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"""
Hierarchical clustering (:mod:`scipy.cluster.hierarchy`)
========================================================
.. currentmodule:: scipy.cluster.hierarchy
These functions cut hierarchical clusterings into flat clusterings
or find the roots of the forest formed by a cut by providing the flat
cluster ids of each observation.
.. autosummary::
:toctree: generated/
fcluster
fclusterdata
leaders
These are routines for agglomerative clustering.
.. autosummary::
:toctree: generated/
linkage
single
complete
average
weighted
centroid
median
ward
These routines compute statistics on hierarchies.
.. autosummary::
:toctree: generated/
cophenet
from_mlab_linkage
inconsistent
maxinconsts
maxdists
maxRstat
to_mlab_linkage
Routines for visualizing flat clusters.
.. autosummary::
:toctree: generated/
dendrogram
These are data structures and routines for representing hierarchies as
tree objects.
.. autosummary::
:toctree: generated/
ClusterNode
leaves_list
to_tree
cut_tree
optimal_leaf_ordering
These are predicates for checking the validity of linkage and
inconsistency matrices as well as for checking isomorphism of two
flat cluster assignments.
.. autosummary::
:toctree: generated/
is_valid_im
is_valid_linkage
is_isomorphic
is_monotonic
correspond
num_obs_linkage
Utility routines for plotting:
.. autosummary::
:toctree: generated/
set_link_color_palette
"""
from __future__ import division, print_function, absolute_import
# Copyright (C) Damian Eads, 2007-2008. New BSD License.
# hierarchy.py (derived from cluster.py, http://scipy-cluster.googlecode.com)
#
# Author: Damian Eads
# Date: September 22, 2007
#
# Copyright (c) 2007, 2008, Damian Eads
#
# 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 author 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
# OWNER 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.
import warnings
import bisect
from collections import deque
import numpy as np
from . import _hierarchy, _optimal_leaf_ordering
import scipy.spatial.distance as distance
from scipy._lib.six import string_types
from scipy._lib.six import xrange
_LINKAGE_METHODS = {'single': 0, 'complete': 1, 'average': 2, 'centroid': 3,
'median': 4, 'ward': 5, 'weighted': 6}
_EUCLIDEAN_METHODS = ('centroid', 'median', 'ward')
__all__ = ['ClusterNode', 'average', 'centroid', 'complete', 'cophenet',
'correspond', 'cut_tree', 'dendrogram', 'fcluster', 'fclusterdata',
'from_mlab_linkage', 'inconsistent', 'is_isomorphic',
'is_monotonic', 'is_valid_im', 'is_valid_linkage', 'leaders',
'leaves_list', 'linkage', 'maxRstat', 'maxdists', 'maxinconsts',
'median', 'num_obs_linkage', 'optimal_leaf_ordering',
'set_link_color_palette', 'single', 'to_mlab_linkage', 'to_tree',
'ward', 'weighted', 'distance']
class ClusterWarning(UserWarning):
pass
def _warning(s):
warnings.warn('scipy.cluster: %s' % s, ClusterWarning, stacklevel=3)
def _copy_array_if_base_present(a):
"""
Copy the array if its base points to a parent array.
"""
if a.base is not None:
return a.copy()
elif np.issubsctype(a, np.float32):
return np.array(a, dtype=np.double)
else:
return a
def _copy_arrays_if_base_present(T):
"""
Accept a tuple of arrays T. Copies the array T[i] if its base array
points to an actual array. Otherwise, the reference is just copied.
This is useful if the arrays are being passed to a C function that
does not do proper striding.
"""
l = [_copy_array_if_base_present(a) for a in T]
return l
def _randdm(pnts):
"""
Generate a random distance matrix stored in condensed form.
Parameters
----------
pnts : int
The number of points in the distance matrix. Has to be at least 2.
Returns
-------
D : ndarray
A ``pnts * (pnts - 1) / 2`` sized vector is returned.
"""
if pnts >= 2:
D = np.random.rand(pnts * (pnts - 1) / 2)
else:
raise ValueError("The number of points in the distance matrix "
"must be at least 2.")
return D
def single(y):
"""
Perform single/min/nearest linkage on the condensed distance matrix ``y``.
Parameters
----------
y : ndarray
The upper triangular of the distance matrix. The result of
``pdist`` is returned in this form.
Returns
-------
Z : ndarray
The linkage matrix.
See Also
--------
linkage: for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import single, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = single(y)
>>> Z
array([[ 0., 1., 1., 2.],
[ 2., 12., 1., 3.],
[ 3., 4., 1., 2.],
[ 5., 14., 1., 3.],
[ 6., 7., 1., 2.],
[ 8., 16., 1., 3.],
[ 9., 10., 1., 2.],
[11., 18., 1., 3.],
[13., 15., 2., 6.],
[17., 20., 2., 9.],
[19., 21., 2., 12.]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 7, 8, 9, 10, 11, 12, 4, 5, 6, 1, 2, 3], dtype=int32)
>>> fcluster(Z, 1, criterion='distance')
array([3, 3, 3, 4, 4, 4, 2, 2, 2, 1, 1, 1], dtype=int32)
>>> fcluster(Z, 2, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='single', metric='euclidean')
def complete(y):
"""
Perform complete/max/farthest point linkage on a condensed distance matrix.
Parameters
----------
y : ndarray
The upper triangular of the distance matrix. The result of
``pdist`` is returned in this form.
Returns
-------
Z : ndarray
A linkage matrix containing the hierarchical clustering. See
the `linkage` function documentation for more information
on its structure.
See Also
--------
linkage: for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import complete, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = complete(y)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.41421356, 3. ],
[ 5. , 13. , 1.41421356, 3. ],
[ 8. , 14. , 1.41421356, 3. ],
[11. , 15. , 1.41421356, 3. ],
[16. , 17. , 4.12310563, 6. ],
[18. , 19. , 4.12310563, 6. ],
[20. , 21. , 5.65685425, 12. ]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], dtype=int32)
>>> fcluster(Z, 1.5, criterion='distance')
array([1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4], dtype=int32)
>>> fcluster(Z, 4.5, criterion='distance')
array([1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2], dtype=int32)
>>> fcluster(Z, 6, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='complete', metric='euclidean')
def average(y):
"""
Perform average/UPGMA linkage on a condensed distance matrix.
Parameters
----------
y : ndarray
The upper triangular of the distance matrix. The result of
``pdist`` is returned in this form.
Returns
-------
Z : ndarray
A linkage matrix containing the hierarchical clustering. See
`linkage` for more information on its structure.
See Also
--------
linkage: for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import average, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = average(y)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.20710678, 3. ],
[ 5. , 13. , 1.20710678, 3. ],
[ 8. , 14. , 1.20710678, 3. ],
[11. , 15. , 1.20710678, 3. ],
[16. , 17. , 3.39675184, 6. ],
[18. , 19. , 3.39675184, 6. ],
[20. , 21. , 4.09206523, 12. ]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], dtype=int32)
>>> fcluster(Z, 1.5, criterion='distance')
array([1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4], dtype=int32)
>>> fcluster(Z, 4, criterion='distance')
array([1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2], dtype=int32)
>>> fcluster(Z, 6, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='average', metric='euclidean')
def weighted(y):
"""
Perform weighted/WPGMA linkage on the condensed distance matrix.
See `linkage` for more information on the return
structure and algorithm.
Parameters
----------
y : ndarray
The upper triangular of the distance matrix. The result of
``pdist`` is returned in this form.
Returns
-------
Z : ndarray
A linkage matrix containing the hierarchical clustering. See
`linkage` for more information on its structure.
See Also
--------
linkage : for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import weighted, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = weighted(y)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 9. , 11. , 1. , 2. ],
[ 2. , 12. , 1.20710678, 3. ],
[ 8. , 13. , 1.20710678, 3. ],
[ 5. , 14. , 1.20710678, 3. ],
[10. , 15. , 1.20710678, 3. ],
[18. , 19. , 3.05595762, 6. ],
[16. , 17. , 3.32379407, 6. ],
[20. , 21. , 4.06357713, 12. ]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 7, 8, 9, 1, 2, 3, 10, 11, 12, 4, 6, 5], dtype=int32)
>>> fcluster(Z, 1.5, criterion='distance')
array([3, 3, 3, 1, 1, 1, 4, 4, 4, 2, 2, 2], dtype=int32)
>>> fcluster(Z, 4, criterion='distance')
array([2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1], dtype=int32)
>>> fcluster(Z, 6, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='weighted', metric='euclidean')
def centroid(y):
"""
Perform centroid/UPGMC linkage.
See `linkage` for more information on the input matrix,
return structure, and algorithm.
The following are common calling conventions:
1. ``Z = centroid(y)``
Performs centroid/UPGMC linkage on the condensed distance
matrix ``y``.
2. ``Z = centroid(X)``
Performs centroid/UPGMC linkage on the observation matrix ``X``
using Euclidean distance as the distance metric.
Parameters
----------
y : ndarray
A condensed distance matrix. A condensed
distance matrix is a flat array containing the upper
triangular of the distance matrix. This is the form that
``pdist`` returns. Alternatively, a collection of
m observation vectors in n dimensions may be passed as
a m by n array.
Returns
-------
Z : ndarray
A linkage matrix containing the hierarchical clustering. See
the `linkage` function documentation for more information
on its structure.
See Also
--------
linkage: for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import centroid, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = centroid(y)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 2. , 12. , 1.11803399, 3. ],
[ 5. , 13. , 1.11803399, 3. ],
[ 8. , 15. , 1.11803399, 3. ],
[11. , 14. , 1.11803399, 3. ],
[18. , 19. , 3.33333333, 6. ],
[16. , 17. , 3.33333333, 6. ],
[20. , 21. , 3.33333333, 12. ]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 7, 8, 9, 10, 11, 12, 1, 2, 3, 4, 5, 6], dtype=int32)
>>> fcluster(Z, 1.1, criterion='distance')
array([5, 5, 6, 7, 7, 8, 1, 1, 2, 3, 3, 4], dtype=int32)
>>> fcluster(Z, 2, criterion='distance')
array([3, 3, 3, 4, 4, 4, 1, 1, 1, 2, 2, 2], dtype=int32)
>>> fcluster(Z, 4, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='centroid', metric='euclidean')
def median(y):
"""
Perform median/WPGMC linkage.
See `linkage` for more information on the return structure
and algorithm.
The following are common calling conventions:
1. ``Z = median(y)``
Performs median/WPGMC linkage on the condensed distance matrix
``y``. See ``linkage`` for more information on the return
structure and algorithm.
2. ``Z = median(X)``
Performs median/WPGMC linkage on the observation matrix ``X``
using Euclidean distance as the distance metric. See `linkage`
for more information on the return structure and algorithm.
Parameters
----------
y : ndarray
A condensed distance matrix. A condensed
distance matrix is a flat array containing the upper
triangular of the distance matrix. This is the form that
``pdist`` returns. Alternatively, a collection of
m observation vectors in n dimensions may be passed as
a m by n array.
Returns
-------
Z : ndarray
The hierarchical clustering encoded as a linkage matrix.
See Also
--------
linkage: for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import median, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = median(y)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 2. , 12. , 1.11803399, 3. ],
[ 5. , 13. , 1.11803399, 3. ],
[ 8. , 15. , 1.11803399, 3. ],
[11. , 14. , 1.11803399, 3. ],
[18. , 19. , 3. , 6. ],
[16. , 17. , 3.5 , 6. ],
[20. , 21. , 3.25 , 12. ]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 7, 8, 9, 10, 11, 12, 1, 2, 3, 4, 5, 6], dtype=int32)
>>> fcluster(Z, 1.1, criterion='distance')
array([5, 5, 6, 7, 7, 8, 1, 1, 2, 3, 3, 4], dtype=int32)
>>> fcluster(Z, 2, criterion='distance')
array([3, 3, 3, 4, 4, 4, 1, 1, 1, 2, 2, 2], dtype=int32)
>>> fcluster(Z, 4, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='median', metric='euclidean')
def ward(y):
"""
Perform Ward's linkage on a condensed distance matrix.
See `linkage` for more information on the return structure
and algorithm.
The following are common calling conventions:
1. ``Z = ward(y)``
Performs Ward's linkage on the condensed distance matrix ``y``.
2. ``Z = ward(X)``
Performs Ward's linkage on the observation matrix ``X`` using
Euclidean distance as the distance metric.
Parameters
----------
y : ndarray
A condensed distance matrix. A condensed
distance matrix is a flat array containing the upper
triangular of the distance matrix. This is the form that
``pdist`` returns. Alternatively, a collection of
m observation vectors in n dimensions may be passed as
a m by n array.
Returns
-------
Z : ndarray
The hierarchical clustering encoded as a linkage matrix. See
`linkage` for more information on the return structure and
algorithm.
See Also
--------
linkage: for advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdist : pairwise distance metrics
Examples
--------
>>> from scipy.cluster.hierarchy import ward, fcluster
>>> from scipy.spatial.distance import pdist
First we need a toy dataset to play with::
x x x x
x x
x x
x x x x
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
Then we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = ward(y)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[11. , 15. , 1.29099445, 3. ],
[16. , 17. , 5.77350269, 6. ],
[18. , 19. , 5.77350269, 6. ],
[20. , 21. , 8.16496581, 12. ]])
The linkage matrix ``Z`` represents a dendrogram - see
`scipy.cluster.hierarchy.linkage` for a detailed explanation of its
contents.
We can use `scipy.cluster.hierarchy.fcluster` to see to which cluster
each initial point would belong given a distance threshold:
>>> fcluster(Z, 0.9, criterion='distance')
array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], dtype=int32)
>>> fcluster(Z, 1.1, criterion='distance')
array([1, 1, 2, 3, 3, 4, 5, 5, 6, 7, 7, 8], dtype=int32)
>>> fcluster(Z, 3, criterion='distance')
array([1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4], dtype=int32)
>>> fcluster(Z, 9, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also `scipy.cluster.hierarchy.dendrogram` can be used to generate a
plot of the dendrogram.
"""
return linkage(y, method='ward', metric='euclidean')
def linkage(y, method='single', metric='euclidean', optimal_ordering=False):
"""
Perform hierarchical/agglomerative clustering.
The input y may be either a 1d condensed distance matrix
or a 2d array of observation vectors.
If y is a 1d condensed distance matrix,
then y must be a :math:`\\binom{n}{2}` sized
vector where n is the number of original observations paired
in the distance matrix. The behavior of this function is very
similar to the MATLAB linkage function.
A :math:`(n-1)` by 4 matrix ``Z`` is returned. At the
:math:`i`-th iteration, clusters with indices ``Z[i, 0]`` and
``Z[i, 1]`` are combined to form cluster :math:`n + i`. A
cluster with an index less than :math:`n` corresponds to one of
the :math:`n` original observations. The distance between
clusters ``Z[i, 0]`` and ``Z[i, 1]`` is given by ``Z[i, 2]``. The
fourth value ``Z[i, 3]`` represents the number of original
observations in the newly formed cluster.
The following linkage methods are used to compute the distance
:math:`d(s, t)` between two clusters :math:`s` and
:math:`t`. The algorithm begins with a forest of clusters that
have yet to be used in the hierarchy being formed. When two
clusters :math:`s` and :math:`t` from this forest are combined
into a single cluster :math:`u`, :math:`s` and :math:`t` are
removed from the forest, and :math:`u` is added to the
forest. When only one cluster remains in the forest, the algorithm
stops, and this cluster becomes the root.
A distance matrix is maintained at each iteration. The ``d[i,j]``
entry corresponds to the distance between cluster :math:`i` and
:math:`j` in the original forest.
At each iteration, the algorithm must update the distance matrix
to reflect the distance of the newly formed cluster u with the
remaining clusters in the forest.
Suppose there are :math:`|u|` original observations
:math:`u[0], \\ldots, u[|u|-1]` in cluster :math:`u` and
:math:`|v|` original objects :math:`v[0], \\ldots, v[|v|-1]` in
cluster :math:`v`. Recall :math:`s` and :math:`t` are
combined to form cluster :math:`u`. Let :math:`v` be any
remaining cluster in the forest that is not :math:`u`.
The following are methods for calculating the distance between the
newly formed cluster :math:`u` and each :math:`v`.
* method='single' assigns
.. math::
d(u,v) = \\min(dist(u[i],v[j]))
for all points :math:`i` in cluster :math:`u` and
:math:`j` in cluster :math:`v`. This is also known as the
Nearest Point Algorithm.
* method='complete' assigns
.. math::
d(u, v) = \\max(dist(u[i],v[j]))
for all points :math:`i` in cluster u and :math:`j` in
cluster :math:`v`. This is also known by the Farthest Point
Algorithm or Voor Hees Algorithm.
* method='average' assigns
.. math::
d(u,v) = \\sum_{ij} \\frac{d(u[i], v[j])}
{(|u|*|v|)}
for all points :math:`i` and :math:`j` where :math:`|u|`
and :math:`|v|` are the cardinalities of clusters :math:`u`
and :math:`v`, respectively. This is also called the UPGMA
algorithm.
* method='weighted' assigns
.. math::
d(u,v) = (dist(s,v) + dist(t,v))/2
where cluster u was formed with cluster s and t and v
is a remaining cluster in the forest. (also called WPGMA)
* method='centroid' assigns
.. math::
dist(s,t) = ||c_s-c_t||_2
where :math:`c_s` and :math:`c_t` are the centroids of
clusters :math:`s` and :math:`t`, respectively. When two
clusters :math:`s` and :math:`t` are combined into a new
cluster :math:`u`, the new centroid is computed over all the
original objects in clusters :math:`s` and :math:`t`. The
distance then becomes the Euclidean distance between the
centroid of :math:`u` and the centroid of a remaining cluster
:math:`v` in the forest. This is also known as the UPGMC
algorithm.
* method='median' assigns :math:`d(s,t)` like the ``centroid``
method. When two clusters :math:`s` and :math:`t` are combined
into a new cluster :math:`u`, the average of centroids s and t
give the new centroid :math:`u`. This is also known as the
WPGMC algorithm.
* method='ward' uses the Ward variance minimization algorithm.
The new entry :math:`d(u,v)` is computed as follows,
.. math::
d(u,v) = \\sqrt{\\frac{|v|+|s|}
{T}d(v,s)^2
+ \\frac{|v|+|t|}
{T}d(v,t)^2
- \\frac{|v|}
{T}d(s,t)^2}
where :math:`u` is the newly joined cluster consisting of
clusters :math:`s` and :math:`t`, :math:`v` is an unused
cluster in the forest, :math:`T=|v|+|s|+|t|`, and
:math:`|*|` is the cardinality of its argument. This is also
known as the incremental algorithm.
Warning: When the minimum distance pair in the forest is chosen, there
may be two or more pairs with the same minimum distance. This
implementation may choose a different minimum than the MATLAB
version.
Parameters
----------
y : ndarray
A condensed distance matrix. A condensed distance matrix
is a flat array containing the upper triangular of the distance matrix.
This is the form that ``pdist`` returns. Alternatively, a collection of
:math:`m` observation vectors in :math:`n` dimensions may be passed as
an :math:`m` by :math:`n` array. All elements of the condensed distance
matrix must be finite, i.e. no NaNs or infs.
method : str, optional
The linkage algorithm to use. See the ``Linkage Methods`` section below
for full descriptions.
metric : str or function, optional
The distance metric to use in the case that y is a collection of
observation vectors; ignored otherwise. See the ``pdist``
function for a list of valid distance metrics. A custom distance
function can also be used.
optimal_ordering : bool, optional
If True, the linkage matrix will be reordered so that the distance
between successive leaves is minimal. This results in a more intuitive
tree structure when the data are visualized. defaults to False, because
this algorithm can be slow, particularly on large datasets [2]_. See
also the `optimal_leaf_ordering` function.
.. versionadded:: 1.0.0
Returns
-------
Z : ndarray
The hierarchical clustering encoded as a linkage matrix.
Notes
-----
1. For method 'single' an optimized algorithm based on minimum spanning
tree is implemented. It has time complexity :math:`O(n^2)`.
For methods 'complete', 'average', 'weighted' and 'ward' an algorithm
called nearest-neighbors chain is implemented. It also has time
complexity :math:`O(n^2)`.
For other methods a naive algorithm is implemented with :math:`O(n^3)`
time complexity.
All algorithms use :math:`O(n^2)` memory.
Refer to [1]_ for details about the algorithms.
2. Methods 'centroid', 'median' and 'ward' are correctly defined only if
Euclidean pairwise metric is used. If `y` is passed as precomputed
pairwise distances, then it is a user responsibility to assure that
these distances are in fact Euclidean, otherwise the produced result
will be incorrect.
See Also
--------
scipy.spatial.distance.pdist : pairwise distance metrics
References
----------
.. [1] Daniel Mullner, "Modern hierarchical, agglomerative clustering
algorithms", :arXiv:`1109.2378v1`.
.. [2] Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola, "Fast optimal
leaf ordering for hierarchical clustering", 2001. Bioinformatics
:doi:`10.1093/bioinformatics/17.suppl_1.S22`
Examples
--------
>>> from scipy.cluster.hierarchy import dendrogram, linkage
>>> from matplotlib import pyplot as plt
>>> X = [[i] for i in [2, 8, 0, 4, 1, 9, 9, 0]]
>>> Z = linkage(X, 'ward')
>>> fig = plt.figure(figsize=(25, 10))
>>> dn = dendrogram(Z)
>>> Z = linkage(X, 'single')
>>> fig = plt.figure(figsize=(25, 10))
>>> dn = dendrogram(Z)
>>> plt.show()
"""
if method not in _LINKAGE_METHODS:
raise ValueError("Invalid method: {0}".format(method))
y = _convert_to_double(np.asarray(y, order='c'))
if y.ndim == 1:
distance.is_valid_y(y, throw=True, name='y')
[y] = _copy_arrays_if_base_present([y])
elif y.ndim == 2:
if method in _EUCLIDEAN_METHODS and metric != 'euclidean':
raise ValueError("Method '{0}' requires the distance metric "
"to be Euclidean".format(method))
if y.shape[0] == y.shape[1] and np.allclose(np.diag(y), 0):
if np.all(y >= 0) and np.allclose(y, y.T):
_warning('The symmetric non-negative hollow observation '
'matrix looks suspiciously like an uncondensed '
'distance matrix')
y = distance.pdist(y, metric)
else:
raise ValueError("`y` must be 1 or 2 dimensional.")
if not np.all(np.isfinite(y)):
raise ValueError("The condensed distance matrix must contain only "
"finite values.")
n = int(distance.num_obs_y(y))
method_code = _LINKAGE_METHODS[method]
if method == 'single':
result = _hierarchy.mst_single_linkage(y, n)
elif method in ['complete', 'average', 'weighted', 'ward']:
result = _hierarchy.nn_chain(y, n, method_code)
else:
result = _hierarchy.fast_linkage(y, n, method_code)
if optimal_ordering:
return optimal_leaf_ordering(result, y)
else:
return result
class ClusterNode(object):
"""
A tree node class for representing a cluster.
Leaf nodes correspond to original observations, while non-leaf nodes
correspond to non-singleton clusters.
The `to_tree` function converts a matrix returned by the linkage
function into an easy-to-use tree representation.
All parameter names are also attributes.
Parameters
----------
id : int
The node id.
left : ClusterNode instance, optional
The left child tree node.
right : ClusterNode instance, optional
The right child tree node.
dist : float, optional
Distance for this cluster in the linkage matrix.
count : int, optional
The number of samples in this cluster.
See Also
--------
to_tree : for converting a linkage matrix ``Z`` into a tree object.
"""
def __init__(self, id, left=None, right=None, dist=0, count=1):
if id < 0:
raise ValueError('The id must be non-negative.')
if dist < 0:
raise ValueError('The distance must be non-negative.')
if (left is None and right is not None) or \
(left is not None and right is None):
raise ValueError('Only full or proper binary trees are permitted.'
' This node has one child.')
if count < 1:
raise ValueError('A cluster must contain at least one original '
'observation.')
self.id = id
self.left = left
self.right = right
self.dist = dist
if self.left is None:
self.count = count
else:
self.count = left.count + right.count
def __lt__(self, node):
if not isinstance(node, ClusterNode):
raise ValueError("Can't compare ClusterNode "
"to type {}".format(type(node)))
return self.dist < node.dist
def __gt__(self, node):
if not isinstance(node, ClusterNode):
raise ValueError("Can't compare ClusterNode "
"to type {}".format(type(node)))
return self.dist > node.dist
def __eq__(self, node):
if not isinstance(node, ClusterNode):
raise ValueError("Can't compare ClusterNode "
"to type {}".format(type(node)))
return self.dist == node.dist
def get_id(self):
"""
The identifier of the target node.
For ``0 <= i < n``, `i` corresponds to original observation i.
For ``n <= i < 2n-1``, `i` corresponds to non-singleton cluster formed
at iteration ``i-n``.
Returns
-------
id : int
The identifier of the target node.
"""
return self.id
def get_count(self):
"""
The number of leaf nodes (original observations) belonging to
the cluster node nd. If the target node is a leaf, 1 is
returned.
Returns
-------
get_count : int
The number of leaf nodes below the target node.
"""
return self.count
def get_left(self):
"""
Return a reference to the left child tree object.
Returns
-------
left : ClusterNode
The left child of the target node. If the node is a leaf,
None is returned.
"""
return self.left
def get_right(self):
"""
Return a reference to the right child tree object.
Returns
-------
right : ClusterNode
The left child of the target node. If the node is a leaf,
None is returned.
"""
return self.right
def is_leaf(self):
"""
Return True if the target node is a leaf.
Returns
-------
leafness : bool
True if the target node is a leaf node.
"""
return self.left is None
def pre_order(self, func=(lambda x: x.id)):
"""
Perform pre-order traversal without recursive function calls.
When a leaf node is first encountered, ``func`` is called with
the leaf node as its argument, and its result is appended to
the list.
For example, the statement::
ids = root.pre_order(lambda x: x.id)
returns a list of the node ids corresponding to the leaf nodes
of the tree as they appear from left to right.
Parameters
----------
func : function
Applied to each leaf ClusterNode object in the pre-order traversal.
Given the ``i``-th leaf node in the pre-order traversal ``n[i]``,
the result of ``func(n[i])`` is stored in ``L[i]``. If not
provided, the index of the original observation to which the node
corresponds is used.
Returns
-------
L : list
The pre-order traversal.
"""
# Do a preorder traversal, caching the result. To avoid having to do
# recursion, we'll store the previous index we've visited in a vector.
n = self.count
curNode = [None] * (2 * n)
lvisited = set()
rvisited = set()
curNode[0] = self
k = 0
preorder = []
while k >= 0:
nd = curNode[k]
ndid = nd.id
if nd.is_leaf():
preorder.append(func(nd))
k = k - 1
else:
if ndid not in lvisited:
curNode[k + 1] = nd.left
lvisited.add(ndid)
k = k + 1
elif ndid not in rvisited:
curNode[k + 1] = nd.right
rvisited.add(ndid)
k = k + 1
# If we've visited the left and right of this non-leaf
# node already, go up in the tree.
else:
k = k - 1
return preorder
_cnode_bare = ClusterNode(0)
_cnode_type = type(ClusterNode)
def _order_cluster_tree(Z):
"""
Return clustering nodes in bottom-up order by distance.
Parameters
----------
Z : scipy.cluster.linkage array
The linkage matrix.
Returns
-------
nodes : list
A list of ClusterNode objects.
"""
q = deque()
tree = to_tree(Z)
q.append(tree)
nodes = []
while q:
node = q.popleft()
if not node.is_leaf():
bisect.insort_left(nodes, node)
q.append(node.get_right())
q.append(node.get_left())
return nodes
def cut_tree(Z, n_clusters=None, height=None):
"""
Given a linkage matrix Z, return the cut tree.
Parameters
----------
Z : scipy.cluster.linkage array
The linkage matrix.
n_clusters : array_like, optional
Number of clusters in the tree at the cut point.
height : array_like, optional
The height at which to cut the tree. Only possible for ultrametric
trees.
Returns
-------
cutree : array
An array indicating group membership at each agglomeration step. I.e.,
for a full cut tree, in the first column each data point is in its own
cluster. At the next step, two nodes are merged. Finally all
singleton and non-singleton clusters are in one group. If `n_clusters`
or `height` is given, the columns correspond to the columns of
`n_clusters` or `height`.
Examples
--------
>>> from scipy import cluster
>>> np.random.seed(23)
>>> X = np.random.randn(50, 4)
>>> Z = cluster.hierarchy.ward(X)
>>> cutree = cluster.hierarchy.cut_tree(Z, n_clusters=[5, 10])
>>> cutree[:10]
array([[0, 0],
[1, 1],
[2, 2],
[3, 3],
[3, 4],
[2, 2],
[0, 0],
[1, 5],
[3, 6],
[4, 7]])
"""
nobs = num_obs_linkage(Z)
nodes = _order_cluster_tree(Z)
if height is not None and n_clusters is not None:
raise ValueError("At least one of either height or n_clusters "
"must be None")
elif height is None and n_clusters is None: # return the full cut tree
cols_idx = np.arange(nobs)
elif height is not None:
heights = np.array([x.dist for x in nodes])
cols_idx = np.searchsorted(heights, height)
else:
cols_idx = nobs - np.searchsorted(np.arange(nobs), n_clusters)
try:
n_cols = len(cols_idx)
except TypeError: # scalar
n_cols = 1
cols_idx = np.array([cols_idx])
groups = np.zeros((n_cols, nobs), dtype=int)
last_group = np.arange(nobs)
if 0 in cols_idx:
groups[0] = last_group
for i, node in enumerate(nodes):
idx = node.pre_order()
this_group = last_group.copy()
this_group[idx] = last_group[idx].min()
this_group[this_group > last_group[idx].max()] -= 1
if i + 1 in cols_idx:
groups[np.nonzero(i + 1 == cols_idx)[0]] = this_group
last_group = this_group
return groups.T
def to_tree(Z, rd=False):
"""
Convert a linkage matrix into an easy-to-use tree object.
The reference to the root `ClusterNode` object is returned (by default).
Each `ClusterNode` object has a ``left``, ``right``, ``dist``, ``id``,
and ``count`` attribute. The left and right attributes point to
ClusterNode objects that were combined to generate the cluster.
If both are None then the `ClusterNode` object is a leaf node, its count
must be 1, and its distance is meaningless but set to 0.
*Note: This function is provided for the convenience of the library
user. ClusterNodes are not used as input to any of the functions in this
library.*
Parameters
----------
Z : ndarray
The linkage matrix in proper form (see the `linkage`
function documentation).
rd : bool, optional
When False (default), a reference to the root `ClusterNode` object is
returned. Otherwise, a tuple ``(r, d)`` is returned. ``r`` is a
reference to the root node while ``d`` is a list of `ClusterNode`
objects - one per original entry in the linkage matrix plus entries
for all clustering steps. If a cluster id is
less than the number of samples ``n`` in the data that the linkage
matrix describes, then it corresponds to a singleton cluster (leaf
node).
See `linkage` for more information on the assignment of cluster ids
to clusters.
Returns
-------
tree : ClusterNode or tuple (ClusterNode, list of ClusterNode)
If ``rd`` is False, a `ClusterNode`.
If ``rd`` is True, a list of length ``2*n - 1``, with ``n`` the number
of samples. See the description of `rd` above for more details.
See Also
--------
linkage, is_valid_linkage, ClusterNode
Examples
--------
>>> from scipy.cluster import hierarchy
>>> x = np.random.rand(10).reshape(5, 2)
>>> Z = hierarchy.linkage(x)
>>> hierarchy.to_tree(Z)
<scipy.cluster.hierarchy.ClusterNode object at ...
>>> rootnode, nodelist = hierarchy.to_tree(Z, rd=True)
>>> rootnode
<scipy.cluster.hierarchy.ClusterNode object at ...
>>> len(nodelist)
9
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
# Number of original objects is equal to the number of rows minus 1.
n = Z.shape[0] + 1
# Create a list full of None's to store the node objects
d = [None] * (n * 2 - 1)
# Create the nodes corresponding to the n original objects.
for i in xrange(0, n):
d[i] = ClusterNode(i)
nd = None
for i in xrange(0, n - 1):
fi = int(Z[i, 0])
fj = int(Z[i, 1])
if fi > i + n:
raise ValueError(('Corrupt matrix Z. Index to derivative cluster '
'is used before it is formed. See row %d, '
'column 0') % fi)
if fj > i + n:
raise ValueError(('Corrupt matrix Z. Index to derivative cluster '
'is used before it is formed. See row %d, '
'column 1') % fj)
nd = ClusterNode(i + n, d[fi], d[fj], Z[i, 2])
# ^ id ^ left ^ right ^ dist
if Z[i, 3] != nd.count:
raise ValueError(('Corrupt matrix Z. The count Z[%d,3] is '
'incorrect.') % i)
d[n + i] = nd
if rd:
return (nd, d)
else:
return nd
def optimal_leaf_ordering(Z, y, metric='euclidean'):
"""
Given a linkage matrix Z and distance, reorder the cut tree.
Parameters
----------
Z : ndarray
The hierarchical clustering encoded as a linkage matrix. See
`linkage` for more information on the return structure and
algorithm.
y : ndarray
The condensed distance matrix from which Z was generated.
Alternatively, a collection of m observation vectors in n
dimensions may be passed as a m by n array.
metric : str or function, optional
The distance metric to use in the case that y is a collection of
observation vectors; ignored otherwise. See the ``pdist``
function for a list of valid distance metrics. A custom distance
function can also be used.
Returns
-------
Z_ordered : ndarray
A copy of the linkage matrix Z, reordered to minimize the distance
between adjacent leaves.
Examples
--------
>>> from scipy.cluster import hierarchy
>>> np.random.seed(23)
>>> X = np.random.randn(10,10)
>>> Z = hierarchy.ward(X)
>>> hierarchy.leaves_list(Z)
array([0, 5, 3, 9, 6, 8, 1, 4, 2, 7], dtype=int32)
>>> hierarchy.leaves_list(hierarchy.optimal_leaf_ordering(Z, X))
array([3, 9, 0, 5, 8, 2, 7, 4, 1, 6], dtype=int32)
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
y = _convert_to_double(np.asarray(y, order='c'))
if y.ndim == 1:
distance.is_valid_y(y, throw=True, name='y')
[y] = _copy_arrays_if_base_present([y])
elif y.ndim == 2:
if y.shape[0] == y.shape[1] and np.allclose(np.diag(y), 0):
if np.all(y >= 0) and np.allclose(y, y.T):
_warning('The symmetric non-negative hollow observation '
'matrix looks suspiciously like an uncondensed '
'distance matrix')
y = distance.pdist(y, metric)
else:
raise ValueError("`y` must be 1 or 2 dimensional.")
if not np.all(np.isfinite(y)):
raise ValueError("The condensed distance matrix must contain only "
"finite values.")
return _optimal_leaf_ordering.optimal_leaf_ordering(Z, y)
def _convert_to_bool(X):
if X.dtype != bool:
X = X.astype(bool)
if not X.flags.contiguous:
X = X.copy()
return X
def _convert_to_double(X):
if X.dtype != np.double:
X = X.astype(np.double)
if not X.flags.contiguous:
X = X.copy()
return X
def cophenet(Z, Y=None):
"""
Calculate the cophenetic distances between each observation in
the hierarchical clustering defined by the linkage ``Z``.
Suppose ``p`` and ``q`` are original observations in
disjoint clusters ``s`` and ``t``, respectively and
``s`` and ``t`` are joined by a direct parent cluster
``u``. The cophenetic distance between observations
``i`` and ``j`` is simply the distance between
clusters ``s`` and ``t``.
Parameters
----------
Z : ndarray
The hierarchical clustering encoded as an array
(see `linkage` function).
Y : ndarray (optional)
Calculates the cophenetic correlation coefficient ``c`` of a
hierarchical clustering defined by the linkage matrix `Z`
of a set of :math:`n` observations in :math:`m`
dimensions. `Y` is the condensed distance matrix from which
`Z` was generated.
Returns
-------
c : ndarray
The cophentic correlation distance (if ``Y`` is passed).
d : ndarray
The cophenetic distance matrix in condensed form. The
:math:`ij` th entry is the cophenetic distance between
original observations :math:`i` and :math:`j`.
See Also
--------
linkage: for a description of what a linkage matrix is.
scipy.spatial.distance.squareform: transforming condensed matrices into square ones.
Examples
--------
>>> from scipy.cluster.hierarchy import single, cophenet
>>> from scipy.spatial.distance import pdist, squareform
Given a dataset ``X`` and a linkage matrix ``Z``, the cophenetic distance
between two points of ``X`` is the distance between the largest two
distinct clusters that each of the points:
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
``X`` corresponds to this dataset ::
x x x x
x x
x x
x x x x
>>> Z = single(pdist(X))
>>> Z
array([[ 0., 1., 1., 2.],
[ 2., 12., 1., 3.],
[ 3., 4., 1., 2.],
[ 5., 14., 1., 3.],
[ 6., 7., 1., 2.],
[ 8., 16., 1., 3.],
[ 9., 10., 1., 2.],
[11., 18., 1., 3.],
[13., 15., 2., 6.],
[17., 20., 2., 9.],
[19., 21., 2., 12.]])
>>> cophenet(Z)
array([1., 1., 2., 2., 2., 2., 2., 2., 2., 2., 2., 1., 2., 2., 2., 2., 2.,
2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 1., 1., 2., 2.,
2., 2., 2., 2., 1., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.,
1., 1., 2., 2., 2., 1., 2., 2., 2., 2., 2., 2., 1., 1., 1.])
The output of the `scipy.cluster.hierarchy.cophenet` method is
represented in condensed form. We can use
`scipy.spatial.distance.squareform` to see the output as a
regular matrix (where each element ``ij`` denotes the cophenetic distance
between each ``i``, ``j`` pair of points in ``X``):
>>> squareform(cophenet(Z))
array([[0., 1., 1., 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[1., 0., 1., 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[1., 1., 0., 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[2., 2., 2., 0., 1., 1., 2., 2., 2., 2., 2., 2.],
[2., 2., 2., 1., 0., 1., 2., 2., 2., 2., 2., 2.],
[2., 2., 2., 1., 1., 0., 2., 2., 2., 2., 2., 2.],
[2., 2., 2., 2., 2., 2., 0., 1., 1., 2., 2., 2.],
[2., 2., 2., 2., 2., 2., 1., 0., 1., 2., 2., 2.],
[2., 2., 2., 2., 2., 2., 1., 1., 0., 2., 2., 2.],
[2., 2., 2., 2., 2., 2., 2., 2., 2., 0., 1., 1.],
[2., 2., 2., 2., 2., 2., 2., 2., 2., 1., 0., 1.],
[2., 2., 2., 2., 2., 2., 2., 2., 2., 1., 1., 0.]])
In this example, the cophenetic distance between points on ``X`` that are
very close (i.e. in the same corner) is 1. For other pairs of points is 2,
because the points will be located in clusters at different
corners - thus the distance between these clusters will be larger.
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
Zs = Z.shape
n = Zs[0] + 1
zz = np.zeros((n * (n-1)) // 2, dtype=np.double)
# Since the C code does not support striding using strides.
# The dimensions are used instead.
Z = _convert_to_double(Z)
_hierarchy.cophenetic_distances(Z, zz, int(n))
if Y is None:
return zz
Y = np.asarray(Y, order='c')
distance.is_valid_y(Y, throw=True, name='Y')
z = zz.mean()
y = Y.mean()
Yy = Y - y
Zz = zz - z
numerator = (Yy * Zz)
denomA = Yy**2
denomB = Zz**2
c = numerator.sum() / np.sqrt((denomA.sum() * denomB.sum()))
return (c, zz)
def inconsistent(Z, d=2):
r"""
Calculate inconsistency statistics on a linkage matrix.
Parameters
----------
Z : ndarray
The :math:`(n-1)` by 4 matrix encoding the linkage (hierarchical
clustering). See `linkage` documentation for more information on its
form.
d : int, optional
The number of links up to `d` levels below each non-singleton cluster.
Returns
-------
R : ndarray
A :math:`(n-1)` by 4 matrix where the ``i``'th row contains the link
statistics for the non-singleton cluster ``i``. The link statistics are
computed over the link heights for links :math:`d` levels below the
cluster ``i``. ``R[i,0]`` and ``R[i,1]`` are the mean and standard
deviation of the link heights, respectively; ``R[i,2]`` is the number
of links included in the calculation; and ``R[i,3]`` is the
inconsistency coefficient,
.. math:: \frac{\mathtt{Z[i,2]} - \mathtt{R[i,0]}} {R[i,1]}
Notes
-----
This function behaves similarly to the MATLAB(TM) ``inconsistent``
function.
Examples
--------
>>> from scipy.cluster.hierarchy import inconsistent, linkage
>>> from matplotlib import pyplot as plt
>>> X = [[i] for i in [2, 8, 0, 4, 1, 9, 9, 0]]
>>> Z = linkage(X, 'ward')
>>> print(Z)
[[ 5. 6. 0. 2. ]
[ 2. 7. 0. 2. ]
[ 0. 4. 1. 2. ]
[ 1. 8. 1.15470054 3. ]
[ 9. 10. 2.12132034 4. ]
[ 3. 12. 4.11096096 5. ]
[11. 13. 14.07183949 8. ]]
>>> inconsistent(Z)
array([[ 0. , 0. , 1. , 0. ],
[ 0. , 0. , 1. , 0. ],
[ 1. , 0. , 1. , 0. ],
[ 0.57735027, 0.81649658, 2. , 0.70710678],
[ 1.04044011, 1.06123822, 3. , 1.01850858],
[ 3.11614065, 1.40688837, 2. , 0.70710678],
[ 6.44583366, 6.76770586, 3. , 1.12682288]])
"""
Z = np.asarray(Z, order='c')
Zs = Z.shape
is_valid_linkage(Z, throw=True, name='Z')
if (not d == np.floor(d)) or d < 0:
raise ValueError('The second argument d must be a nonnegative '
'integer value.')
# Since the C code does not support striding using strides.
# The dimensions are used instead.
[Z] = _copy_arrays_if_base_present([Z])
n = Zs[0] + 1
R = np.zeros((n - 1, 4), dtype=np.double)
_hierarchy.inconsistent(Z, R, int(n), int(d))
return R
def from_mlab_linkage(Z):
"""
Convert a linkage matrix generated by MATLAB(TM) to a new
linkage matrix compatible with this module.
The conversion does two things:
* the indices are converted from ``1..N`` to ``0..(N-1)`` form,
and
* a fourth column ``Z[:,3]`` is added where ``Z[i,3]`` represents the
number of original observations (leaves) in the non-singleton
cluster ``i``.
This function is useful when loading in linkages from legacy data
files generated by MATLAB.
Parameters
----------
Z : ndarray
A linkage matrix generated by MATLAB(TM).
Returns
-------
ZS : ndarray
A linkage matrix compatible with ``scipy.cluster.hierarchy``.
See Also
--------
linkage: for a description of what a linkage matrix is.
to_mlab_linkage: transform from SciPy to MATLAB format.
Examples
--------
>>> import numpy as np
>>> from scipy.cluster.hierarchy import ward, from_mlab_linkage
Given a linkage matrix in MATLAB format ``mZ``, we can use
`scipy.cluster.hierarchy.from_mlab_linkage` to import
it into SciPy format:
>>> mZ = np.array([[1, 2, 1], [4, 5, 1], [7, 8, 1],
... [10, 11, 1], [3, 13, 1.29099445],
... [6, 14, 1.29099445],
... [9, 15, 1.29099445],
... [12, 16, 1.29099445],
... [17, 18, 5.77350269],
... [19, 20, 5.77350269],
... [21, 22, 8.16496581]])
>>> Z = from_mlab_linkage(mZ)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[ 11. , 15. , 1.29099445, 3. ],
[ 16. , 17. , 5.77350269, 6. ],
[ 18. , 19. , 5.77350269, 6. ],
[ 20. , 21. , 8.16496581, 12. ]])
As expected, the linkage matrix ``Z`` returned includes an
additional column counting the number of original samples in
each cluster. Also, all cluster indexes are reduced by 1
(MATLAB format uses 1-indexing, whereas SciPy uses 0-indexing).
"""
Z = np.asarray(Z, dtype=np.double, order='c')
Zs = Z.shape
# If it's empty, return it.
if len(Zs) == 0 or (len(Zs) == 1 and Zs[0] == 0):
return Z.copy()
if len(Zs) != 2:
raise ValueError("The linkage array must be rectangular.")
# If it contains no rows, return it.
if Zs[0] == 0:
return Z.copy()
Zpart = Z.copy()
if Zpart[:, 0:2].min() != 1.0 and Zpart[:, 0:2].max() != 2 * Zs[0]:
raise ValueError('The format of the indices is not 1..N')
Zpart[:, 0:2] -= 1.0
CS = np.zeros((Zs[0],), dtype=np.double)
_hierarchy.calculate_cluster_sizes(Zpart, CS, int(Zs[0]) + 1)
return np.hstack([Zpart, CS.reshape(Zs[0], 1)])
def to_mlab_linkage(Z):
"""
Convert a linkage matrix to a MATLAB(TM) compatible one.
Converts a linkage matrix ``Z`` generated by the linkage function
of this module to a MATLAB(TM) compatible one. The return linkage
matrix has the last column removed and the cluster indices are
converted to ``1..N`` indexing.
Parameters
----------
Z : ndarray
A linkage matrix generated by ``scipy.cluster.hierarchy``.
Returns
-------
to_mlab_linkage : ndarray
A linkage matrix compatible with MATLAB(TM)'s hierarchical
clustering functions.
The return linkage matrix has the last column removed
and the cluster indices are converted to ``1..N`` indexing.
See Also
--------
linkage: for a description of what a linkage matrix is.
from_mlab_linkage: transform from Matlab to SciPy format.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, to_mlab_linkage
>>> from scipy.spatial.distance import pdist
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[11. , 15. , 1.29099445, 3. ],
[16. , 17. , 5.77350269, 6. ],
[18. , 19. , 5.77350269, 6. ],
[20. , 21. , 8.16496581, 12. ]])
After a linkage matrix ``Z`` has been created, we can use
`scipy.cluster.hierarchy.to_mlab_linkage` to convert it
into MATLAB format:
>>> mZ = to_mlab_linkage(Z)
>>> mZ
array([[ 1. , 2. , 1. ],
[ 4. , 5. , 1. ],
[ 7. , 8. , 1. ],
[ 10. , 11. , 1. ],
[ 3. , 13. , 1.29099445],
[ 6. , 14. , 1.29099445],
[ 9. , 15. , 1.29099445],
[ 12. , 16. , 1.29099445],
[ 17. , 18. , 5.77350269],
[ 19. , 20. , 5.77350269],
[ 21. , 22. , 8.16496581]])
The new linkage matrix ``mZ`` uses 1-indexing for all the
clusters (instead of 0-indexing). Also, the last column of
the original linkage matrix has been dropped.
"""
Z = np.asarray(Z, order='c', dtype=np.double)
Zs = Z.shape
if len(Zs) == 0 or (len(Zs) == 1 and Zs[0] == 0):
return Z.copy()
is_valid_linkage(Z, throw=True, name='Z')
ZP = Z[:, 0:3].copy()
ZP[:, 0:2] += 1.0
return ZP
def is_monotonic(Z):
"""
Return True if the linkage passed is monotonic.
The linkage is monotonic if for every cluster :math:`s` and :math:`t`
joined, the distance between them is no less than the distance
between any previously joined clusters.
Parameters
----------
Z : ndarray
The linkage matrix to check for monotonicity.
Returns
-------
b : bool
A boolean indicating whether the linkage is monotonic.
See Also
--------
linkage: for a description of what a linkage matrix is.
Examples
--------
>>> from scipy.cluster.hierarchy import median, ward, is_monotonic
>>> from scipy.spatial.distance import pdist
By definition, some hierarchical clustering algorithms - such as
`scipy.cluster.hierarchy.ward` - produce monotonic assignments of
samples to clusters; however, this is not always true for other
hierarchical methods - e.g. `scipy.cluster.hierarchy.median`.
Given a linkage matrix ``Z`` (as the result of a hierarchical clustering
method) we can test programmatically whether if is has the monotonicity
property or not, using `scipy.cluster.hierarchy.is_monotonic`:
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[11. , 15. , 1.29099445, 3. ],
[16. , 17. , 5.77350269, 6. ],
[18. , 19. , 5.77350269, 6. ],
[20. , 21. , 8.16496581, 12. ]])
>>> is_monotonic(Z)
True
>>> Z = median(pdist(X))
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 2. , 12. , 1.11803399, 3. ],
[ 5. , 13. , 1.11803399, 3. ],
[ 8. , 15. , 1.11803399, 3. ],
[11. , 14. , 1.11803399, 3. ],
[18. , 19. , 3. , 6. ],
[16. , 17. , 3.5 , 6. ],
[20. , 21. , 3.25 , 12. ]])
>>> is_monotonic(Z)
False
Note that this method is equivalent to just verifying that the distances
in the third column of the linkage matrix appear in a monotonically
increasing order.
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
# We expect the i'th value to be greater than its successor.
return (Z[1:, 2] >= Z[:-1, 2]).all()
def is_valid_im(R, warning=False, throw=False, name=None):
"""Return True if the inconsistency matrix passed is valid.
It must be a :math:`n` by 4 array of doubles. The standard
deviations ``R[:,1]`` must be nonnegative. The link counts
``R[:,2]`` must be positive and no greater than :math:`n-1`.
Parameters
----------
R : ndarray
The inconsistency matrix to check for validity.
warning : bool, optional
When True, issues a Python warning if the linkage
matrix passed is invalid.
throw : bool, optional
When True, throws a Python exception if the linkage
matrix passed is invalid.
name : str, optional
This string refers to the variable name of the invalid
linkage matrix.
Returns
-------
b : bool
True if the inconsistency matrix is valid.
See Also
--------
linkage: for a description of what a linkage matrix is.
inconsistent: for the creation of a inconsistency matrix.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, inconsistent, is_valid_im
>>> from scipy.spatial.distance import pdist
Given a data set ``X``, we can apply a clustering method to obtain a
linkage matrix ``Z``. `scipy.cluster.hierarchy.inconsistent` can
be also used to obtain the inconsistency matrix ``R`` associated to
this clustering process:
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
>>> R = inconsistent(Z)
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[11. , 15. , 1.29099445, 3. ],
[16. , 17. , 5.77350269, 6. ],
[18. , 19. , 5.77350269, 6. ],
[20. , 21. , 8.16496581, 12. ]])
>>> R
array([[1. , 0. , 1. , 0. ],
[1. , 0. , 1. , 0. ],
[1. , 0. , 1. , 0. ],
[1. , 0. , 1. , 0. ],
[1.14549722, 0.20576415, 2. , 0.70710678],
[1.14549722, 0.20576415, 2. , 0.70710678],
[1.14549722, 0.20576415, 2. , 0.70710678],
[1.14549722, 0.20576415, 2. , 0.70710678],
[2.78516386, 2.58797734, 3. , 1.15470054],
[2.78516386, 2.58797734, 3. , 1.15470054],
[6.57065706, 1.38071187, 3. , 1.15470054]])
Now we can use `scipy.cluster.hierarchy.is_valid_im` to verify that
``R`` is correct:
>>> is_valid_im(R)
True
However, if ``R`` is wrongly constructed (e.g one of the standard
deviations is set to a negative value) then the check will fail:
>>> R[-1,1] = R[-1,1] * -1
>>> is_valid_im(R)
False
"""
R = np.asarray(R, order='c')
valid = True
name_str = "%r " % name if name else ''
try:
if type(R) != np.ndarray:
raise TypeError('Variable %spassed as inconsistency matrix is not '
'a numpy array.' % name_str)
if R.dtype != np.double:
raise TypeError('Inconsistency matrix %smust contain doubles '
'(double).' % name_str)
if len(R.shape) != 2:
raise ValueError('Inconsistency matrix %smust have shape=2 (i.e. '
'be two-dimensional).' % name_str)
if R.shape[1] != 4:
raise ValueError('Inconsistency matrix %smust have 4 columns.' %
name_str)
if R.shape[0] < 1:
raise ValueError('Inconsistency matrix %smust have at least one '
'row.' % name_str)
if (R[:, 0] < 0).any():
raise ValueError('Inconsistency matrix %scontains negative link '
'height means.' % name_str)
if (R[:, 1] < 0).any():
raise ValueError('Inconsistency matrix %scontains negative link '
'height standard deviations.' % name_str)
if (R[:, 2] < 0).any():
raise ValueError('Inconsistency matrix %scontains negative link '
'counts.' % name_str)
except Exception as e:
if throw:
raise
if warning:
_warning(str(e))
valid = False
return valid
def is_valid_linkage(Z, warning=False, throw=False, name=None):
"""
Check the validity of a linkage matrix.
A linkage matrix is valid if it is a two dimensional array (type double)
with :math:`n` rows and 4 columns. The first two columns must contain
indices between 0 and :math:`2n-1`. For a given row ``i``, the following
two expressions have to hold:
.. math::
0 \\leq \\mathtt{Z[i,0]} \\leq i+n-1
0 \\leq Z[i,1] \\leq i+n-1
I.e. a cluster cannot join another cluster unless the cluster being joined
has been generated.
Parameters
----------
Z : array_like
Linkage matrix.
warning : bool, optional
When True, issues a Python warning if the linkage
matrix passed is invalid.
throw : bool, optional
When True, throws a Python exception if the linkage
matrix passed is invalid.
name : str, optional
This string refers to the variable name of the invalid
linkage matrix.
Returns
-------
b : bool
True if the inconsistency matrix is valid.
See Also
--------
linkage: for a description of what a linkage matrix is.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, is_valid_linkage
>>> from scipy.spatial.distance import pdist
All linkage matrices generated by the clustering methods in this module
will be valid (i.e. they will have the appropriate dimensions and the two
required expressions will hold for all the rows).
We can check this using `scipy.cluster.hierarchy.is_valid_linkage`:
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[11. , 15. , 1.29099445, 3. ],
[16. , 17. , 5.77350269, 6. ],
[18. , 19. , 5.77350269, 6. ],
[20. , 21. , 8.16496581, 12. ]])
>>> is_valid_linkage(Z)
True
However, is we create a linkage matrix in a wrong way - or if we modify
a valid one in a way that any of the required expressions don't hold
anymore, then the check will fail:
>>> Z[3][1] = 20 # the cluster number 20 is not defined at this point
>>> is_valid_linkage(Z)
False
"""
Z = np.asarray(Z, order='c')
valid = True
name_str = "%r " % name if name else ''
try:
if type(Z) != np.ndarray:
raise TypeError('Passed linkage argument %sis not a valid array.' %
name_str)
if Z.dtype != np.double:
raise TypeError('Linkage matrix %smust contain doubles.' % name_str)
if len(Z.shape) != 2:
raise ValueError('Linkage matrix %smust have shape=2 (i.e. be '
'two-dimensional).' % name_str)
if Z.shape[1] != 4:
raise ValueError('Linkage matrix %smust have 4 columns.' % name_str)
if Z.shape[0] == 0:
raise ValueError('Linkage must be computed on at least two '
'observations.')
n = Z.shape[0]
if n > 1:
if ((Z[:, 0] < 0).any() or (Z[:, 1] < 0).any()):
raise ValueError('Linkage %scontains negative indices.' %
name_str)
if (Z[:, 2] < 0).any():
raise ValueError('Linkage %scontains negative distances.' %
name_str)
if (Z[:, 3] < 0).any():
raise ValueError('Linkage %scontains negative counts.' %
name_str)
if _check_hierarchy_uses_cluster_before_formed(Z):
raise ValueError('Linkage %suses non-singleton cluster before '
'it is formed.' % name_str)
if _check_hierarchy_uses_cluster_more_than_once(Z):
raise ValueError('Linkage %suses the same cluster more than once.'
% name_str)
except Exception as e:
if throw:
raise
if warning:
_warning(str(e))
valid = False
return valid
def _check_hierarchy_uses_cluster_before_formed(Z):
n = Z.shape[0] + 1
for i in xrange(0, n - 1):
if Z[i, 0] >= n + i or Z[i, 1] >= n + i:
return True
return False
def _check_hierarchy_uses_cluster_more_than_once(Z):
n = Z.shape[0] + 1
chosen = set([])
for i in xrange(0, n - 1):
if (Z[i, 0] in chosen) or (Z[i, 1] in chosen) or Z[i, 0] == Z[i, 1]:
return True
chosen.add(Z[i, 0])
chosen.add(Z[i, 1])
return False
def _check_hierarchy_not_all_clusters_used(Z):
n = Z.shape[0] + 1
chosen = set([])
for i in xrange(0, n - 1):
chosen.add(int(Z[i, 0]))
chosen.add(int(Z[i, 1]))
must_chosen = set(range(0, 2 * n - 2))
return len(must_chosen.difference(chosen)) > 0
def num_obs_linkage(Z):
"""
Return the number of original observations of the linkage matrix passed.
Parameters
----------
Z : ndarray
The linkage matrix on which to perform the operation.
Returns
-------
n : int
The number of original observations in the linkage.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, num_obs_linkage
>>> from scipy.spatial.distance import pdist
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
``Z`` is a linkage matrix obtained after using the Ward clustering method
with ``X``, a dataset with 12 data points.
>>> num_obs_linkage(Z)
12
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
return (Z.shape[0] + 1)
def correspond(Z, Y):
"""
Check for correspondence between linkage and condensed distance matrices.
They must have the same number of original observations for
the check to succeed.
This function is useful as a sanity check in algorithms that make
extensive use of linkage and distance matrices that must
correspond to the same set of original observations.
Parameters
----------
Z : array_like
The linkage matrix to check for correspondence.
Y : array_like
The condensed distance matrix to check for correspondence.
Returns
-------
b : bool
A boolean indicating whether the linkage matrix and distance
matrix could possibly correspond to one another.
See Also
--------
linkage: for a description of what a linkage matrix is.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, correspond
>>> from scipy.spatial.distance import pdist
This method can be used to check if a given linkage matrix ``Z`` has been
obtained from the application of a cluster method over a dataset ``X``:
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> X_condensed = pdist(X)
>>> Z = ward(X_condensed)
Here we can compare ``Z`` and ``X`` (in condensed form):
>>> correspond(Z, X_condensed)
True
"""
is_valid_linkage(Z, throw=True)
distance.is_valid_y(Y, throw=True)
Z = np.asarray(Z, order='c')
Y = np.asarray(Y, order='c')
return distance.num_obs_y(Y) == num_obs_linkage(Z)
def fcluster(Z, t, criterion='inconsistent', depth=2, R=None, monocrit=None):
"""
Form flat clusters from the hierarchical clustering defined by
the given linkage matrix.
Parameters
----------
Z : ndarray
The hierarchical clustering encoded with the matrix returned
by the `linkage` function.
t : scalar
For criteria 'inconsistent', 'distance' or 'monocrit',
this is the threshold to apply when forming flat clusters.
For 'maxclust' or 'maxclust_monocrit' criteria,
this would be max number of clusters requested.
criterion : str, optional
The criterion to use in forming flat clusters. This can
be any of the following values:
``inconsistent`` :
If a cluster node and all its
descendants have an inconsistent value less than or equal
to `t` then all its leaf descendants belong to the
same flat cluster. When no non-singleton cluster meets
this criterion, every node is assigned to its own
cluster. (Default)
``distance`` :
Forms flat clusters so that the original
observations in each flat cluster have no greater a
cophenetic distance than `t`.
``maxclust`` :
Finds a minimum threshold ``r`` so that
the cophenetic distance between any two original
observations in the same flat cluster is no more than
``r`` and no more than `t` flat clusters are formed.
``monocrit`` :
Forms a flat cluster from a cluster node c
with index i when ``monocrit[j] <= t``.
For example, to threshold on the maximum mean distance
as computed in the inconsistency matrix R with a
threshold of 0.8 do::
MR = maxRstat(Z, R, 3)
cluster(Z, t=0.8, criterion='monocrit', monocrit=MR)
``maxclust_monocrit`` :
Forms a flat cluster from a
non-singleton cluster node ``c`` when ``monocrit[i] <=
r`` for all cluster indices ``i`` below and including
``c``. ``r`` is minimized such that no more than ``t``
flat clusters are formed. monocrit must be
monotonic. For example, to minimize the threshold t on
maximum inconsistency values so that no more than 3 flat
clusters are formed, do::
MI = maxinconsts(Z, R)
cluster(Z, t=3, criterion='maxclust_monocrit', monocrit=MI)
depth : int, optional
The maximum depth to perform the inconsistency calculation.
It has no meaning for the other criteria. Default is 2.
R : ndarray, optional
The inconsistency matrix to use for the 'inconsistent'
criterion. This matrix is computed if not provided.
monocrit : ndarray, optional
An array of length n-1. `monocrit[i]` is the
statistics upon which non-singleton i is thresholded. The
monocrit vector must be monotonic, i.e. given a node c with
index i, for all node indices j corresponding to nodes
below c, ``monocrit[i] >= monocrit[j]``.
Returns
-------
fcluster : ndarray
An array of length ``n``. ``T[i]`` is the flat cluster number to
which original observation ``i`` belongs.
See Also
--------
linkage : for information about hierarchical clustering methods work.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, fcluster
>>> from scipy.spatial.distance import pdist
All cluster linkage methods - e.g. `scipy.cluster.hierarchy.ward`
generate a linkage matrix ``Z`` as their output:
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
>>> Z
array([[ 0. , 1. , 1. , 2. ],
[ 3. , 4. , 1. , 2. ],
[ 6. , 7. , 1. , 2. ],
[ 9. , 10. , 1. , 2. ],
[ 2. , 12. , 1.29099445, 3. ],
[ 5. , 13. , 1.29099445, 3. ],
[ 8. , 14. , 1.29099445, 3. ],
[11. , 15. , 1.29099445, 3. ],
[16. , 17. , 5.77350269, 6. ],
[18. , 19. , 5.77350269, 6. ],
[20. , 21. , 8.16496581, 12. ]])
This matrix represents a dendrogram, where the first and second elements
are the two clusters merged at each step, the third element is the
distance between these clusters, and the fourth element is the size of
the new cluster - the number of original data points included.
`scipy.cluster.hierarchy.fcluster` can be used to flatten the
dendrogram, obtaining as a result an assignation of the original data
points to single clusters.
This assignation mostly depends on a distance threshold ``t`` - the maximum
inter-cluster distance allowed:
>>> fcluster(Z, t=0.9, criterion='distance')
array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], dtype=int32)
>>> fcluster(Z, t=1.1, criterion='distance')
array([1, 1, 2, 3, 3, 4, 5, 5, 6, 7, 7, 8], dtype=int32)
>>> fcluster(Z, t=3, criterion='distance')
array([1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4], dtype=int32)
>>> fcluster(Z, t=9, criterion='distance')
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
In the first case, the threshold ``t`` is too small to allow any two
samples in the data to form a cluster, so 12 different clusters are
returned.
In the second case, the threshold is large enough to allow the first
4 points to be merged with their nearest neighbors. So here only 8
clusters are returned.
The third case, with a much higher threshold, allows for up to 8 data
points to be connected - so 4 clusters are returned here.
Lastly, the threshold of the fourth case is large enough to allow for
all data points to be merged together - so a single cluster is returned.
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
n = Z.shape[0] + 1
T = np.zeros((n,), dtype='i')
# Since the C code does not support striding using strides.
# The dimensions are used instead.
[Z] = _copy_arrays_if_base_present([Z])
if criterion == 'inconsistent':
if R is None:
R = inconsistent(Z, depth)
else:
R = np.asarray(R, order='c')
is_valid_im(R, throw=True, name='R')
# Since the C code does not support striding using strides.
# The dimensions are used instead.
[R] = _copy_arrays_if_base_present([R])
_hierarchy.cluster_in(Z, R, T, float(t), int(n))
elif criterion == 'distance':
_hierarchy.cluster_dist(Z, T, float(t), int(n))
elif criterion == 'maxclust':
_hierarchy.cluster_maxclust_dist(Z, T, int(n), int(t))
elif criterion == 'monocrit':
[monocrit] = _copy_arrays_if_base_present([monocrit])
_hierarchy.cluster_monocrit(Z, monocrit, T, float(t), int(n))
elif criterion == 'maxclust_monocrit':
[monocrit] = _copy_arrays_if_base_present([monocrit])
_hierarchy.cluster_maxclust_monocrit(Z, monocrit, T, int(n), int(t))
else:
raise ValueError('Invalid cluster formation criterion: %s'
% str(criterion))
return T
def fclusterdata(X, t, criterion='inconsistent',
metric='euclidean', depth=2, method='single', R=None):
"""
Cluster observation data using a given metric.
Clusters the original observations in the n-by-m data
matrix X (n observations in m dimensions), using the euclidean
distance metric to calculate distances between original observations,
performs hierarchical clustering using the single linkage algorithm,
and forms flat clusters using the inconsistency method with `t` as the
cut-off threshold.
A one-dimensional array ``T`` of length ``n`` is returned. ``T[i]`` is
the index of the flat cluster to which the original observation ``i``
belongs.
Parameters
----------
X : (N, M) ndarray
N by M data matrix with N observations in M dimensions.
t : scalar
For criteria 'inconsistent', 'distance' or 'monocrit',
this is the threshold to apply when forming flat clusters.
For 'maxclust' or 'maxclust_monocrit' criteria,
this would be max number of clusters requested.
criterion : str, optional
Specifies the criterion for forming flat clusters. Valid
values are 'inconsistent' (default), 'distance', or 'maxclust'
cluster formation algorithms. See `fcluster` for descriptions.
metric : str, optional
The distance metric for calculating pairwise distances. See
``distance.pdist`` for descriptions and linkage to verify
compatibility with the linkage method.
depth : int, optional
The maximum depth for the inconsistency calculation. See
`inconsistent` for more information.
method : str, optional
The linkage method to use (single, complete, average,
weighted, median centroid, ward). See `linkage` for more
information. Default is "single".
R : ndarray, optional
The inconsistency matrix. It will be computed if necessary
if it is not passed.
Returns
-------
fclusterdata : ndarray
A vector of length n. T[i] is the flat cluster number to
which original observation i belongs.
See Also
--------
scipy.spatial.distance.pdist : pairwise distance metrics
Notes
-----
This function is similar to the MATLAB function ``clusterdata``.
Examples
--------
>>> from scipy.cluster.hierarchy import fclusterdata
This is a convenience method that abstracts all the steps to perform in a
typical SciPy's hierarchical clustering workflow.
* Transform the input data into a condensed matrix with `scipy.spatial.distance.pdist`.
* Apply a clustering method.
* Obtain flat clusters at a user defined distance threshold ``t`` using `scipy.cluster.hierarchy.fcluster`.
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> fclusterdata(X, t=1)
array([3, 3, 3, 4, 4, 4, 2, 2, 2, 1, 1, 1], dtype=int32)
The output here (for the dataset ``X``, distance threshold ``t``, and the
default settings) is four clusters with three data points each.
"""
X = np.asarray(X, order='c', dtype=np.double)
if type(X) != np.ndarray or len(X.shape) != 2:
raise TypeError('The observation matrix X must be an n by m numpy '
'array.')
Y = distance.pdist(X, metric=metric)
Z = linkage(Y, method=method)
if R is None:
R = inconsistent(Z, d=depth)
else:
R = np.asarray(R, order='c')
T = fcluster(Z, criterion=criterion, depth=depth, R=R, t=t)
return T
def leaves_list(Z):
"""
Return a list of leaf node ids.
The return corresponds to the observation vector index as it appears
in the tree from left to right. Z is a linkage matrix.
Parameters
----------
Z : ndarray
The hierarchical clustering encoded as a matrix. `Z` is
a linkage matrix. See `linkage` for more information.
Returns
-------
leaves_list : ndarray
The list of leaf node ids.
See Also
--------
dendrogram: for information about dendrogram structure.
Examples
--------
>>> from scipy.cluster.hierarchy import ward, dendrogram, leaves_list
>>> from scipy.spatial.distance import pdist
>>> from matplotlib import pyplot as plt
>>> X = [[0, 0], [0, 1], [1, 0],
... [0, 4], [0, 3], [1, 4],
... [4, 0], [3, 0], [4, 1],
... [4, 4], [3, 4], [4, 3]]
>>> Z = ward(pdist(X))
The linkage matrix ``Z`` represents a dendrogram, that is, a tree that
encodes the structure of the clustering performed.
`scipy.cluster.hierarchy.leaves_list` shows the mapping between
indexes in the ``X`` dataset and leaves in the dendrogram:
>>> leaves_list(Z)
array([ 2, 0, 1, 5, 3, 4, 8, 6, 7, 11, 9, 10], dtype=int32)
>>> fig = plt.figure(figsize=(25, 10))
>>> dn = dendrogram(Z)
>>> plt.show()
"""
Z = np.asarray(Z, order='c')
is_valid_linkage(Z, throw=True, name='Z')
n = Z.shape[0] + 1
ML = np.zeros((n,), dtype='i')
[Z] = _copy_arrays_if_base_present([Z])
_hierarchy.prelist(Z, ML, int(n))
return ML
# Maps number of leaves to text size.
#
# p <= 20, size="12"
# 20 < p <= 30, size="10"
# 30 < p <= 50, size="8"
# 50 < p <= np.inf, size="6"
_dtextsizes = {20: 12, 30: 10, 50: 8, 85: 6, np.inf: 5}
_drotation = {20: 0, 40: 45, np.inf: 90}
_dtextsortedkeys = list(_dtextsizes.keys())
_dtextsortedkeys.sort()
_drotationsortedkeys = list(_drotation.keys())
_drotationsortedkeys.sort()
def _remove_dups(L):
"""
Remove duplicates AND preserve the original order of the elements.
The set class is not guaranteed to do this.
"""
seen_before = set([])
L2 = []
for i in L:
if i not in seen_before:
seen_before.add(i)
L2.append(i)
return L2
def _get_tick_text_size(p):
for k in _dtextsortedkeys:
if p <= k:
return _dtextsizes[k]
def _get_tick_rotation(p):
for k in _drotationsortedkeys:
if p <= k:
return _drotation[k]
def _plot_dendrogram(icoords, dcoords, ivl, p, n, mh, orientation,
no_labels, color_list, leaf_font_size=None,
leaf_rotation=None, contraction_marks=None,
ax=None, above_threshold_color='b'):
# Import matplotlib here so that it's not imported unless dendrograms
# are plotted. Raise an informative error if importing fails.
try:
# if an axis is provided, don't use pylab at all
if ax is None:
import matplotlib.pylab
import matplotlib.patches
import matplotlib.collections
except ImportError:
raise ImportError("You must install the matplotlib library to plot "
"the dendrogram. Use no_plot=True to calculate the "
"dendrogram without plotting.")
if ax is None:
ax = matplotlib.pylab.gca()
# if we're using pylab, we want to trigger a draw at the end
trigger_redraw = True
else:
trigger_redraw = False
# Independent variable plot width
ivw = len(ivl) * 10
# Dependent variable plot height
dvw = mh + mh * 0.05
iv_ticks = np.arange(5, len(ivl) * 10 + 5, 10)
if orientation in ('top', 'bottom'):
if orientation == 'top':
ax.set_ylim([0, dvw])
ax.set_xlim([0, ivw])
else:
ax.set_ylim([dvw, 0])
ax.set_xlim([0, ivw])
xlines = icoords
ylines = dcoords
if no_labels:
ax.set_xticks([])
ax.set_xticklabels([])
else:
ax.set_xticks(iv_ticks)
if orientation == 'top':
ax.xaxis.set_ticks_position('bottom')
else:
ax.xaxis.set_ticks_position('top')
# Make the tick marks invisible because they cover up the links
for line in ax.get_xticklines():
line.set_visible(False)
leaf_rot = (float(_get_tick_rotation(len(ivl)))
if (leaf_rotation is None) else leaf_rotation)
leaf_font = (float(_get_tick_text_size(len(ivl)))
if (leaf_font_size is None) else leaf_font_size)
ax.set_xticklabels(ivl, rotation=leaf_rot, size=leaf_font)
elif orientation in ('left', 'right'):
if orientation == 'left':
ax.set_xlim([dvw, 0])
ax.set_ylim([0, ivw])
else:
ax.set_xlim([0, dvw])
ax.set_ylim([0, ivw])
xlines = dcoords
ylines = icoords
if no_labels:
ax.set_yticks([])
ax.set_yticklabels([])
else:
ax.set_yticks(iv_ticks)
if orientation == 'left':
ax.yaxis.set_ticks_position('right')
else:
ax.yaxis.set_ticks_position('left')
# Make the tick marks invisible because they cover up the links
for line in ax.get_yticklines():
line.set_visible(False)
leaf_font = (float(_get_tick_text_size(len(ivl)))
if (leaf_font_size is None) else leaf_font_size)
if leaf_rotation is not None:
ax.set_yticklabels(ivl, rotation=leaf_rotation, size=leaf_font)
else:
ax.set_yticklabels(ivl, size=leaf_font)
# Let's use collections instead. This way there is a separate legend item
# for each tree grouping, rather than stupidly one for each line segment.
colors_used = _remove_dups(color_list)
color_to_lines = {}
for color in colors_used:
color_to_lines[color] = []
for (xline, yline, color) in zip(xlines, ylines, color_list):
color_to_lines[color].append(list(zip(xline, yline)))
colors_to_collections = {}
# Construct the collections.
for color in colors_used:
coll = matplotlib.collections.LineCollection(color_to_lines[color],
colors=(color,))
colors_to_collections[color] = coll
# Add all the groupings below the color threshold.
for color in colors_used:
if color != above_threshold_color:
ax.add_collection(colors_to_collections[color])
# If there's a grouping of links above the color threshold, it goes last.
if above_threshold_color in colors_to_collections:
ax.add_collection(colors_to_collections[above_threshold_color])
if contraction_marks is not None:
Ellipse = matplotlib.patches.Ellipse
for (x, y) in contraction_marks:
if orientation in ('left', 'right'):
e = Ellipse((y, x), width=dvw / 100, height=1.0)
else:
e = Ellipse((x, y), width=1.0, height=dvw / 100)
ax.add_artist(e)
e.set_clip_box(ax.bbox)
e.set_alpha(0.5)
e.set_facecolor('k')
if trigger_redraw:
matplotlib.pylab.draw_if_interactive()
_link_line_colors = ['g', 'r', 'c', 'm', 'y', 'k']
def set_link_color_palette(palette):
"""
Set list of matplotlib color codes for use by dendrogram.
Note that this palette is global (i.e. setting it once changes the colors
for all subsequent calls to `dendrogram`) and that it affects only the
the colors below ``color_threshold``.
Note that `dendrogram` also accepts a custom coloring function through its
``link_color_func`` keyword, which is more flexible and non-global.
Parameters
----------
palette : list of str or None
A list of matplotlib color codes. The order of the color codes is the
order in which the colors are cycled through when color thresholding in
the dendrogram.
If ``None``, resets the palette to its default (which is
``['g', 'r', 'c', 'm', 'y', 'k']``).
Returns
-------
None
See Also
--------
dendrogram
Notes
-----
Ability to reset the palette with ``None`` added in SciPy 0.17.0.
Examples
--------
>>> from scipy.cluster import hierarchy
>>> ytdist = np.array([662., 877., 255., 412., 996., 295., 468., 268.,
... 400., 754., 564., 138., 219., 869., 669.])
>>> Z = hierarchy.linkage(ytdist, 'single')
>>> dn = hierarchy.dendrogram(Z, no_plot=True)
>>> dn['color_list']
['g', 'b', 'b', 'b', 'b']
>>> hierarchy.set_link_color_palette(['c', 'm', 'y', 'k'])
>>> dn = hierarchy.dendrogram(Z, no_plot=True)
>>> dn['color_list']
['c', 'b', 'b', 'b', 'b']
>>> dn = hierarchy.dendrogram(Z, no_plot=True, color_threshold=267,
... above_threshold_color='k')
>>> dn['color_list']
['c', 'm', 'm', 'k', 'k']
Now reset the color palette to its default:
>>> hierarchy.set_link_color_palette(None)
"""
if palette is None:
# reset to its default
palette = ['g', 'r', 'c', 'm', 'y', 'k']
elif type(palette) not in (list, tuple):
raise TypeError("palette must be a list or tuple")
_ptypes = [isinstance(p, string_types) for p in palette]
if False in _ptypes:
raise TypeError("all palette list elements must be color strings")
for i in list(_link_line_colors):
_link_line_colors.remove(i)
_link_line_colors.extend(list(palette))
def dendrogram(Z, p=30, truncate_mode=None, color_threshold=None,
get_leaves=True, orientation='top', labels=None,
count_sort=False, distance_sort=False, show_leaf_counts=True,
no_plot=False, no_labels=False, leaf_font_size=None,
leaf_rotation=None, leaf_label_func=None,
show_contracted=False, link_color_func=None, ax=None,
above_threshold_color='b'):
"""
Plot the hierarchical clustering as a dendrogram.
The dendrogram illustrates how each cluster is
composed by drawing a U-shaped link between a non-singleton
cluster and its children. The top of the U-link indicates a
cluster merge. The two legs of the U-link indicate which clusters
were merged. The length of the two legs of the U-link represents
the distance between the child clusters. It is also the
cophenetic distance between original observations in the two
children clusters.
Parameters
----------
Z : ndarray
The linkage matrix encoding the hierarchical clustering to
render as a dendrogram. See the ``linkage`` function for more
information on the format of ``Z``.
p : int, optional
The ``p`` parameter for ``truncate_mode``.
truncate_mode : str, optional
The dendrogram can be hard to read when the original
observation matrix from which the linkage is derived is
large. Truncation is used to condense the dendrogram. There
are several modes:
``None``
No truncation is performed (default).
Note: ``'none'`` is an alias for ``None`` that's kept for
backward compatibility.
``'lastp'``
The last ``p`` non-singleton clusters formed in the linkage are the
only non-leaf nodes in the linkage; they correspond to rows
``Z[n-p-2:end]`` in ``Z``. All other non-singleton clusters are
contracted into leaf nodes.
``'level'``
No more than ``p`` levels of the dendrogram tree are displayed.
A "level" includes all nodes with ``p`` merges from the last merge.
Note: ``'mtica'`` is an alias for ``'level'`` that's kept for
backward compatibility.
color_threshold : double, optional
For brevity, let :math:`t` be the ``color_threshold``.
Colors all the descendent links below a cluster node
:math:`k` the same color if :math:`k` is the first node below
the cut threshold :math:`t`. All links connecting nodes with
distances greater than or equal to the threshold are colored
blue. If :math:`t` is less than or equal to zero, all nodes
are colored blue. If ``color_threshold`` is None or
'default', corresponding with MATLAB(TM) behavior, the
threshold is set to ``0.7*max(Z[:,2])``.
get_leaves : bool, optional
Includes a list ``R['leaves']=H`` in the result
dictionary. For each :math:`i`, ``H[i] == j``, cluster node
``j`` appears in position ``i`` in the left-to-right traversal
of the leaves, where :math:`j < 2n-1` and :math:`i < n`.
orientation : str, optional
The direction to plot the dendrogram, which can be any
of the following strings:
``'top'``
Plots the root at the top, and plot descendent links going downwards.
(default).
``'bottom'``
Plots the root at the bottom, and plot descendent links going
upwards.
``'left'``
Plots the root at the left, and plot descendent links going right.
``'right'``
Plots the root at the right, and plot descendent links going left.
labels : ndarray, optional
By default ``labels`` is None so the index of the original observation
is used to label the leaf nodes. Otherwise, this is an :math:`n`
-sized list (or tuple). The ``labels[i]`` value is the text to put
under the :math:`i` th leaf node only if it corresponds to an original
observation and not a non-singleton cluster.
count_sort : str or bool, optional
For each node n, the order (visually, from left-to-right) n's
two descendent links are plotted is determined by this
parameter, which can be any of the following values:
``False``
Nothing is done.
``'ascending'`` or ``True``
The child with the minimum number of original objects in its cluster
is plotted first.
``'descending'``
The child with the maximum number of original objects in its cluster
is plotted first.
Note ``distance_sort`` and ``count_sort`` cannot both be True.
distance_sort : str or bool, optional
For each node n, the order (visually, from left-to-right) n's
two descendent links are plotted is determined by this
parameter, which can be any of the following values:
``False``
Nothing is done.
``'ascending'`` or ``True``
The child with the minimum distance between its direct descendents is
plotted first.
``'descending'``
The child with the maximum distance between its direct descendents is
plotted first.
Note ``distance_sort`` and ``count_sort`` cannot both be True.
show_leaf_counts : bool, optional
When True, leaf nodes representing :math:`k>1` original
observation are labeled with the number of observations they
contain in parentheses.
no_plot : bool, optional
When True, the final rendering is not performed. This is
useful if only the data structures computed for the rendering
are needed or if matplotlib is not available.
no_labels : bool, optional
When True, no labels appear next to the leaf nodes in the
rendering of the dendrogram.
leaf_rotation : double, optional
Specifies the angle (in degrees) to rotate the leaf
labels. When unspecified, the rotation is based on the number of
nodes in the dendrogram (default is 0).
leaf_font_size : int, optional
Specifies the font size (in points) of the leaf labels. When
unspecified, the size based on the number of nodes in the
dendrogram.
leaf_label_func : lambda or function, optional
When leaf_label_func is a callable function, for each
leaf with cluster index :math:`k < 2n-1`. The function
is expected to return a string with the label for the
leaf.
Indices :math:`k < n` correspond to original observations
while indices :math:`k \\geq n` correspond to non-singleton
clusters.
For example, to label singletons with their node id and
non-singletons with their id, count, and inconsistency
coefficient, simply do::
# First define the leaf label function.
def llf(id):
if id < n:
return str(id)
else:
return '[%d %d %1.2f]' % (id, count, R[n-id,3])
# The text for the leaf nodes is going to be big so force
# a rotation of 90 degrees.
dendrogram(Z, leaf_label_func=llf, leaf_rotation=90)
show_contracted : bool, optional
When True the heights of non-singleton nodes contracted
into a leaf node are plotted as crosses along the link
connecting that leaf node. This really is only useful when
truncation is used (see ``truncate_mode`` parameter).
link_color_func : callable, optional
If given, `link_color_function` is called with each non-singleton id
corresponding to each U-shaped link it will paint. The function is
expected to return the color to paint the link, encoded as a matplotlib
color string code. For example::
dendrogram(Z, link_color_func=lambda k: colors[k])
colors the direct links below each untruncated non-singleton node
``k`` using ``colors[k]``.
ax : matplotlib Axes instance, optional
If None and `no_plot` is not True, the dendrogram will be plotted
on the current axes. Otherwise if `no_plot` is not True the
dendrogram will be plotted on the given ``Axes`` instance. This can be
useful if the dendrogram is part of a more complex figure.
above_threshold_color : str, optional
This matplotlib color string sets the color of the links above the
color_threshold. The default is 'b'.
Returns
-------
R : dict
A dictionary of data structures computed to render the
dendrogram. Its has the following keys:
``'color_list'``
A list of color names. The k'th element represents the color of the
k'th link.
``'icoord'`` and ``'dcoord'``
Each of them is a list of lists. Let ``icoord = [I1, I2, ..., Ip]``
where ``Ik = [xk1, xk2, xk3, xk4]`` and ``dcoord = [D1, D2, ..., Dp]``
where ``Dk = [yk1, yk2, yk3, yk4]``, then the k'th link painted is
``(xk1, yk1)`` - ``(xk2, yk2)`` - ``(xk3, yk3)`` - ``(xk4, yk4)``.
``'ivl'``
A list of labels corresponding to the leaf nodes.
``'leaves'``
For each i, ``H[i] == j``, cluster node ``j`` appears in position
``i`` in the left-to-right traversal of the leaves, where
:math:`j < 2n-1` and :math:`i < n`. If ``j`` is less than ``n``, the
``i``-th leaf node corresponds to an original observation.
Otherwise, it corresponds to a non-singleton cluster.
See Also
--------
linkage, set_link_color_palette
Notes
-----
It is expected that the distances in ``Z[:,2]`` be monotonic, otherwise
crossings appear in the dendrogram.
Examples
--------
>>> from scipy.cluster import hierarchy
>>> import matplotlib.pyplot as plt
A very basic example:
>>> ytdist = np.array([662., 877., 255., 412., 996., 295., 468., 268.,
... 400., 754., 564., 138., 219., 869., 669.])
>>> Z = hierarchy.linkage(ytdist, 'single')
>>> plt.figure()
>>> dn = hierarchy.dendrogram(Z)
Now plot in given axes, improve the color scheme and use both vertical and
horizontal orientations:
>>> hierarchy.set_link_color_palette(['m', 'c', 'y', 'k'])
>>> fig, axes = plt.subplots(1, 2, figsize=(8, 3))
>>> dn1 = hierarchy.dendrogram(Z, ax=axes[0], above_threshold_color='y',
... orientation='top')
>>> dn2 = hierarchy.dendrogram(Z, ax=axes[1],
... above_threshold_color='#bcbddc',
... orientation='right')
>>> hierarchy.set_link_color_palette(None) # reset to default after use
>>> plt.show()
"""
# This feature was thought about but never implemented (still useful?):
#
# ... = dendrogram(..., leaves_order=None)
#
# Plots the leaves in the order specified by a vector of
# original observation indices. If the vector contains duplicates
# or results in a crossing, an exception will be thrown. Passing
# None orders leaf nodes based on the order they appear in the
# pre-order traversal.
Z = np.asarray(Z, order='c')
if orientation not in ["top", "left", "bottom", "right"]:
raise ValueError("orientation must be one of 'top', 'left', "
"'bottom', or 'right'")
is_valid_linkage(Z, throw=True, name='Z')
Zs = Z.shape
n = Zs[0] + 1
if type(p) in (int, float):
p = int(p)
else:
raise TypeError('The second argument must be a number')
if truncate_mode not in ('lastp', 'mlab', 'mtica', 'level', 'none', None):
# 'mlab' and 'mtica' are kept working for backwards compat.
raise ValueError('Invalid truncation mode.')
if truncate_mode == 'lastp' or truncate_mode == 'mlab':
if p > n or p == 0:
p = n
if truncate_mode == 'mtica':
# 'mtica' is an alias
truncate_mode = 'level'
if truncate_mode == 'level':
if p <= 0:
p = np.inf
if get_leaves:
lvs = []
else:
lvs = None
icoord_list = []
dcoord_list = []
color_list = []
current_color = [0]
currently_below_threshold = [False]
ivl = [] # list of leaves
if color_threshold is None or (isinstance(color_threshold, string_types) and
color_threshold == 'default'):
color_threshold = max(Z[:, 2]) * 0.7
R = {'icoord': icoord_list, 'dcoord': dcoord_list, 'ivl': ivl,
'leaves': lvs, 'color_list