",                      type="string", help="format of the input [compulsory] [format: transcript file format]")
    parser.add_option("-x", "--x",          dest="x",              action="store",                      type="string", help="tag for the x value [format: string]")
    parser.add_option("-y", "--y",          dest="y",              action="store",                      type="string", help="tag for the y value [format: string]")
    parser.add_option("-z", "--z",          dest="z",              action="store",      default=None,   type="string", help="tag for the z value [format: string]")
    parser.add_option("-X", "--xDefault",   dest="xDefault",       action="store",      default=None,   type="float",  help="value for x when tag is not present [format: float]")
    parser.add_option("-Y", "--yDefault",   dest="yDefault",       action="store",      default=None,   type="float",  help="value for y when tag is not present [format: float]")
    parser.add_option("-Z", "--zDefault",   dest="zDefault",       action="store",      default=None,   type="float",  help="value for z when tag is not present [format: float]")
    parser.add_option("-o", "--output",     dest="outputFileName", action="store",                      type="string", help="output file names [format: output file in PNG format]")
    parser.add_option("-s", "--shape",      dest="shape",          action="store", default="barplot",   type="string", help="shape of the plot [format: choice (barplot, line, points, heatPoints)]")
    parser.add_option("-n", "--nbBars",     dest="nbBars",         action="store",      default=2,                type="int",    help="number of bars in barplot [format: int]")
    parser.add_option("-k", "--keep",       dest="keep",           action="store_true", default=False,                 help="keep temporary files [format: bool]")
    parser.add_option("-r", "--regression", dest="regression",     action="store_true", default=False,                 help="plot regression line (in 'points' format) [format: bool]")
    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]")
    parser.add_option("-v", "--verbosity",  dest="verbosity",      action="store",      default=1,      type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    plot = Plot(options.verbosity)
    plot.setInputFileName(options.inputFileName, options.format)
    plot.setOutputFileName(options.outputFileName)
    plot.setXData(options.x, options.xDefault)
    plot.setYData(options.y, options.yDefault)
    plot.setZData(options.z, options.zDefault)
    plot.setShape(options.shape)
    plot.setNbBars(options.nbBars)
    plot.setRegression(options.regression)
    plot.setLog(options.log)
    plot.keepTmpFiles(options.keep)
    plot.run()