def view(self, spec='p', **kwargs):
"""Visualization of the Hi-C map and domains (if present). The function makes use
of :func:`.showMatrix`.
:arg spec: a string specifies how to preprocess the matrix. Blank for no preprocessing,
'p' for showing only data from *p*-th to *100-p*-th percentile. '_' is to suppress
creating a new figure and paint to the current one instead. The letter specifications
can be applied sequentially, e.g. 'p_'.
:type spec: str
:arg p: specifies the percentile threshold.
:type p: double
"""
dm_kwargs = {}
keys = list(kwargs.keys())
for k in keys:
if k.startswith('dm_'):
dm_kwargs[k[3:]] = kwargs.pop(k)
elif k.startswith('domain_'):
dm_kwargs[k[7:]] = kwargs.pop(k)
M = self.map
if 'p' in spec:
p = kwargs.pop('p', 5)
lp = kwargs.pop('lp', p)
hp = kwargs.pop('hp', 100 - p)
vmin = np.percentile(M, lp)
vmax = np.percentile(M, hp)
else:
vmin = vmax = None
if not 'vmin' in kwargs:
kwargs['vmin'] = vmin
if not 'vmax' in kwargs:
kwargs['vmax'] = vmax
im = showMatrix(M, **kwargs)
domains = self.getDomainList()
if len(domains) > 1:
showDomains(domains, **dm_kwargs)
return im
def view(self, spec='p', **kwargs):
"""Visualization of the Hi-C map and domains (if present). The function makes use
of :func:`.showMap`."""
dm_kwargs = {}
keys = kwargs.keys()
for k in keys:
if k.startswith('dm_'):
dm_kwargs[k[3:]] = kwargs.pop(k)
elif k.startswith('domain_'):
dm_kwargs[k[7:]] = kwargs.pop(k)
im = showMap(self.map, spec, **kwargs)
domains = self.getDomainList()
if len(domains) > 1:
showDomains(domains, **dm_kwargs)
return im