Source code for conkit.plot.contactmapmatrix
# BSD 3-Clause License
#
# Copyright (c) 2016-21, University of Liverpool
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# * Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""A module to produce a contact map plot"""
from __future__ import division
from __future__ import print_function
__author__ = "Felix Simkovic"
__date__ = "10 Jan 2018"
__version__ = "0.13.3"
import matplotlib.collections as mcoll
import matplotlib.pyplot as plt
import numpy as np
from conkit.core.struct import Gap
from conkit.misc import normalize
from conkit.plot.figure import Figure
from conkit.plot.tools import ColorDefinitions, _isinstance
[docs]class ContactMapMatrixFigure(Figure):
"""A Figure object specifically for a :obj:`~conkit.core.contactmap.ContactMap`
This figure will illustrate the contacts in a contact
map matrix. This plot is a very common representation of contacts.
With this figure, you can illustrate either your contact
map by itself, compared against a second contact map, and/or
matched against contacts extracted from a contact map.
Attributes
----------
hierarchy : :obj:`~conkit.core.contactmap.ContactMap`
The default contact map hierarchy
other : :obj:`~conkit.core.contactmap.ContactMap`
The second contact map hierarchy
altloc : bool
Use the :attr:`~conkit.core.contact.Contact.res_altloc` positions [default: False]
Examples
--------
>>> import conkit
>>> cmap = conkit.io.read('toxd/toxd.mat', 'ccmpred').top_map
>>> conkit.plot.ContactMapMatrixFigure(cmap)
"""
def __init__(self, hierarchy, other=None, altloc=False, lim=None, **kwargs):
"""A new contact map plot
Parameters
----------
hierarchy : :obj:`~conkit.core.contactmap.ContactMap`
The default contact map hierarchy
other : :obj:`~conkit.core.contactmap.ContactMap`, optional
The second contact map hierarchy
altloc : bool, optional
Use the :attr:`~conkit.core.contact.Contact.res_altloc` positions [default: False]
lim : tuple, list, optional
The [min, max] residue numbers to show
**kwargs
General :obj:`~conkit.plot.figure.Figure` keyword arguments
"""
super(ContactMapMatrixFigure, self).__init__(**kwargs)
self._hierarchy = None
self._other = None
self._lim = None
self.altloc = altloc
self.hierarchy = hierarchy
if other:
self.other = other
if lim:
self.lim = lim
self.draw()
def __repr__(self):
return self.__class__.__name__
@property
def hierarchy(self):
return self._hierarchy
@hierarchy.setter
def hierarchy(self, hierarchy):
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._hierarchy = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" % hierarchy.__class__.__name__)
@property
def other(self):
return self._other
@other.setter
def other(self, hierarchy):
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._other = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" % hierarchy.__class__.__name__)
@property
def lim(self):
return self._lim
@lim.setter
def lim(self, lim):
if isinstance(lim, (list, tuple)) and len(lim) == 2:
self._lim = lim
elif isinstance(lim, (list, tuple)):
raise ValueError("A list with 2 entries is required!")
else:
raise TypeError("A list with [min, max] limits is required!")
[docs] def draw(self):
_hierarchy = self._hierarchy.rescale()
self_data = np.array([c for c in _hierarchy.as_list() if all(ci != Gap.IDENTIFIER for ci in c)])
self_colors = ContactMapMatrixFigure._determine_color(_hierarchy)
self_rawsc = np.array(
[c.raw_score for c in _hierarchy if all(ci != Gap.IDENTIFIER for ci in [c.res1_seq, c.res2_seq])]
)
if self._other:
_other = self._other.rescale()
other_data = np.array([c for c in _other.as_list() if any(ci != Gap.IDENTIFIER for ci in c)])
other_colors = ContactMapMatrixFigure._determine_color(_other)
other_rawsc = np.array(
[c.raw_score for c in _other if all(ci != Gap.IDENTIFIER for ci in [c.res1_seq, c.res2_seq])]
)
else:
other_data = self_data
other_colors = self_colors
other_rawsc = self_rawsc
self._patch_scatter(
self_data[:, 1], self_data[:, 0], symbol="s", facecolor=self_colors, radius=1.0, linewidth=0
)
self._patch_scatter(
other_data[:, 0], other_data[:, 1], symbol="s", facecolor=other_colors, radius=1.0, linewidth=0
)
self.define_axis_settings(self_data, other_data)
# TODO: deprecate this in 0.14
if self._file_name:
self.savefig(self._file_name, dpi=self._dpi)
[docs] def define_axis_settings(self, data_1, data_2):
if self.lim:
min_max_data = np.arange(self.lim[0], self.lim[1] + 1)
self.ax.set_xlim(self.lim[0] - 0.5, self.lim[1] + 0.5)
self.ax.set_ylim(self.lim[0] - 0.5, self.lim[1] + 0.5)
else:
min_max_data = np.append(data_1[:, 0], data_1[:, 1])
min_max_data = np.append(min_max_data, data_2[:, 0])
min_max_data = np.append(min_max_data, data_2[:, 1])
self.ax.set_xlim(min_max_data.min(), min_max_data.max() + 1.0)
self.ax.set_ylim(min_max_data.min(), min_max_data.max() + 1.0)
gap = 10 * (min_max_data.max() - min_max_data.min()) // 100
if gap < 1:
gap = 1
tick_range = np.arange(min_max_data.min(), min_max_data.max(), gap, dtype=np.int64)
self.ax.set_xticks(tick_range + 0.5)
self.ax.set_xticklabels(tick_range)
self.ax.set_yticks(tick_range + 0.5)
self.ax.set_yticklabels(tick_range)
self.ax.set_xlabel("Residue number")
self.ax.set_ylabel("Residue number")
@staticmethod
def _determine_color(h):
"""Determine the color of the contacts in order"""
greys = plt.get_cmap("Greys")
return [greys(contact.raw_score) for contact in h]