Perform clustering of isolates using a hard SNP distance cutoff.

This function uses a hard SNP distance cutoff to define clusters naïvely, without using the phylogenetic tree.

Usage

get_tn_clusters_snp_thresh(snp_dist, snp_thresh, hclust_method = "complete")

Arguments

snp_dist

A matrix of SNP distances between isolates constructed using a model of DNA evolution. See get_snp_dist_matrix() for a useful function to generate this.

snp_thresh

A threshold for defining clusters.

hclust_method

A string indicating the method to use for hierarchical clustering. See stats::hclust() for more details. Default is "complete".

Value

A numeric vector indicating the cluster that each isolate belongs to.