Hierarchical clustering of TCRs by TCRdist

Convenience wrapper that computes the pairwise TCRdist matrix and performs hierarchical clustering via stats::hclust().

Usage

tcrdist_hclust(
  tcr_df = NULL,
  organism = NULL,
  method = "average",
  max_tcrs = 2000L,
  dist_matrix = NULL
)

Arguments

tcr_df

Data.frame with TCR columns (optional if dist_matrix is provided).

organism

Character string ("human" or "mouse") (optional if dist_matrix is provided).

method

Clustering method for stats::hclust(). Default "average" (UPGMA).

max_tcrs

Integer. Subsample if N exceeds this. Default 2000L.

dist_matrix

Optional precomputed distance matrix. If provided, tcr_df and organism are not used for distance computation.

Value

A named list:

hclust

An hclust object.

dist_matrix

The pairwise distance matrix used.

indices

Integer vector of row indices used (after potential subsampling).

See also

cluster_tcrs, neighborhood_test, plot_tcrdist_dendrogram

Examples

if (FALSE) { # \dontrun{
result <- tcrdist_hclust(tcr_df, "human")
plot(result$hclust)
clusters <- cutree(result$hclust, k = 5)
} # }