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