Source code for conkit.plot.precisionevaluation
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"""A module to produce a precision evaluation plot"""
from __future__ import division
__author__ = "Felix Simkovic"
__date__ = "07 Feb 2017"
__version__ = "0.13.3"
import matplotlib.pyplot as plt
import numpy as np
from conkit.plot.figure import Figure
from conkit.plot.tools import ColorDefinitions, _isinstance
[docs]class PrecisionEvaluationFigure(Figure):
"""A Figure object specifically for a Precision evaluation.
This figure will illustrate the precision scores of a contact
map at different precision scores. These can be determined at
various start and end points with different stepwise increases
in between.
Attributes
----------
hierarchy : :obj:`~conkit.core.contactmap.ContactMap`
The contact map hierarchy
cutoff_step : float
The cutoff step
min_cutoff : float
The minimum cutoff factor
max_cutoff : float
The maximum cutoff factor
Examples
--------
>>> import conkit
>>> cmap = conkit.io.read('toxd/toxd.mat', 'ccmpred').top_map
>>> cmap.sequence = conkit.io.read('toxd/toxd.fasta', 'fasta').top_sequence
>>> pdb = conkit.io.read('toxd/toxd.pdb', 'pdb').top_map
>>> cmap.match(pdb, inplace=True)
>>> conkit.plot.PrecisionEvaluationFigure(cmap)
"""
def __init__(self, hierarchy, min_cutoff=0.0, max_cutoff=100.0, cutoff_step=0.2, **kwargs):
"""A precision evaluation figure
Parameters
----------
hierarchy : :obj:`~conkit.core.contactmap.ContactMap`
The contact map hierarchy
min_cutoff : float, optional
The minimum factor
max_cutoff : float, optional
The maximum facotr
cutoff_step : float, optional
The cutoff step
**kwargs
General :obj:`~conkit.plot.figure.Figure` keyword arguments
"""
super(PrecisionEvaluationFigure, self).__init__(**kwargs)
self._hierarchy = None
self._cutoff_boundaries = [0.0, 100.0]
self._cutoff_step = 0.2
self.hierarchy = hierarchy
self.cutoff_step = cutoff_step
self.min_cutoff = min_cutoff
self.max_cutoff = max_cutoff
self.draw()
def __repr__(self):
return self.__class__.__name__
@property
def cutoff_step(self):
"""The cutoff step"""
return self._cutoff_step
@cutoff_step.setter
def cutoff_step(self, cutoff_step):
"""Define the cutoff step"""
self._cutoff_step = cutoff_step
@property
def hierarchy(self):
"""A ConKit :obj:`~conkit.core.contactmap.ContactMap`"""
return self._hierarchy
@hierarchy.setter
def hierarchy(self, hierarchy):
"""Define the ConKit :obj:`~conkit.core.contactmap.ContactMap`
Raises
------
:exc:`RuntimeError`
The hierarchy is not an alignment
"""
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._hierarchy = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" % hierarchy.__class__.__name__)
@property
def min_cutoff(self):
"""The minimum cutoff factor
Raises
------
:obj:`ValueError`
The minimum cutoff value is larger than or equal to the maximum
"""
if self._cutoff_boundaries[0] >= self._cutoff_boundaries[1]:
msg = "The minimum cutoff value is larger than or equal to the maximum"
raise ValueError(msg)
return self._cutoff_boundaries[0]
@min_cutoff.setter
def min_cutoff(self, min_cutoff):
"""Define the minimum cutoff factor"""
if min_cutoff < 0.0:
raise ValueError("Minimum factor cannot be negative")
self._cutoff_boundaries[0] = min_cutoff
@property
def max_cutoff(self):
"""The maximum cutoff factor
Raises
------
:obj:`ValueError`
The maximum cutoff value is smaller than the the minimum
"""
if self._cutoff_boundaries[1] < self._cutoff_boundaries[0]:
msg = "The maximum cutoff value is smaller than the the minimum"
raise ValueError(msg)
return self._cutoff_boundaries[1]
@max_cutoff.setter
def max_cutoff(self, max_cutoff):
"""Define the maximum cutoff factor"""
if max_cutoff > 100:
raise ValueError("Maximum factor cannot be greater than 100")
self._cutoff_boundaries[1] = max_cutoff
[docs] def draw(self):
factors = np.arange(self.min_cutoff, self.max_cutoff + 0.1, self.cutoff_step)
precisions = np.zeros(factors.shape[0])
for i, factor in enumerate(factors):
ncontacts = int(self._hierarchy.sequence.seq_len * factor)
m = self._hierarchy[:ncontacts]
precisions[i] = m.precision
self.ax.plot(
factors,
precisions,
color=ColorDefinitions.GENERAL,
marker=None,
linestyle="-",
label="Precision score",
zorder=1,
)
self.ax.axhline(0.5, color=ColorDefinitions.PRECISION50, linestyle="-", label="50% Precision", zorder=0)
if self.min_cutoff <= 1.0:
self.ax.axvline(1.0, color=ColorDefinitions.FACTOR1, linestyle="-", label="Factor L", zorder=0)
if self.min_cutoff <= 0.5:
self.ax.axvline(0.5, color=ColorDefinitions.FACTOR1, linestyle="--", label="Factor L/2", zorder=0)
if self.min_cutoff <= 0.2:
self.ax.axvline(0.2, color=ColorDefinitions.FACTOR1, linestyle="-.", label="Factor L/5", zorder=0)
if self.min_cutoff <= 0.1:
self.ax.axvline(0.1, color=ColorDefinitions.FACTOR1, linestyle=":", label="Factor L/10", zorder=0)
self.ax.set_xlim(self.min_cutoff, self.max_cutoff)
xticks = (self.ax.get_xticks() * self._hierarchy.sequence.seq_len).astype(np.int64)
self.ax.set_xticklabels(xticks)
self.ax.set_ylim(0.0, 1.0)
self.ax.set_xlabel("Number of Contacts")
self.ax.set_ylabel("Precision")
if self.legend:
self.ax.legend(bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), loc=3, ncol=3, mode="expand", borderaxespad=0.0)
# TODO: deprecate this in 0.14
if self._file_name:
self.savefig(self._file_name, dpi=self._dpi)