conkit.plot.contactdensity module¶
A module to produce a domain boundary plot
-
class
ContactDensityFigure
(hierarchy, bw_method='bowman', **kwargs)[source]¶ Bases:
conkit.plot.figure.Figure
A Figure object specifically for a contact density illustration.
This figure is an adaptation of the algorithm published by Sadowski (2013) [1].
[1] Sadowski M. (2013). Prediction of protein domain boundaries from inverse covariances. Proteins 81(2), 253-260. -
hierarchy
¶ The default contact map hierarchy
Type: ContactMap
Examples
>>> import conkit >>> cmap = conkit.io.read('toxd/toxd.mat', 'ccmpred').top_map >>> conkit.plot.ContactDensityFigure(cmap)
-
bw_method
The method to estimate the bandwidth
For a full list of options, please refer to
get_contact_density()
-
hierarchy
-