https://github.com/galaxyproject/galaxy
Tip revision: 55beabf25a91e9363e9acbe773ca803e4c557409 authored by John Chilton on 04 July 2020, 14:26:59 UTC
Version 20.5.0 of test-base (tag galaxy-test-base-20.5.0).
Version 20.5.0 of test-base (tag galaxy-test-base-20.5.0).
Tip revision: 55beabf
bar_chart.py
#!/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 | anton@bx.psu.edu
"""
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 = sys.argv[3].split(',')
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 Exception:
stop_err("Check arguments\n")
try:
int(col_list[0])
except Exception:
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 Exception:
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 Exception:
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)