--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/plotTranscriptList.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,255 @@
+#! /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".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# 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.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+"""
+Plot the data from the data files
+"""
+import sys
+import math
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.RPlotter import RPlotter
+
+
+class PlotTranscriptList(object):
+
+    def __init__(self, verbosity = 0):
+        self.inputFileName    = None
+        self.format                 = None
+        self.x                            = None
+        self.y                            = None
+        self.z                            = None
+        self.xDefault             = None
+        self.yDefault             = None
+        self.zDefault             = None
+        self.xLabel                 = None
+        self.yLabel                 = None
+        self.shape                    = None
+        self.bucket                 = None
+        self.keep                     = None
+        self.log                        = None
+        self.verbosity            = None
+
+
+    def setPlotter(self, outputFileName, keep, log, xLabel, yLabel):
+        self.plotter = RPlotter(outputFileName, self.verbosity, keep)
+        if self.shape != "barplot":
+            self.plotter.setLog(log)
+        self.plotter.setXLabel(xLabel)
+        self.plotter.setYLabel(yLabel)
+
+
+    def setShape(self, shape):
+        if self.shape == "line":
+            pass
+        elif shape == "barplot":
+            self.plotter.setBarplot(True)
+        elif shape == "points":
+            self.plotter.setPoints(True)
+        elif shape == "heatPoints":
+            self.plotter.setHeatPoints(True)
+        else:
+            sys.exit("Do not understand shape '%s'" % (shape))
+
+
+    def setInput(self, inputFileName, format):
+        self.parser = TranscriptContainer(inputFileName, format, self.verbosity)
+
+
+    def getValues(self, transcript):
+        x, y, z = None, None, None
+        x = transcript.getTagValue(self.x)
+        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:
+                sys.exit("Error! Transcript %s do not have the x-tag %s" % (transcript, self.x))
+        if y == None and self.shape != "line" and self.shape != "barplot":
+            if self.yDefault != None:
+                y = self.yDefault
+            else:
+                sys.exit("Error! Transcript %s do not have the y-tag %s" % (transcript, self.y))
+        if self.z != None:
+            if z == None:
+                if self.zDefault != None:
+                    z = self.zDefault
+                else:
+                    sys.exit("Error! Transcript %s do not have the z-tag %s" % (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 readFile(self):
+        cpt            = 1
+        line         = {}
+        heatLine = {}
+        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 == "points":
+                line[name] = (x, y)
+            elif self.shape == "heatPoints":
+                line[name] = (x, y)
+                heatLine[name] = z
+            elif self.shape == "line" or self.shape == "barplot":
+                if x not in line:
+                    line[x] = 1
+                else:
+                    line[x] += 1
+            else:
+                sys.exit("Do not understand shape '%s'" % (self.shape))
+        return line, heatLine
+
+
+    def putLineInBuckets(self, line):
+        tmpLine = line
+        line        = {}
+        for key, value in tmpLine.iteritems():
+            line[int(key / float(self.bucket)) * self.bucket] = value
+        return line
+
+
+    def clusterInBarplot(self, line):
+        nbZeros        = 0
+        minValue     = min(line.keys())
+        maxValue     = max(line.keys())
+        if self.log != "":
+            if minValue == 0:
+                minValue = 1000000000
+                for value in line:
+                    if value < minValue:
+                        if value == 0:
+                            nbZeros += 1
+                        else:
+                            minValue = value
+            minValue = math.log(minValue)
+            maxValue = math.log(maxValue)
+        bucketSize = (maxValue - minValue) / self.bucket
+        tmpLine        = line
+        line             = {}
+        for i in range(int(self.bucket) + 1):
+            line[i * bucketSize + minValue] = 0
+        for key, value in tmpLine.iteritems():
+            if self.log != "" and key != 0:
+                key = math.log(key)
+            bucketKey = int((key - minValue) / bucketSize) * bucketSize + minValue
+            if self.log == "" or key != 0:
+                line[bucketKey] += value
+#     if self.log != "":
+#         tmpLine = line
+#         line        = {}
+#         for key, value in tmpLine.iteritems():
+#             line[math.exp(key)] = value
+        print "%d zeros have been removed" % (nbZeros)
+        return line
+
+
+    def getSpearmanRho(self):
+        rho = self.plotter.getSpearmanRho()
+        if rho == None:
+            print "Cannot compute Spearman rho."
+        else:
+            print "Spearman rho: %f" % (rho)
+
+
+    def run(self):
+        line, heatLine = self.readFile()
+
+        if self.shape == "line" and self.bucket != None:
+            line = self.putLineInBuckets(line)
+        if self.shape == "barplot":
+            line = self.clusterInBarplot(line)
+
+        if self.shape == "points" or self.shape == "barplot" or self.shape == "line":
+            self.plotter.addLine(line)
+        elif self.shape == "heatPoints":
+            self.plotter.addLine(line)
+            self.plotter.addHeatLine(heatLine)
+        else:
+            sys.exit("Do not understand shape '%s'" % (self.shape))
+
+        self.plotter.plot()
+
+        if self.shape == "points" or self.shape == "heatPoints":
+            self.getSpearmanRho()
+
+
+
+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("-n", "--xLabel",dest="xLabel",action="store",default="",type="string", help="label on the x-axis [format: string] [default: ]")
+    parser.add_option("-m", "--yLabel",dest="yLabel",action="store",default="", type="string", help="label on the y-axis [format: string] [default: ]")
+    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", type="string", help="shape of the plot [format: choice (barplot, line, points, heatPoints)]")
+    parser.add_option("-b", "--bucket",dest="bucket",action="store",default=None,type="float",help="bucket size (for the line plot) [format: int] [default: 1]")
+    parser.add_option("-k", "--keep",dest="keep",action="store_true", default=False, help="keep temporary files [format: bool]")
+    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: ]")
+    parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1, type="int",help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    plotTranscriptList = PlotTranscriptList(options.verbosity)
+    plotTranscriptList.x                = options.x
+    plotTranscriptList.y                = options.y
+    plotTranscriptList.z                = options.z
+    plotTranscriptList.xDefault = options.xDefault
+    plotTranscriptList.yDefault = options.yDefault
+    plotTranscriptList.zDefault = options.zDefault
+    plotTranscriptList.shape        = options.shape
+    plotTranscriptList.bucket     = options.bucket
+    plotTranscriptList.log            = options.log
+    plotTranscriptList.setPlotter(options.outputFileName, options.keep, options.log, options.xLabel, options.yLabel)
+    plotTranscriptList.setShape(options.shape)
+    plotTranscriptList.setInput(options.inputFileName, options.format)
+    plotTranscriptList.run()
+