Plot max intra-cluster vs. min inter-cluster genetic distance

Plots each cluster's maximum within-cluster distance against the minimum distance to an isolate in another cluster. Points below y = x are clusters whose internal diversity exceeds their separation from the nearest other cluster.

Usage

plot_intra_vs_inter_cluster_distance(clusters, snp_dist)

Arguments

clusters

Vector named by sequence IDs giving each sequence's cluster; singletons dropped but their sequences still count as unclustered isolates.

snp_dist

Matrix of SNP distances between isolates; row and column names define the full isolate universe, including unclustered isolates.

Value

A ggplot object, suitable for saving with ggsave().