Plot the per-isolate genetic distance needed to cluster each isolate, by cluster — plot_genetic_distance_by

For every non-singleton cluster, plots the genetic distance an SNV-threshold clustering would need to place each isolate in the cluster (clusters on x, distance on y, one jittered point per isolate). Single linkage uses each isolate's nearest cluster-mate; "complete" uses the farthest. A boxplot summarizes each cluster.

Usage

plot_genetic_distance_by_cluster(
  clusters,
  snp_dist,
  linkage = c("single", "complete")
)

Arguments

clusters: Vector named by sequence IDs giving each sequence's cluster; singletons dropped.
snp_dist: Matrix of SNP distances between isolates.
linkage: Linkage rule, "single" or "complete".

Value

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