Cluster isolates using a hard SNP distance cutoff — get_tn_clusters_snp

Defines clusters with a hard SNP distance cutoff, via hierarchical clustering of the distance matrix cut at snp_thresh. This is the naive baseline to the threshold-free get_tn_clusters_sv_index(). The resulting clusters are then reconciled with a phylogenetic tree so that each is monophyletic.

Usage

get_tn_clusters_snp_thresh(
  snp_dist,
  snp_thresh,
  hclust_method = "single",
  tree = NULL,
  monophyly_method = c("break_down", "expand")
)

Arguments

snp_dist: A matrix of SNP distances between isolates. See get_snp_dist_matrix().
snp_thresh: SNP distance at which to cut the hierarchical clustering into clusters.
hclust_method: Linkage method for hierarchical clustering, passed to stats::hclust().
tree: An optional phylogenetic tree of class phylo over the same isolates (e.g. from get_phylo_tree()). When supplied, clusters are forced to be monophyletic with respect to it; otherwise monophyly is enforced on the dendrogram implied by the SNP distances.
monophyly_method: How a non-monophyletic cluster is reconciled with the tree. "expand" grows the cluster to the smallest clade containing all its members, absorbing any intervening isolates; "break_down" splits it into the largest monophyletic clades it already contains, pulling in no foreign isolates.

Value

A numeric vector giving the cluster each isolate belongs to.