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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, by_length=False, dpi=300):
"""
*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']
*by_length* if True, then instead of plotting number of intervals, plot combined
lengths of intervals
*dpi* is the dpi setting passed to matplotlib savefig
"""
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)
count_features = lambda x:x.count()
if by_length:
count_features = lambda x:x.total_coverage()
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(count_features(a - b - c)), **kwargs)
# Unique to B
ax.text(center + 2 * offset, center + offset, str(count_features(b - a - c)), **kwargs)
# Unique to C
ax.text(center, center - 2 * offset, str(count_features(c - a - b)), **kwargs)
# A and B not C
ax.text(
center, center + 2 * offset - 0.5 * offset, str(count_features(a + b - c)), **kwargs
)
# A and C not B
ax.text(
center - 1.2 * offset, center - 0.5 * offset, str(count_features(a + c - b)), **kwargs
)
# B and C not A
ax.text(
center + 1.2 * offset, center - 0.5 * offset, str(count_features(b + c - a)), **kwargs
)
# all
ax.text(center, center, str(count_features(a + b + c)), **kwargs)
ax.legend(loc="best")
fig.savefig(outfn, dpi=dpi)
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()
|
