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1 #!/usr/bin/env python
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2
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3
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4 """
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5 histogram_gnuplot.py <datafile> <xtic column> <column_list> <title> <ylabel> <yrange_min> <yrange_max> <grath_file>
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6 a generic histogram builder based on gnuplot backend
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7
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8 data_file - tab delimited file with data
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9 xtic_column - column containing labels for x ticks [integer, 0 means no ticks]
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10 column_list - comma separated list of columns to plot
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11 title - title for the entire histrogram
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12 ylabel - y axis label
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13 yrange_max - minimal value at the y axis (integer)
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14 yrange_max - maximal value at the y_axis (integer)
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15 to set yrange to autoscaling assign 0 to yrange_min and yrange_max
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16 graph_file - file to write histogram image to
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17 img_size - as X,Y pair in pixels (e.g., 800,600 or 600,800 etc.)
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18
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19
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20 This tool required gnuplot and gnuplot.py
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21
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22 anton nekrutenko | anton@bx.psu.edu
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23
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24 """
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25
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26 import Gnuplot, Gnuplot.funcutils
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27 import sys, string, tempfile, os
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28
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29 assert sys.version_info[:2] >= ( 2, 4 )
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30
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31 def stop_err(msg):
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32 sys.stderr.write(msg)
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33 sys.exit()
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34
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35 def main(tmpFileName):
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36 skipped_lines_count = 0
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37 skipped_lines_index = []
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38 gf = open(tmpFileName, 'w')
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39
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40
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41 try:
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42 in_file = open( sys.argv[1], 'r' )
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43 xtic = int( sys.argv[2] )
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44 col_list = string.split( sys.argv[3],"," )
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45 title = 'set title "' + sys.argv[4] + '"'
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46 ylabel = 'set ylabel "' + sys.argv[5] + '"'
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47 ymin = sys.argv[6]
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48 ymax = sys.argv[7]
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49 img_file = sys.argv[8]
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50 img_size = sys.argv[9]
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51 except:
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52 stop_err("Check arguments\n")
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53
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54 try:
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55 int( col_list[0] )
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56 except:
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57 stop_err('You forgot to set columns for plotting\n')
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58
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59
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60 for i, line in enumerate( in_file ):
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61 valid = True
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62 line = line.rstrip('\r\n')
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63 if line and not line.startswith( '#' ):
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64 row = []
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65 try:
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66 fields = line.split( '\t' )
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67 for col in col_list:
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68 row.append( str( float( fields[int( col )-1] ) ) )
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69
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70 except:
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71 valid = False
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72 skipped_lines_count += 1
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73 skipped_lines_index.append(i)
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74
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75 else:
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76 valid = False
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77 skipped_lines_count += 1
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78 skipped_lines_index.append(i)
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79
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80 if valid and xtic > 0:
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81 row.append( fields[xtic-1] )
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82 elif valid and xtic == 0:
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83 row.append( str( i ) )
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84
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85 if valid:
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86 gf.write( '\t'.join( row ) )
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87 gf.write( '\n' )
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88
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89 if skipped_lines_count < i:
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90
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91 #prepare 'using' clause of plot statement
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92
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93 g_plot_command = ' ';
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94
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95 #set the first column
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96 if xtic > 0:
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97 g_plot_command = "'%s' using 1:xticlabels(%s) ti 'Column %s', " % ( tmpFileName, str( len( row ) ), col_list[0] )
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98 else:
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99 g_plot_command = "'%s' using 1 ti 'Column %s', " % ( tmpFileName, col_list[0] )
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100
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101 #set subsequent columns
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102
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103 for i in range(1,len(col_list)):
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104 g_plot_command += "'%s' using %s t 'Column %s', " % ( tmpFileName, str( i+1 ), col_list[i] )
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105
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106 g_plot_command = g_plot_command.rstrip( ', ' )
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107
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108 yrange = 'set yrange [' + ymin + ":" + ymax + ']'
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109
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110 try:
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111 g = Gnuplot.Gnuplot()
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112 g('reset')
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113 g('set boxwidth 0.9 absolute')
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114 g('set style fill solid 1.00 border -1')
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115 g('set style histogram clustered gap 5 title offset character 0, 0, 0')
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116 g('set xtics border in scale 1,0.5 nomirror rotate by 90 offset character 0, 0, 0')
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117 g('set key invert reverse Left outside')
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118 if xtic == 0: g('unset xtics')
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119 g(title)
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120 g(ylabel)
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121 g_term = 'set terminal png tiny size ' + img_size
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122 g(g_term)
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123 g_out = 'set output "' + img_file + '"'
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124 if ymin != ymax:
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125 g(yrange)
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126 g(g_out)
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127 g('set style data histograms')
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128 g.plot(g_plot_command)
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129 except:
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130 stop_err("Gnuplot error: Data cannot be plotted")
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131 else:
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132 sys.stderr.write('Column(s) %s of your dataset do not contain valid numeric data' %sys.argv[3] )
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133
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134 if skipped_lines_count > 0:
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135 sys.stdout.write('\nWARNING. You dataset contain(s) %d invalid lines starting with line #%d. These lines were skipped while building the graph.\n' % ( skipped_lines_count, skipped_lines_index[0]+1 ) )
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136
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137
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138 if __name__ == "__main__":
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139 # The tempfile initialization is here because while inside the main() it seems to create a condition
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140 # when the file is removed before gnuplot has a chance of accessing it
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141 gp_data_file = tempfile.NamedTemporaryFile('w')
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142 Gnuplot.gp.GnuplotOpts.default_term = 'png'
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143 main(gp_data_file.name)
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144
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