Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/misc/MultipleRPlotter.py @ 4:1fc014126d55

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Uploaded
author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents e0f8dcca02ed
children
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0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #
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2 # Copyright INRA-URGI 2009-2012
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3 #
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30
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31 import os
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32 import subprocess
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33 import random
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34 import math
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35 from SMART.Java.Python.misc.RPlotter import RPlotter
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36
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37 NBCOLORS = 9
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38
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39 """
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40 Plot multiple curves with RPlotter
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41 """
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42
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43 class MultipleRPlotter(object):
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44 """
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45 Plot some curves
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46 @ivar fileName: name of the file
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47 @type fileName: string
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48 @ivar height: height of the file
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49 @type height: int
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50 @ivar width: width of the file
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51 @type width: int
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52 @ivar plots: plots to be included
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53 @type plots: list of L{RPlotter{RPlotter}}
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54 @ivar keep: keep script lines
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55 @type keep: boolean
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56 @ivar format: format of the file
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57 @type format: string
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58 """
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59
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60 def __init__(self, fileName, verbosity = 0, keep = False):
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61 """
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62 Constructor
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63 @param fileName: name of the file to produce
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64 @type fileName: string
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65 @param verbosity: verbosity
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66 @type verbosity: int
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67 @param keep: keep temporary files
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68 @type keep: boolean
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69 """
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70 self.fileName = fileName
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71 self.verbosity = verbosity
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72 self.keep = keep
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73 self.format = "png"
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74 self.width = 1000
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75 self.height = 500
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76 self.plots = []
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77 self.scriptFileName = "tmpScript-%d.R" % (os.getpid())
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78
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79 def __del__(self):
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80 """
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81 Destructor
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82 Remove script files
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83 """
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84 if not self.keep:
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85 if os.path.exists(self.scriptFileName):
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86 os.remove(self.scriptFileName)
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87 outputFileName = "%sout" % (self.scriptFileName)
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88 if os.path.exists(outputFileName):
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89 os.remove(outputFileName)
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90
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91 def setFormat(self, format):
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92 """
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93 Set the format of the picture
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94 @param format: the format
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95 @type format: string
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96 """
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97 if format not in ("png", "pdf", "jpeg", "bmp", "tiff"):
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98 raise Exception("Format '%s' is not supported by RPlotter" % (format))
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99 self.format = format
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100
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101
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102 def setWidth(self, width):
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103 """
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104 Set the dimensions of the image produced
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105 @param width: width of the image
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106 @type width: int
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107 """
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108 self.width = width
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109
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110
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111 def setHeight(self, height):
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112 """
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113 Set the dimensions of the image produced
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114 @param height: heigth of the image
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115 @type height: int
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116 """
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117 self.height = height
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118
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119
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120 def setImageSize(self, width, height):
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121 """
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122 Set the dimensions of the image produced
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123 @param width: width of the image
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124 @type width: int
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125 @param height: heigth of the image
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126 @type height: int
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127 """
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128 self.width = width
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129 self.height = height
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130
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131 def addPlot(self, plot):
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132 """
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133 Add a plot
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134 @param plots: plot to be included
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135 @type plots: L{RPlotter{RPlotter}}
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136 """
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137 self.plots.append(plot)
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138
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139 def plot(self):
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140 """
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141 Plot the figures
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142 """
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143 scriptHandle = open(self.scriptFileName, "w")
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144 scriptHandle.write("library(RColorBrewer)\n")
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145 scriptHandle.write("colorPanel = brewer.pal(n=%d, name=\"Set1\")\n" % (NBCOLORS))
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146 scriptHandle.write("%s(%s = \"%s\", width = %d, height = %d, bg = \"white\")\n" % (self.format, "filename" if self.format != "pdf" else "file", self.fileName, self.width, self.height))
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147 scriptHandle.write("par(mfrow=c(%d, 1))\n" % (len(self.plots)))
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148 for plot in self.plots:
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149 scriptHandle.write(plot.getScript())
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150 scriptHandle.write("dev.off()\n")
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151 scriptHandle.close()
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152 rCommand = "R"
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153 if "SMARTRPATH" in os.environ:
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154 rCommand = os.environ["SMARTRPATH"]
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155 command = "\"%s\" CMD BATCH %s" % (rCommand, self.scriptFileName)
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156 status = subprocess.call(command, shell=True)
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157 if status != 0:
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158 self.keep = True
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159 raise Exception("Problem with the execution of script file %s, status is: %s" % (self.scriptFileName, status))
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160