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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """
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32 Plot the data from the data files
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33 """
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34 import sys
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35 import math
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36 from optparse import OptionParser
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37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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38 from SMART.Java.Python.misc.RPlotter import RPlotter
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39
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40
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41 class PlotTranscriptList(object):
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42
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43 def __init__(self, verbosity = 0):
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44 self.inputFileName = None
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45 self.format = None
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46 self.x = None
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47 self.y = None
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48 self.z = None
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49 self.xDefault = None
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50 self.yDefault = None
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51 self.zDefault = None
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52 self.xLabel = None
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53 self.yLabel = None
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54 self.shape = None
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55 self.bucket = None
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56 self.keep = None
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57 self.log = None
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58 self.verbosity = None
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59
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60
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61 def setPlotter(self, outputFileName, keep, log, xLabel, yLabel):
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62 self.plotter = RPlotter(outputFileName, self.verbosity, keep)
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63 if self.shape != "barplot":
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64 self.plotter.setLog(log)
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65 self.plotter.setXLabel(xLabel)
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66 self.plotter.setYLabel(yLabel)
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67
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68
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69 def setShape(self, shape):
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70 if self.shape == "line":
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71 pass
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72 elif shape == "barplot":
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73 self.plotter.setBarplot(True)
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74 elif shape == "points":
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75 self.plotter.setPoints(True)
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76 elif shape == "heatPoints":
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77 self.plotter.setHeatPoints(True)
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78 else:
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79 sys.exit("Do not understand shape '%s'" % (shape))
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80
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81
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82 def setInput(self, inputFileName, format):
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83 self.parser = TranscriptContainer(inputFileName, format, self.verbosity)
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84
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85
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86 def getValues(self, transcript):
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87 x, y, z = None, None, None
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88 x = transcript.getTagValue(self.x)
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89 if self.y != None:
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90 y = transcript.getTagValue(self.y)
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91 if self.z != None:
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92 z = transcript.getTagValue(self.z)
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93 if x == None:
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94 if self.xDefault != None:
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95 x = self.xDefault
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96 else:
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97 sys.exit("Error! Transcript %s do not have the x-tag %s" % (transcript, self.x))
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98 if y == None and self.shape != "line" and self.shape != "barplot":
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99 if self.yDefault != None:
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100 y = self.yDefault
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101 else:
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102 sys.exit("Error! Transcript %s do not have the y-tag %s" % (transcript, self.y))
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103 if self.z != None:
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104 if z == None:
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105 if self.zDefault != None:
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106 z = self.zDefault
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107 else:
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108 sys.exit("Error! Transcript %s do not have the z-tag %s" % (transcript, self.z))
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109 x = float(x)
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110 if self.y != None:
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111 y = float(y)
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112 if self.z != None:
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113 z = float(z)
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114 return (x, y, z)
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115
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116
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117 def readFile(self):
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118 cpt = 1
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119 line = {}
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120 heatLine = {}
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121 for transcript in self.parser.getIterator():
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122 x, y, z = self.getValues(transcript)
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123
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124 name = transcript.name
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125 if name == "unnamed transcript":
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126 name = "transcript %d" % (cpt)
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127 cpt += 1
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128 if self.shape == "points":
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129 line[name] = (x, y)
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130 elif self.shape == "heatPoints":
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131 line[name] = (x, y)
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132 heatLine[name] = z
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133 elif self.shape == "line" or self.shape == "barplot":
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134 if x not in line:
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135 line[x] = 1
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136 else:
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137 line[x] += 1
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138 else:
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139 sys.exit("Do not understand shape '%s'" % (self.shape))
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140 return line, heatLine
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141
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142
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143 def putLineInBuckets(self, line):
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144 tmpLine = line
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145 line = {}
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146 for key, value in tmpLine.iteritems():
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147 line[int(key / float(self.bucket)) * self.bucket] = value
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148 return line
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149
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150
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151 def clusterInBarplot(self, line):
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152 nbZeros = 0
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153 minValue = min(line.keys())
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154 maxValue = max(line.keys())
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155 if self.log != "":
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156 if minValue == 0:
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157 minValue = 1000000000
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158 for value in line:
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159 if value < minValue:
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160 if value == 0:
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161 nbZeros += 1
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162 else:
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163 minValue = value
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164 minValue = math.log(minValue)
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165 maxValue = math.log(maxValue)
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166 bucketSize = (maxValue - minValue) / self.bucket
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167 tmpLine = line
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168 line = {}
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169 for i in range(int(self.bucket) + 1):
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170 line[i * bucketSize + minValue] = 0
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171 for key, value in tmpLine.iteritems():
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172 if self.log != "" and key != 0:
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173 key = math.log(key)
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174 bucketKey = int((key - minValue) / bucketSize) * bucketSize + minValue
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175 if self.log == "" or key != 0:
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176 line[bucketKey] += value
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177 # if self.log != "":
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178 # tmpLine = line
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179 # line = {}
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180 # for key, value in tmpLine.iteritems():
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181 # line[math.exp(key)] = value
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182 print "%d zeros have been removed" % (nbZeros)
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183 return line
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184
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185
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186 def getSpearmanRho(self):
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187 rho = self.plotter.getSpearmanRho()
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188 if rho == None:
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189 print "Cannot compute Spearman rho."
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190 else:
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191 print "Spearman rho: %f" % (rho)
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192
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193
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194 def run(self):
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195 line, heatLine = self.readFile()
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196
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197 if self.shape == "line" and self.bucket != None:
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198 line = self.putLineInBuckets(line)
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199 if self.shape == "barplot":
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200 line = self.clusterInBarplot(line)
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201
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202 if self.shape == "points" or self.shape == "barplot" or self.shape == "line":
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203 self.plotter.addLine(line)
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204 elif self.shape == "heatPoints":
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205 self.plotter.addLine(line)
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206 self.plotter.addHeatLine(heatLine)
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207 else:
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208 sys.exit("Do not understand shape '%s'" % (self.shape))
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209
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210 self.plotter.plot()
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211
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212 if self.shape == "points" or self.shape == "heatPoints":
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213 self.getSpearmanRho()
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214
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215
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216
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217 if __name__ == "__main__":
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218
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219 # parse command line
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220 description = "Plot v1.0.2: Plot some information from a list of transcripts. [Category: Visualization]"
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221
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222 parser = OptionParser(description = description)
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223 parser.add_option("-i", "--input",dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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224 parser.add_option("-f", "--format",dest="format", action="store",type="string", help="format of the input [compulsory] [format: transcript file format]")
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225 parser.add_option("-x", "--x",dest="x",action="store", type="string", help="tag for the x value [format: string]")
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226 parser.add_option("-y", "--y",dest="y",action="store", type="string", help="tag for the y value [format: string]")
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227 parser.add_option("-z", "--z",dest="z", action="store", default=None,type="string", help="tag for the z value [format: string]")
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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]")
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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]")
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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]")
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231 parser.add_option("-n", "--xLabel",dest="xLabel",action="store",default="",type="string", help="label on the x-axis [format: string] [default: ]")
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232 parser.add_option("-m", "--yLabel",dest="yLabel",action="store",default="", type="string", help="label on the y-axis [format: string] [default: ]")
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233 parser.add_option("-o", "--output",dest="outputFileName",action="store",type="string", help="output file names [format: output file in PNG format]")
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234 parser.add_option("-s", "--shape",dest="shape",action="store", type="string", help="shape of the plot [format: choice (barplot, line, points, heatPoints)]")
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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]")
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236 parser.add_option("-k", "--keep",dest="keep",action="store_true", default=False, help="keep temporary files [format: bool]")
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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: ]")
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238 parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1, type="int",help="trace level [format: int]")
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239 (options, args) = parser.parse_args()
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240
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241 plotTranscriptList = PlotTranscriptList(options.verbosity)
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242 plotTranscriptList.x = options.x
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243 plotTranscriptList.y = options.y
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244 plotTranscriptList.z = options.z
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245 plotTranscriptList.xDefault = options.xDefault
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246 plotTranscriptList.yDefault = options.yDefault
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247 plotTranscriptList.zDefault = options.zDefault
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248 plotTranscriptList.shape = options.shape
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249 plotTranscriptList.bucket = options.bucket
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250 plotTranscriptList.log = options.log
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251 plotTranscriptList.setPlotter(options.outputFileName, options.keep, options.log, options.xLabel, options.yLabel)
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252 plotTranscriptList.setShape(options.shape)
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253 plotTranscriptList.setInput(options.inputFileName, options.format)
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254 plotTranscriptList.run()
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255
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