"""
CorrPlot functionalities.
It comes from `corrplot.py <https://raw.githubusercontent.com/biokit/biokit/master/biokit/viz/corrplot.py>`_
which I copied here because the module does not properly work on Python 3 (import issues).
See also `biokit license <https://github.com/biokit/biokit/blob/master/LICENSE>`_.
:author: Thomas Cokelaer
:references: http://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html
:githublink:`%|py|12`
"""
import numpy
from scipy.cluster.hierarchy import dendrogram, fcluster
import pandas
from .linkage import Linkage
from ._colormap import cmap_builder
[docs]class Corrplot(Linkage):
"""
An implementation of correlation plotting tools (corrplot).
the class requires `scipy <http://www.scipy.org/>`_.
Here is a simple example with a correlation matrix as an input (stored in
a pandas dataframe):
.. plot::
:width: 50%
:include-source:
import pandas
import numpy
letters = "ABCDEFGHIJKLM"[0:10]
df = pandas.DataFrame(dict(( (k, numpy.random.random(10)+ord(k)-65) for k in letters)))
import matplotlib.pyplot as plt
plt.close('all')
plt.style.use('ggplot')
from pyensae.graph_helper import Corrplot
c = Corrplot(df)
c.plot()
plt.show()
This class requires module `colormap <https://pypi.python.org/pypi/colormap>`_.
:githublink:`%|py|46`
"""
[docs] def __init__(self, data, na=0):
"""
Plots the content of square matrix that contains correlation values.
:param data: input can be a dataframe (Pandas), or list of lists (python) or
a numpy matrix. Note, however, that values must be between -1 and 1. If not,
or if the matrix (or list of lists) is not squared, then correlation is
computed. The data or computed correlation is stored in :attr:`df` attribute.
:param na: replace NA values with this value (default 0)
The :attr:`params` contains some tunable parameters for the colorbar in the
:meth:`plot` method.
::
# can be a list of lists, the correlation matrix is then a 2x2 matrix
c = Corrplot([[1,1], [2,4], [3,3], [4,4]])
:githublink:`%|py|66`
"""
super(Corrplot, self).__init__() # pylint: disable=R1725
# we delay import in case this is not needed
self.cmap_builder = cmap_builder
self.df = pandas.DataFrame(data, copy=True)
compute_correlation = False
w, h = self.df.shape
if self.df.max().max() > 1 or self.df.min().min() < -1:
compute_correlation = True
if w != h:
compute_correlation = True
if list(self.df.index) != list(self.df.columns):
compute_correlation = True
if compute_correlation:
cor = self.df.corr()
self.df = cor
# replace NA with zero
self.df.fillna(na, inplace=True)
#: tunable parameters for the :meth:`plot` method.
self.params = {
'colorbar.N': 100,
'colorbar.shrink': .8,
'colorbar.orientation': 'vertical'}
[docs] def _set_default_cmap(self):
self.cm = self.cmap_builder('#AA0000', 'white', 'darkblue')
[docs] def order(self, method='complete', metric='euclidean', inplace=False):
"""
Rearranges the order of rows and columns after clustering.
:param method: any scipy method (e.g., single, average, centroid,
median, ward). See scipy.cluster.hierarchy.linkage
:param metric: any scipy distance (euclidean, hamming, jaccard)
See scipy.spatial.distance or scipy.cluster.hieararchy
:param bool inplace: if set to True, the dataframe is replaced
You probably do not need to use that method. Use :meth:`plot` and
the two parameters order_metric and order_method instead.
:githublink:`%|py|112`
"""
if None is method or None is metric:
return self.df
Y = self.linkage(self.df, method=method, metric=metric)
ind1 = fcluster(Y, 0.7 * max(Y[:, 2]), 'distance')
Z = dendrogram(Y, no_plot=True)
idx1 = Z['leaves']
cor2 = self.df.iloc[idx1].T.iloc[idx1].T
if inplace is True:
self.df = cor2
else:
return cor2
self.Y = Y
self.Z = Z
self.idx1 = idx1
self.ind1 = ind1
return cor2
[docs] def plot(self, fig=None, grid=True,
rotation=30, lower=None, upper=None,
shrink=0.9, axisbg='white', colorbar=True, label_color='black',
fontsize='small', edgecolor='black', method='ellipse',
order_method='complete', order_metric='euclidean', cmap=None,
ax=None, binarise_color=False, figsize=None):
"""
Plots the correlation matrix from the content of :attr:`df`
(dataframe).
By default, the correlation is shown on the upper and lower triangle and is
symmetric wrt to the diagonal. The symbols are ellipses. The symbols can
be changed to e.g. rectangle. The symbols are shown on upper and lower sides but
you could choose a symbol for the upper side and another for the lower side using
the **lower** and **upper** parameters.
:param fig: Create a new figure by default. If an instance of an existing
figure is provided, the corrplot is overlayed on the figure provided.
Can also be the number of the figure.
:param grid: add grid (Defaults to grey color). You can set it to False or a color.
:param rotation: rotate labels on y-axis
:param lower: if set to a valid method, plots the data on the lower
left triangle
:param upper: if set to a valid method, plots the data on the upper
left triangle
:param float shrink: maximum space used (in percent) by a symbol.
If negative values are provided, the absolute value is taken.
If greater than 1, the symbols wiill overlap.
:param axisbg: color of the background (defaults to white).
:param colorbar: add the colorbar (defaults to True).
:param str label_color: (defaults to black).
:param fontsize: size of the fonts defaults to 'small'.
:param method: shape to be used in 'ellipse', 'square', 'rectangle',
'color', 'text', 'circle', 'number', 'pie'.
:param order_method: see :meth:`order <pyensae.graphhelper.corrplot.Corrplot.order>`.
:param order_metric: see : meth:`order`.
:param cmap: a valid cmap from matplotlib or colormap package (e.g.,
'jet', or 'copper'). Default is red/white/blue colors.
:param binarise_color: two colors only, negative, positive
:param ax: a matplotlib axes.
:param figsize: gives that parameter to the new created figure
:return: ax (matplotlib axes)
The colorbar can be tuned with the parameters stored in :attr:`params`.
Here is an example. See notebook for other examples:
::
c = corrplot.Corrplot(dataframe)
c.plot(cmap=('Orange', 'white', 'green'))
c.plot(method='circle')
c.plot(colorbar=False, shrink=.8, upper='circle' )
:githublink:`%|py|183`
"""
import matplotlib.pyplot as plt # pylint: disable=C0415
# default
if cmap is not None:
try:
if isinstance(cmap, str):
self.cm = self.cmap_builder(cmap)
else:
self.cm = self.cmap_builder(*cmap)
except Exception:
self._set_default_cmap()
else:
self._set_default_cmap()
self.shrink = abs(shrink)
self.fontsize = fontsize
self.edgecolor = edgecolor
df = self.order(method=order_method, metric=order_metric)
# figure can be a number or an instance; otherwise creates it
params = dict(facecolor=axisbg)
if isinstance(fig, int):
params["num"] = fig.number
elif fig is not None:
params["num"] = fig.number
else:
params["num"] = None
if figsize is not None:
params["figsize"] = figsize
fig = plt.figure(**params)
# do we have an axes to plot the data in ?
if ax is None:
ax = plt.subplot(1, 1, 1, aspect='equal', facecolor=axisbg)
else:
# if so, clear the axes. Colorbar cannot be removed easily.
plt.sca(ax)
ax.clear()
# subplot resets the bg color, let us set it again
fig.set_facecolor(axisbg)
width, height = df.shape
labels = (df.columns)
if upper is None and lower is None:
mode = 'method'
elif upper and lower:
mode = 'both'
elif lower is not None:
mode = 'lower'
elif upper is not None:
mode = 'upper'
self.binarise_color = binarise_color
if mode == 'upper':
self._add_patches(df, upper, 'upper', ax, diagonal=True)
elif mode == 'lower':
self._add_patches(df, lower, 'lower', ax, diagonal=True)
elif mode == 'method':
self._add_patches(df, method, 'both', ax, diagonal=True)
elif mode == 'both':
self._add_patches(df, upper, 'upper', ax, diagonal=False)
self._add_patches(df, lower, 'lower', ax, diagonal=False)
# shift the limits to englobe the patches correctly
ax.set_xlim(-0.5, width - .5)
ax.set_ylim(-0.5, height - .5)
# set xticks/xlabels on top
ax.xaxis.tick_top()
xtickslocs = numpy.arange(len(labels))
ax.set_xticks(xtickslocs)
ax.set_xticklabels(labels, rotation=rotation, color=label_color,
fontsize=fontsize, ha='left')
ax.invert_yaxis()
ytickslocs = numpy.arange(len(labels))
ax.set_yticks(ytickslocs)
ax.set_yticklabels(labels, fontsize=fontsize, color=label_color)
plt.tight_layout()
if grid is not False:
if grid is True:
grid = 'grey'
for i in range(0, width):
ratio1 = float(i) / width
ratio2 = float(i + 2) / width
# set axis off
# 2 - set xlabels along the diagonal
# set colorbar either on left or bottom
if mode == 'lower':
ax.axvline(i + .5, ymin=1 - ratio1, ymax=0., color=grid)
ax.axhline(i + .5, xmin=0, xmax=ratio2, color=grid)
if mode == 'upper':
ax.axvline(i + .5, ymin=1 - ratio2, ymax=1, color=grid)
ax.axhline(i + .5, xmin=ratio1, xmax=1, color=grid)
if mode in ['method', 'both']:
ax.axvline(i + .5, color=grid)
ax.axhline(i + .5, color=grid)
# can probably be simplified
if mode == 'lower':
ax.axvline(-.5, ymin=0, ymax=1, color='grey')
ax.axvline(width - .5, ymin=0, ymax=1. /
width, color='grey', lw=2)
ax.axhline(width - .5, xmin=0, xmax=1, color='grey', lw=2)
ax.axhline(-.5, xmin=0, xmax=1. / width, color='grey', lw=2)
ax.xticks([])
for i in range(0, width):
ax.text(i, i - .6, labels[i], fontsize=fontsize,
color=label_color,
rotation=rotation, verticalalignment='bottom')
ax.text(-.6, i, labels[i], fontsize=fontsize,
color=label_color,
rotation=0, horizontalalignment='right')
ax.set_axis_off()
# can probably be simplified
elif mode == 'upper':
ax.axvline(width - .5, ymin=0, ymax=1, color='grey', lw=2)
ax.axvline(-.5, ymin=1 - 1. / width,
ymax=1, color='grey', lw=2)
ax.axhline(-.5, xmin=0, xmax=1, color='grey', lw=2)
ax.axhline(width - .5, xmin=1 - 1. / width,
xmax=1, color='grey', lw=2)
ax.yticks([])
for i in range(0, width):
ax.text(-.6 + i, i, labels[i], fontsize=fontsize,
color=label_color, horizontalalignment='right',
rotation=0)
ax.text(i, -.5, labels[i], fontsize=fontsize,
color=label_color, rotation=rotation, verticalalignment='bottom')
ax.set_axis_off()
# set all ticks length to zero
ax = plt.gca()
ax.tick_params(axis='both', which='both', length=0)
if colorbar:
N = self.params['colorbar.N'] + 1
if N < 2:
raise RuntimeError("No colorbar to draw.")
cb = plt.gcf().colorbar(
self.collection, orientation=self.params['colorbar.orientation'],
shrink=self.params['colorbar.shrink'],
boundaries=numpy.linspace(0, 1, N),
ticks=[0, .25, 0.5, 0.75, 1])
cb.ax.set_yticklabels([-1, -.5, 0, .5, 1])
# make sure it goes from -1 to 1 even though actual values may not
# reach that range
# cb.set_clim(0, 1)
# not working in matplotlib 3.3.0
return ax
[docs] def _add_patches(self, df, method, fill, ax, diagonal=True):
from matplotlib.patches import Ellipse, Circle, Rectangle, Wedge
from matplotlib.collections import PatchCollection
width, height = df.shape
patches = []
colors = []
for x in range(width):
for y in range(height):
if fill == 'lower' and x > y:
continue
if fill == 'upper' and x < y:
continue
if diagonal is False and x == y:
continue
datum = (df.iloc[x, y] + 1.) / 2.
d = df.iloc[x, y]
d_abs = numpy.abs(d)
#c = self.pvalues[x, y]
rotate = -45 if d > 0 else +45
#cmap = self.poscm if d >= 0 else self.negcm
if method in ['ellipse', 'square', 'rectangle', 'color']:
if method == 'ellipse':
func = Ellipse
patch = func((x, y), width=1 * self.shrink,
height=(self.shrink - d_abs * self.shrink), angle=rotate)
else:
func = Rectangle
w = h = d_abs * self.shrink
offset = (1 - w) / 2.
if method == 'color':
w = 1
h = 1
offset = 0
patch = func((x + offset - .5, y + offset - .5), width=w,
height=h, angle=0)
if self.edgecolor:
patch.set_edgecolor(self.edgecolor)
# patch.set_facecolor(cmap(d_abs))
colors.append(datum)
if d_abs > 0.05:
patch.set_linestyle('dotted')
# ax.add_artist(patch)
patches.append(patch)
elif method == 'circle':
patch = Circle((x, y), radius=d_abs * self.shrink / 2.)
if self.edgecolor:
patch.set_edgecolor(self.edgecolor)
# patch.set_facecolor(cmap(d_abs))
colors.append(datum)
if d_abs > 0.05:
patch.set_linestyle('dotted')
# ax.add_artist(patch)
patches.append(patch)
elif method in ['number', 'text']:
if d < 0:
edgecolor = self.cm(-1.0)
elif d >= 0:
edgecolor = self.cm(1.0)
d_str = "{:.2f}".format(d).replace(
"0.", ".").replace(".00", "")
ax.text(x, y, d_str, color=edgecolor,
fontsize=self.fontsize, horizontalalignment='center',
weight='bold', alpha=max(0.5, d_abs),
withdash=False)
elif method == 'pie':
S = 360 * d_abs
patch = [
Wedge((x, y), 1 * self.shrink / 2., -90, S - 90),
Wedge((x, y), 1 * self.shrink / 2., S - 90, 360 - 90),
]
# patch[0].set_facecolor(cmap(d_abs))
# patch[1].set_facecolor('white')
colors.append(datum)
colors.append(0.5)
if self.edgecolor:
patch[0].set_edgecolor(self.edgecolor)
patch[1].set_edgecolor(self.edgecolor)
# ax.add_artist(patch[0])
# ax.add_artist(patch[1])
patches.append(patch[0])
patches.append(patch[1])
else:
raise ValueError(
'Method for the symbols is not known. Use e.g, square, circle')
if self.binarise_color:
colors = [1 if color > 0.5 else -1 for color in colors]
if len(patches):
col1 = PatchCollection(
patches, array=numpy.array(colors), cmap=self.cm)
ax.add_collection(col1)
self.collection = col1
