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