def test_calc_r2_windows(self):
variations = VariationsArrays()
chrom = numpy.array([b'chr1'] * 4)
pos = numpy.array([1, 4, 6, 20])
gts = numpy.array([[[0, 0], [1, 1], [0, 0]],
[[0, 0], [1, 1], [0, 0]],
[[1, 1], [0, 0], [1, 1]],
[[0, 0], [0, 1], [-1, -1]]])
variations['/variations/chrom'] = chrom
variations['/variations/pos'] = pos
variations['/calls/GT'] = gts
expected = [1.0, 1.0000002, 1.0, 1.0000002, 1.0, 1.0]
assert numpy.allclose(_calc_r2(gts), expected)
chrom, pos, r2 = calc_r2_windows(variations, 10)
assert numpy.allclose(r2, [1.0000002384185933, numpy.nan],
equal_nan=True)
assert numpy.all(chrom == b'chr1')
def test_calc_r2_windows(self):
variations = VariationsArrays()
chrom = numpy.array([b'chr1'] * 4)
pos = numpy.array([1, 4, 6, 20])
gts = numpy.array([[[0, 0], [1, 1], [0, 0]],
[[0, 0], [1, 1], [0, 0]],
[[1, 1], [0, 0], [1, 1]],
[[0, 0], [0, 1], [-1, -1]]])
variations['/variations/chrom'] = chrom
variations['/variations/pos'] = pos
variations['/calls/GT'] = gts
expected = [1.0, 1.0000002, 1.0, 1.0000002, 1.0, 1.0]
assert numpy.allclose(_calc_r2(gts), expected)
chrom, pos, r2 = calc_r2_windows(variations, 10)
assert numpy.allclose(r2, [1.0000002384185933, numpy.nan],
equal_nan=True)
assert numpy.all(chrom == b'chr1')
def plot_r2(variations, window_size, data_dir, write_bg=False):
# Calculate LD r2 parameter in windows
chrom, pos, r2 = calc_r2_windows(variations, window_size=window_size)
# Plot r2 distribution
fpath = os.path.join(data_dir, 'r2_distrib.png')
distrib, bins = histogram(r2, n_bins=50, range_=(0, 1))
title = 'r2 distribution in windows of {} bp'.format(window_size)
mpl_params={'set_xlabel': {'args': ['r2'], 'kwargs': {}},
'set_ylabel': {'args': ['Number of windows'], 'kwargs': {}},
'set_title': {'args': [title], 'kwargs': {}}}
plot_distrib(distrib, bins, fhand=open(fpath, 'w'), figsize=(7, 7),
mpl_params=mpl_params)
# Manhattan plot
mask = numpy.logical_not(numpy.isnan(r2))
chrom = chrom[mask]
pos = pos[mask]
r2 = r2[mask]
fpath = os.path.join(data_dir, 'r2_manhattan.png')
title = 'r2 along genome in windows of {} bp'.format(window_size)
mpl_params={'set_xlabel': {'args': ['Chromosome'], 'kwargs': {}},
'set_ylabel': {'args': ['r2'], 'kwargs': {}},
'set_title': {'args': [title], 'kwargs': {}}}
manhattan_plot(chrom, pos, r2, fhand=open(fpath, 'w'), figsize=(15, 7),
marker='k', mpl_params=mpl_params)
# Write bg
if write_bg:
fpath = os.path.join(data_dir, 'r2_windows_{}.png'.format(window_size))
bg_fhand = open(fpath, 'w')
pos_r2 = PositionalStatsCalculator(chrom, pos, r2,
window_size=window_size,
step=window_size,
take_windows=False)
description = 'mean r2 in windows of {} bp'.format(window_size)
pos_r2.write(bg_fhand, 'r2', description, track_type='bedgraph')
def plot_r2(variations, window_size, data_dir, write_bg=False):
# Calculate LD r2 parameter in windows
chrom, pos, r2 = calc_r2_windows(variations, window_size=window_size)
# Plot r2 distribution
fpath = os.path.join(data_dir, 'r2_distrib.png')
distrib, bins = histogram(r2, n_bins=50, range_=(0, 1))
title = 'r2 distribution in windows of {} bp'.format(window_size)
mpl_params = {
'set_xlabel': {
'args': ['r2'],
'kwargs': {}
},
'set_ylabel': {
'args': ['Number of windows'],
'kwargs': {}
},
'set_title': {
'args': [title],
'kwargs': {}
}
}
plot_distrib(distrib,
bins,
fhand=open(fpath, 'w'),
figsize=(7, 7),
mpl_params=mpl_params)
# Manhattan plot
mask = numpy.logical_not(numpy.isnan(r2))
chrom = chrom[mask]
pos = pos[mask]
r2 = r2[mask]
fpath = os.path.join(data_dir, 'r2_manhattan.png')
title = 'r2 along genome in windows of {} bp'.format(window_size)
mpl_params = {
'set_xlabel': {
'args': ['Chromosome'],
'kwargs': {}
},
'set_ylabel': {
'args': ['r2'],
'kwargs': {}
},
'set_title': {
'args': [title],
'kwargs': {}
}
}
manhattan_plot(chrom,
pos,
r2,
fhand=open(fpath, 'w'),
figsize=(15, 7),
marker='k',
mpl_params=mpl_params)
# Write bg
if write_bg:
fpath = os.path.join(data_dir, 'r2_windows_{}.png'.format(window_size))
bg_fhand = open(fpath, 'w')
pos_r2 = PositionalStatsCalculator(chrom,
pos,
r2,
window_size=window_size,
step=window_size,
take_windows=False)
description = 'mean r2 in windows of {} bp'.format(window_size)
pos_r2.write(bg_fhand, 'r2', description, track_type='bedgraph')