annotate bar_chart_plot.py @ 1:f1bcd79cd923 draft default tip

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#!/usr/bin/env python
"""
histogram_gnuplot.py <datafile> <xtic column> <column_list> <title> <ylabel> <yrange_min> <yrange_max> <grath_file>
a generic histogram builder based on gnuplot backend

   data_file    - tab delimited file with data
   xtic_column  - column containing labels for x ticks [integer, 0 means no ticks]
   column_list  - comma separated list of columns to plot
   title        - title for the entire histrogram
   ylabel       - y axis label
   yrange_max   - minimal value at the y axis (integer)
   yrange_max   - maximal value at the y_axis (integer)
                  to set yrange to autoscaling assign 0 to yrange_min and yrange_max
   graph_file   - file to write histogram image to
   img_size     - as X,Y pair in pixels (e.g., 800,600 or 600,800 etc.)


   This tool required gnuplot and gnuplot.py

anton nekrutenko | [e-mail]
"""

import string
import sys
import tempfile

import Gnuplot
import Gnuplot.funcutils

assert sys.version_info[:2] >= (2, 4)


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


def main(tmpFileName):
    skipped_lines_count = 0
    skipped_lines_index = []
    gf = open(tmpFileName, 'w')

    try:
        in_file = open(sys.argv[1], 'r')
        xtic = int(sys.argv[2])
        col_list = string.split(sys.argv[3], ",")
        title = 'set title "' + sys.argv[4] + '"'
        ylabel = 'set ylabel "' + sys.argv[5] + '"'
        ymin = sys.argv[6]
        ymax = sys.argv[7]
        img_file = sys.argv[8]
        img_size = sys.argv[9]
    except:
        stop_err("Check arguments\n")

    try:
        int(col_list[0])
    except:
        stop_err('You forgot to set columns for plotting\n')

    for i, line in enumerate(in_file):
        valid = True
        line = line.rstrip('\r\n')
        if line and not line.startswith('#'):
            row = []
            try:
                fields = line.split('\t')
                for col in col_list:
                    row.append(str(float(fields[int(col) - 1])))
            except:
                valid = False
                skipped_lines_count += 1
                skipped_lines_index.append(i)
        else:
            valid = False
            skipped_lines_count += 1
            skipped_lines_index.append(i)

        if valid and xtic > 0:
            row.append(fields[xtic - 1])
        elif valid and xtic == 0:
            row.append(str(i))

        if valid:
            gf.write('\t'.join(row))
            gf.write('\n')

    if skipped_lines_count < i:
        # Prepare 'using' clause of plot statement
        g_plot_command = ' '

        # Set the first column
        if xtic > 0:
            g_plot_command = "'%s' using 1:xticlabels(%s) ti 'Column %s', " % (tmpFileName, str(len(row)), col_list[0])
        else:
            g_plot_command = "'%s' using 1 ti 'Column %s', " % (tmpFileName, col_list[0])

        # Set subsequent columns
        for i in range(1, len(col_list)):
            g_plot_command += "'%s' using %s t 'Column %s', " % (tmpFileName, str(i + 1), col_list[i])

        g_plot_command = g_plot_command.rstrip(', ')

        yrange = 'set yrange [' + ymin + ":" + ymax + ']'

        try:
            g = Gnuplot.Gnuplot()
            g('reset')
            g('set boxwidth 0.9 absolute')
            g('set style fill  solid 1.00 border -1')
            g('set style histogram clustered gap 5 title  offset character 0, 0, 0')
            g('set xtics border in scale 1,0.5 nomirror rotate by 90 offset character 0, 0, 0')
            g('set key invert reverse Left outside')
            if xtic == 0:
                g('unset xtics')
            g(title)
            g(ylabel)
            g_term = 'set terminal png tiny size ' + img_size
            g(g_term)
            g_out = 'set output "' + img_file + '"'
            if ymin != ymax:
                g(yrange)
            g(g_out)
            g('set style data histograms')
            g.plot(g_plot_command)
        except:
            stop_err("Gnuplot error: Data cannot be plotted")
    else:
        sys.stderr.write('Column(s) %s of your dataset do not contain valid numeric data' % sys.argv[3])

    if skipped_lines_count > 0:
        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))


if __name__ == "__main__":
    # The tempfile initialization is here because while inside the main() it seems to create a condition
    # when the file is removed before gnuplot has a chance of accessing it
    gp_data_file = tempfile.NamedTemporaryFile('w')
    Gnuplot.gp.GnuplotOpts.default_term = 'png'
    main(gp_data_file.name)