<reponame>jjavier-bm/conkit<filename>conkit/plot/contactmapmatrix.py
# 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__ = "<NAME>"
__date__ = "10 Jan 2018"
__version__ = "0.13.2"

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


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!")

    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)

    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]

# 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__ = "<NAME>"
__date__ = "10 Jan 2018"
__version__ = "0.13.2"

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


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!")

    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)

    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]
# 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 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) 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 # TODO: deprecate this in 0.14 Determine the color of the contacts in order