# 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.

`fcluster`(Z, t[, criterion, depth, R, monocrit]) | Form flat clusters from the hierarchical clustering defined by the given linkage matrix.
`fclusterdata`(X, t[, criterion, metric, …]) | Cluster observation data using a given metric.
`leaders`(Z, T) | Return the root nodes in a hierarchical clustering.

These are routines for agglomerative clustering.

`linkage`(y[, method, metric, optimal_ordering]) | Perform hierarchical/agglomerative clustering.
`single`(y) | Perform single/min/nearest linkage on the condensed distance matrix `y`.
`complete`(y) | Perform complete/max/farthest point linkage on a condensed distance matrix.
`average`(y) | Perform average/UPGMA linkage on a condensed distance matrix.
`weighted`(y) | Perform weighted/WPGMA linkage on the condensed distance matrix.
`centroid`(y) | Perform centroid/UPGMC linkage.
`median`(y) | Perform median/WPGMC linkage.
`ward`(y) | Perform Ward’s linkage on a condensed distance matrix.

These routines compute statistics on hierarchies.

`cophenet`(Z[, Y]) | Calculate the cophenetic distances between each observation in the hierarchical clustering defined by the linkage `Z`.
`from_mlab_linkage`(Z) | Convert a linkage matrix generated by MATLAB(TM) to a new linkage matrix compatible with this module.
`inconsistent`(Z[, d]) | Calculate inconsistency statistics on a linkage matrix.
`maxinconsts`(Z, R) | Return the maximum inconsistency coefficient for each non-singleton cluster and its children.
`maxdists`(Z) | Return the maximum distance between any non-singleton cluster.
`maxRstat`(Z, R, i) | Return the maximum statistic for each non-singleton cluster and its children.
`to_mlab_linkage`(Z) | Convert a linkage matrix to a MATLAB(TM) compatible one.

Routines for visualizing flat clusters.

`dendrogram`(Z[, p, truncate_mode, …]) | Plot the hierarchical clustering as a dendrogram.

These are data structures and routines for representing hierarchies as tree objects.

`ClusterNode`(id[, left, right, dist, count]) | A tree node class for representing a cluster.
`leaves_list`(Z) | Return a list of leaf node ids.
`to_tree`(Z[, rd]) | Convert a linkage matrix into an easy-to-use tree object.
`cut_tree`(Z[, n_clusters, height]) | Given a linkage matrix Z, return the cut tree.
`optimal_leaf_ordering`(Z, y[, metric]) | 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.

`is_valid_im`(R[, warning, throw, name]) | Return True if the inconsistency matrix passed is valid.
`is_valid_linkage`(Z[, warning, throw, name]) | Check the validity of a linkage matrix.
`is_isomorphic`(T1, T2) | Determine if two different cluster assignments are equivalent.
`is_monotonic`(Z) | Return True if the linkage passed is monotonic.
`correspond`(Z, Y) | Check for correspondence between linkage and condensed distance matrices.
`num_obs_linkage`(Z) | Return the number of original observations of the linkage matrix passed.

Utility routines for plotting:

`set_link_color_palette`(palette) | Set list of matplotlib color codes for use by dendrogram.

Utility classes:

`DisjointSet`([elements]) | Disjoint set data structure for incremental connectivity queries.

scipy.cluster.vq.kmeans2 scipy.cluster.hierarchy.fcluster