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#!/usr/bin/env python
"""
Given 3 files, creates a 3-way Venn diagram of intersections using the Google \
Chart API; see :mod:`pybedtools.contrib.venn_maker` for more flexibility.
The values in the diagram assume:
* unstranded intersections
* no features that are nested inside larger features
"""
import argparse
import sys
import pybedtools
import urllib
def venn_gchart(a, b, c=None, colors=None, labels=None, size="300x300"):
"""
a, b, and c are filenames to BED-like files.
*colors* is a list of 3 hex colors
*labels* is a list of 3 labels
*outfn* is the output PNG you want to create.
*size* is the size in pixels for the PNG
"""
a = pybedtools.BedTool(a)
b = pybedtools.BedTool(b)
if c:
c = pybedtools.BedTool(c)
# The order of values is meaningful to the API, see
# http://code.google.com/apis/chart/docs/gallery/venn_charts.html
if c:
vals = [
len(a),
len(b),
len(c),
len(a + b),
len(a + c),
len(b + c),
len(a + b + c),
]
else:
# insert 0 for size of 3rd circle.
vals = [len(a), len(b), 0, len(a + b)]
labels = labels[:2]
# API doesn't seem to like large numbers, so get fractions instead, then
# join make a comma-separated list of values.
mx = float(max(vals))
vals = [round(i / mx, 4) for i in vals]
valstr = ",".join(map(str, vals))
data = {"cht": "v", "chs": size, "chd": "t:" + valstr}
# Add the optional data, if specified
if labels:
data["chdl"] = "|".join(labels)
if colors:
data["chco"] = ",".join(colors)
return data
def gchart(data, outfn="out.png"):
"""
Sends data to Google Chart API
"""
data = urllib.parse.urlencode(data)
binary_data = data.encode("UTF-8")
url = "https://chart.googleapis.com/chart?"
# Request and get the PNG
req = urllib.request.Request(url, binary_data)
print(url + data)
response = urllib.request.urlopen(req)
f = open(outfn, "w")
f.write(response.read())
f.close()
def main():
"""Create a 3-way Venn diagram using Google Charts API
"""
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(
"--colors",
help="Optional comma-separated list of hex "
"colors for circles a, b, and c. E.g. %(default)s",
default="00FF00,FF0000,0000FF",
)
op.add_argument(
"--labels",
help="Optional comma-separated list of labels for a, b, and c",
default="a,b,c",
)
op.add_argument(
"--size",
default="300x300",
help="Optional size of PNG, in pixels. Default is " '"%(default)s"',
)
op.add_argument(
"-o", default="out.png", help="Output file to save as, in PNG format"
)
op.add_argument(
"--test", action="store_true", help="run test, overriding all other options."
)
options = op.parse_args()
reqd_args = ["a", "b"]
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:
# Example data
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 = "00FF00,FF0000,0000FF"
options.o = "out.png"
options.labels = "a,b,c"
data = venn_gchart(
a=options.a,
b=options.b,
c=options.c,
colors=options.colors.split(","),
labels=options.labels.split(","),
size=options.size,
)
gchart(data, outfn=options.o)
if __name__ == "__main__":
import doctest
if doctest.testmod(optionflags=doctest.ELLIPSIS).failed == 0:
main()
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