def test_venn_mpl():
"""
compares output image to expected
"""
try:
import matplotlib
except ImportError:
import sys
sys.stderr.write('Need matplotlib installed to test venn_mpl')
return
here = os.path.dirname(__file__)
expected_fn = os.path.join(here, 'mpl-expected.png')
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
outfn = 'mplout.png'
venn_mpl.venn_mpl(a=a.fn, b=b.fn, c=c.fn, colors=['r','b','g'], outfn=outfn, labels=['a','b','c'])
# On a different machine, the created image is not visibly different but is
# numerically different. Not sure what a reasonable tolerance is, but this
# seems to work for now....
o = matplotlib.image.imread(outfn)
e = matplotlib.image.imread(expected_fn)
TOLERANCE = 200
SUM = abs((o - e).sum())
assert SUM < TOLERANCE, SUM
os.unlink(outfn)
def test_venn_mpl():
"""
compares output image to expected
"""
try:
import matplotlib
except ImportError:
import sys
sys.stderr.write('Need matplotlib installed to test venn_mpl')
return
here = os.path.dirname(__file__)
expected_fn = os.path.join(here, 'mpl-expected.png')
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
outfn = 'mplout.png'
venn_mpl.venn_mpl(a=a.fn, b=b.fn, c=c.fn, colors=['r','b','g'], outfn=outfn, labels=['a','b','c'])
# On a different machine, the created image is not visibly different but is
# numerically different. Not sure what a reasonable tolerance is, but this
# seems to work for now....
o = matplotlib.image.imread(outfn)
e = matplotlib.image.imread(expected_fn)
TOLERANCE = 200
SUM = abs((o - e).sum())
assert SUM < TOLERANCE, SUM
os.unlink(outfn)
def test_venn_mpl():
"""
compares output image to expected
"""
try:
import matplotlib
except ImportError:
import sys
sys.stderr.write('Need matplotlib installed to test venn_mpl')
return
here = os.path.dirname(__file__)
expected_fn = os.path.join(here, 'mpl-expected.png')
pybedtools.bedtool.random.seed(1)
a = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed')
b = a.random_subset(100).shuffle(genome='hg19', seed=1)
b = b.cat(a.random_subset(100, seed=1))
c = a.random_subset(200).shuffle(genome='hg19', seed=2)
c = c.cat(b.random_subset(100, seed=1))
outfn = 'mplout.png'
venn_mpl.venn_mpl(a=a.fn, b=b.fn, c=c.fn, colors=['r','b','g'], outfn=outfn, labels=['a','b','c'])
# On a different machine, the created image is not visibly different but is
# numerically different. Not sure what a reasonable tolerance is, but this
# seems to work for now....
o = matplotlib.image.imread(outfn)
e = matplotlib.image.imread(expected_fn)
TOLERANCE = 25
assert abs((o - e).sum()) < TOLERANCE
os.unlink(outfn)
import pybedtools
from pybedtools.scripts import venn_mpl
from pybedtools.contrib import venn_maker
rheos = pybedtools.BedTool("/Users/siakhnin/data/giab/RMNISTHS_30xdownsample.chr20.rheos_kde_dels.bed")
delly = pybedtools.BedTool("/Users/siakhnin/data/giab/RMNISTHS_30xdownsample.chr20.no_spikein.delly.pass_only.dels.bed")
giab = pybedtools.BedTool("/Users/siakhnin/data/giab/Personalis_1000_Genomes_deduplicated_deletions_chr20_gt500bp.bed")
venn_mpl.venn_mpl(rheos, delly, giab, labels=["rheos", "delly", "giab"])
venn_maker.venn_maker(["/Users/siakhnin/data/giab/RMNISTHS_30xdownsample.chr20.rheos_kde_dels.bed",
"/Users/siakhnin/data/giab/RMNISTHS_30xdownsample.chr20.no_spikein.delly.pass_only.dels.bed",
"/Users/siakhnin/data/giab/Personalis_1000_Genomes_deduplicated_deletions_chr20_gt500bp.bed"],
names=["rheos","delly","giab"],
run=True,
figure_filename='out.png',
additional_args=['euler.d=TRUE',
'scaled=TRUE',
'cat.col=c("red","blue","green")',
'col=c("red","blue","green")',
'imagetype="png"']
)
