def test_plot_boxplot(self):
distribs = numpy.array(
[
[0, 0, 0, 0, 0, 1, 3, 5, 3, 1],
[0, 0, 0, 0, 1, 3, 5, 3, 1, 0],
[0, 1, 3, 5, 3, 1, 0, 0, 0, 0],
[1, 3, 5, 3, 1, 0, 0, 0, 0, 0],
]
)
mpl_params = {
"set_xlabel": {"args": ["Samples"], "kwargs": {}},
"set_ylabel": {"args": ["Depth"], "kwargs": {}},
}
with NamedTemporaryFile(suffix=".png") as fhand:
plot_boxplot_from_distribs(distribs, fhand=fhand, mpl_params=mpl_params)
def plot_called_gts_distrib_per_depth(h5, depths, data_dir,
chunk_size=SNPS_PER_CHUNK):
# Distribution of the number of samples with a depth higher than
# given values
distribs, _ = calc_called_gts_distrib_per_depth(h5, depths=depths,
chunk_size=chunk_size)
fpath = join(data_dir, 'gts_distribution_per_depth.png')
title = 'Distribution of the number of samples with a depth higher than'
title += ' given values'
mpl_params = {'set_xlabel': {'args': ['Depth'], 'kwargs': {}},
'set_ylabel': {'args': ['Number of samples'], 'kwargs': {}},
'set_title': {'args': [title], 'kwargs': {}},
'set_xticklabels': {'args': [depths],
'kwargs': {'rotation': 90}}}
plot_boxplot_from_distribs(distribs, fhand=open(fpath, 'w'),
figsize=(15, 10), mpl_params=mpl_params,
color='tan')
def test_plot_boxplot(self):
distribs = numpy.array([[0, 0, 0, 0, 0, 1, 3, 5, 3, 1],
[0, 0, 0, 0, 1, 3, 5, 3, 1, 0],
[0, 1, 3, 5, 3, 1, 0, 0, 0, 0],
[1, 3, 5, 3, 1, 0, 0, 0, 0, 0]])
mpl_params = {
'set_xlabel': {
'args': ['Samples'],
'kwargs': {}
},
'set_ylabel': {
'args': ['Depth'],
'kwargs': {}
}
}
with NamedTemporaryFile(suffix='.png') as fhand:
plot_boxplot_from_distribs(distribs,
fhand=fhand,
mpl_params=mpl_params)
def plot_called_gts_distrib_per_depth(h5,
depths,
data_dir,
chunk_size=SNPS_PER_CHUNK):
# Distribution of the number of samples with a depth higher than
# given values
distribs, _ = calc_called_gts_distrib_per_depth(h5,
depths=depths,
chunk_size=chunk_size)
fpath = join(data_dir, 'gts_distribution_per_depth.png')
title = 'Distribution of the number of samples with a depth higher than'
title += ' given values'
mpl_params = {
'set_xlabel': {
'args': ['Depth'],
'kwargs': {}
},
'set_ylabel': {
'args': ['Number of samples'],
'kwargs': {}
},
'set_title': {
'args': [title],
'kwargs': {}
},
'set_xticklabels': {
'args': [depths],
'kwargs': {
'rotation': 90
}
}
}
plot_boxplot_from_distribs(distribs,
fhand=open(fpath, 'w'),
figsize=(15, 10),
mpl_params=mpl_params,
color='tan')