Source code for sequana.viz.linkage
# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.readthedocs.io
#
##############################################################################
"""Heatmap and dendograms"""
import warnings
import scipy.cluster.hierarchy as hierarchy
import scipy.spatial.distance as distance
__all__ = ["Linkage"]
[docs]
class Linkage(object):
"""Linkage used in other tools such as Heatmap"""
methods = ["single", "complete", "average", "weighted", "centroid", "median", "ward"]
metrics = [
"braycurtis",
"canberra",
"chebyshev",
"cityblock",
"correlation",
"cosine",
"dice",
"euclidean",
"hamming",
"jaccard",
"jensenshannon",
"kulsinski",
"mahalanobis",
"matching",
"minkowski",
"rogerstanimoto",
"russellrao",
"seuclidean",
"sokalmichener",
"sokalsneath",
"sqeuclidean",
"yule",
]
def __init__(self):
""".. rubric:: constructor
:param data: a dataframe or possibly a numpy matrix.
"""
pass
[docs]
def check_metric(self, value):
if value not in self.metrics:
raise ValueError(f"value {value} must be in {self.metrics}")
[docs]
def check_method(self, value):
# None is possible
# in R, in addition to single, complete, average, centroid,
# median and ward
# there are ward.D, wardD2 and mcquitty
# default is complete
if value not in self.methods:
raise ValueError(f"value {value} must be in {self.methods}")
[docs]
def linkage(self, df, method, metric):
self.check_metric(metric)
self.check_method(method)
d = distance.pdist(df)
D = distance.squareform(d)
# hierarchy.ClusterWarning
with warnings.catch_warnings():
warnings.filterwarnings("ignore")
Y = hierarchy.linkage(D, method=method, metric=metric)
return Y
