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"""
A module to produce a sequence coverage plot
"""
from __future__ import division
from __future__ import print_function
__author__ = "Felix Simkovic"
__date__ = "07 Feb 2017"
__version__ = "0.1"
import matplotlib.pyplot as plt
import numpy as np
from conkit.plot._figure import Figure
from conkit.plot._plottools import ColorDefinitions
[docs]class SequenceCoverageFigure(Figure):
"""A Figure object specifically for a Sequence coverage illustration.
This figure will illustrate the coverage of sequences at each position
in the provided alignment. It counts the frequency of sequences at which
a residue is present and plots it.
This figure can be particularly useful in cases where domain boundaries
could be redefined. It is also useful in cases where only parts of your
alignment are well covered, and thus trimming the alignment might produce
much more accurate Evoluationary Covariance predictions.
Attributes
----------
hierarchy : :obj:`SequenceFile <conkit.core.SequenceFile>`
The Multiple Sequence Alignment hierarchy
Examples
--------
>>> import conkit
>>> msa = conkit.io.read('toxd/toxd.a3m', 'a3m')
>>> conkit.plot.SequenceCoverageFigure(msa)
"""
def __init__(self, hierarchy, **kwargs):
"""A new sequence coverage plot
Parameters
----------
hierarchy : :obj:`SequenceFile <conkit.core.SequenceFile>`
The Multiple Sequence Alignment hierarchy
**kwargs
General :obj:`Figure <conkit.plot._Figure.Figure>` keyword arguments
"""
super(SequenceCoverageFigure, self).__init__(**kwargs)
self._hierarchy = None
self.hierarchy = hierarchy
self._draw()
def __repr__(self):
return "{0}(file_name=\"{1}\")".format(self.__class__.__name__, self.file_name)
@property
def hierarchy(self):
"""A ConKit :obj:`SequenceFile <conkit.core.SequenceFile>`"""
return self._hierarchy
@hierarchy.setter
def hierarchy(self, hierarchy):
"""Define the ConKit :obj:`SequenceFile <conkit.core.SequenceFile>`
Raises
------
RuntimeError
The hierarchy is not an alignment
"""
if hierarchy:
Figure._check_hierarchy(hierarchy, "SequenceFile")
if not hierarchy.is_alignment:
raise RuntimeError("Provided hierarchy does not show characteristics of an alignment")
self._hierarchy = hierarchy
def _draw(self):
"""Draw the actual plot"""
residues = np.arange(1, self._hierarchy.top_sequence.seq_len + 1)
aa_counts = np.asarray(self._hierarchy.calculate_freq()) * self._hierarchy.nseq
fig, ax = plt.subplots()
ax.plot(
residues,
aa_counts,
color=ColorDefinitions.GENERAL,
marker='o',
markersize=5,
linestyle='-',
label='Amino acid count',
zorder=1)
# Add lines as quality indicators
ax.axhline(
self._hierarchy.top_sequence.seq_len * 5, color=ColorDefinitions.L5CUTOFF, label='5 x Nresidues', zorder=0)
if any(x >= self._hierarchy.top_sequence.seq_len * 20 for x in aa_counts):
ax.axhline(
self._hierarchy.top_sequence.seq_len * 20,
color=ColorDefinitions.L20CUTOFF,
label='20 x Nresidues',
zorder=0)
# Prettify the plot
ax.set_xlim(residues[0], residues[-1])
xticks = ax.get_xticks().astype(np.int64) + residues[0]
# Remove any excess xticks
xticks = np.delete(xticks, [i for i, t in enumerate(xticks) if t > residues[-1]])
ax.set_xticks(xticks)
ax.set_xticklabels(xticks)
ax.set_xlabel('Residue number')
ax.set_ylabel('Sequence Count')
ax.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, ncol=3, mode="expand", borderaxespad=0.)
# Make axes length proportional and remove whitespace around the plot
aspectratio = Figure._correct_aspect(ax, 0.3)
ax.set(aspect=aspectratio)
fig.tight_layout()
fig.savefig(self.file_name, bbox_inches='tight', dpi=self.dpi)