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#!/usr/bin/env python
"""
Given 3 files, creates a 3-way Venn diagram of intersections using matplotlib; \
see :mod:`pybedtools.contrib.venn_maker` for more flexibility.
Numbers are placed on the diagram. If you don't have matplotlib installed.
try venn_gchart.py to use the Google Chart API instead.
The values in the diagram assume:
* unstranded intersections
* no features that are nested inside larger features
"""
import argparse
import sys
import os
import pybedtools
def venn_mpl(a, b, c, colors=None, outfn='out.png', labels=None):
"""
*a*, *b*, and *c* are filenames to BED-like files.
*colors* is a list of matplotlib colors for the Venn diagram circles.
*outfn* is the resulting output file. This is passed directly to
fig.savefig(), so you can supply extensions of .png, .pdf, or whatever your
matplotlib installation supports.
*labels* is a list of labels to use for each of the files; by default the
labels are ['a','b','c']
"""
try:
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
except ImportError:
sys.stderr.write('matplotlib is required to make a Venn diagram with %s\n' % os.path.basename(sys.argv[0]))
sys.exit(1)
a = pybedtools.BedTool(a)
b = pybedtools.BedTool(b)
c = pybedtools.BedTool(c)
if colors is None:
colors = ['r','b','g']
radius = 6.0
center = 0.0
offset = radius / 2
if labels is None:
labels = ['a','b','c']
circle_a = Circle(xy = (center-offset, center+offset), radius=radius, edgecolor=colors[0], label=labels[0])
circle_b = Circle(xy = (center+offset, center+offset), radius=radius, edgecolor=colors[1], label=labels[1])
circle_c = Circle(xy = (center, center-offset), radius=radius, edgecolor=colors[2], label=labels[2])
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111)
for circle in (circle_a, circle_b, circle_c):
circle.set_facecolor('none')
circle.set_linewidth(3)
ax.add_patch(circle)
ax.axis('tight')
ax.axis('equal')
ax.set_axis_off()
kwargs = dict(horizontalalignment='center')
# Unique to A
ax.text( center-2*offset, center+offset, str((a - b - c).count()), **kwargs)
# Unique to B
ax.text( center+2*offset, center+offset, str((b - a - c).count()), **kwargs)
# Unique to C
ax.text( center, center-2*offset, str((c - a - b).count()), **kwargs)
# A and B not C
ax.text( center, center+2*offset-0.5*offset, str((a + b - c).count()), **kwargs)
# A and C not B
ax.text( center-1.2*offset, center-0.5*offset, str((a + c - b).count()), **kwargs)
# B and C not A
ax.text( center+1.2*offset, center-0.5*offset, str((b + c - a).count()), **kwargs)
# all
ax.text( center, center, str((a + b + c).count()), **kwargs)
ax.legend(loc='best')
fig.savefig(outfn)
plt.close(fig)
def main():
"""Create a 3-way Venn diagram, using matplotlib"""
op = argparse.ArgumentParser(description=__doc__, prog=sys.argv[0])
op.add_argument('-a', help='File to use for the left-most circle')
op.add_argument('-b', help='File to use for the right-most circle')
op.add_argument('-c', help='File to use for the bottom circle')
op.add_argument('--labels',
help='Optional comma-separated list of '
'labels for a, b, and c', default='a,b,c')
op.add_argument('--colors', default='r,b,g',
help='Comma-separated list of matplotlib-valid colors '
'for circles a, b, and c. E.g., --colors=r,b,k')
op.add_argument('-o', default='out.png',
help='Output file to save as. Extension is '
'meaningful, e.g., out.pdf, out.png, out.svg. Default is "%(default)s"')
op.add_argument('--test', action='store_true', help='run test, overriding all other options.')
options = op.parse_args()
reqd_args = ['a','b','c']
if not options.test:
for ra in reqd_args:
if not getattr(options,ra):
op.print_help()
sys.stderr.write('Missing required arg "%s"\n' % ra)
sys.exit(1)
if options.test:
pybedtools.bedtool.random.seed(1)
a = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed')
b = pybedtools.example_bedtool('venn.b.bed')
c = pybedtools.example_bedtool('venn.c.bed')
options.a = a.fn
options.b = b.fn
options.c = c.fn
options.colors='r,b,g'
options.o = 'out.png'
options.labels = 'a,b,c'
venn_mpl(a=options.a, b=options.b, c=options.c,
colors=options.colors.split(','),
labels=options.labels.split(','),
outfn=options.o)
if __name__ == "__main__":
import doctest
if doctest.testmod(optionflags=doctest.ELLIPSIS).failed == 0:
main()
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