Hierarchical clustering on a symmetric distance matrix. — cluster_set

Wraps stats::hclust to produce a normalized output that mirrors the webtool's pure-JS clusterSetOrder and Python cluster_set_order.

Usage

cluster_set_order(D, linkage = c("average", "complete", "single"))

Arguments

D: Symmetric numeric distance matrix (NxN, zero diagonal).
linkage: One of "average" (UPGMA), "complete", "single".

Value

A list with:

leaf_order: 1-based integer vector — left-to-right ordering of original indices. At each internal node the subtree whose minimum original leaf index is smaller is placed on the left (deterministic; mirrors the webtool / Python convention).
merges: data.frame with columns left, right (0-based cluster ids matching the webtool/Python convention; leaves are 0..N-1, internal nodes are N..2N-2), height (linkage distance), size (number of leaves in the merged cluster).

Examples

D <- matrix(c(0, 0.2, 0.9, 0.2, 0, 0.85, 0.9, 0.85, 0), nrow = 3)
cluster_set_order(D, linkage = "average")
#> $leaf_order
#> [1] 1 2 3
#> 
#> $merges
#>   left right height size
#> 1    0     1  0.200    2
#> 2    2     3  0.875    3
#>