Hierarchical clustering (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.
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Form flat clusters from the hierarchical clustering defined by the given linkage matrix. |
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Cluster observation data using a given metric. |
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Return the root nodes in a hierarchical clustering. |
These are routines for agglomerative clustering.
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Perform hierarchical/agglomerative clustering. |
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Perform single/min/nearest linkage on the condensed distance matrix |
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Perform complete/max/farthest point linkage on a condensed distance matrix. |
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Perform average/UPGMA linkage on a condensed distance matrix. |
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Perform weighted/WPGMA linkage on the condensed distance matrix. |
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Perform centroid/UPGMC linkage. |
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Perform median/WPGMC linkage. |
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Perform Ward's linkage on a condensed distance matrix. |
These routines compute statistics on hierarchies.
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Calculate the cophenetic distances between each observation in the hierarchical clustering defined by the linkage |
Convert a linkage matrix generated by MATLAB(TM) to a new linkage matrix compatible with this module. |
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Calculate inconsistency statistics on a linkage matrix. |
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Return the maximum inconsistency coefficient for each non-singleton cluster and its children. |
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Return the maximum distance between any non-singleton cluster. |
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Return the maximum statistic for each non-singleton cluster and its children. |
Convert a linkage matrix to a MATLAB(TM) compatible one. |
Routines for visualizing flat clusters.
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Plot the hierarchical clustering as a dendrogram. |
These are data structures and routines for representing hierarchies as tree objects.
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A tree node class for representing a cluster. |
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Return a list of leaf node ids. |
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Convert a linkage matrix into an easy-to-use tree object. |
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Given a linkage matrix Z, return the cut tree. |
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Given a linkage matrix Z and distance, reorder the cut tree. |
These are predicates for checking the validity of linkage and inconsistency matrices as well as for checking isomorphism of two flat cluster assignments.
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Return True if the inconsistency matrix passed is valid. |
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Check the validity of a linkage matrix. |
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Determine if two different cluster assignments are equivalent. |
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Return True if the linkage passed is monotonic. |
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Check for correspondence between linkage and condensed distance matrices. |
Return the number of original observations of the linkage matrix passed. |
Utility routines for plotting:
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Set list of matplotlib color codes for use by dendrogram. |
Utility classes:
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Disjoint set data structure for incremental connectivity queries. |