plot_sub_cluster: plot_sub_cluster

In rhierbaps: Clustering Genetic Sequence Data Using the HierBAPS Algorithm

plot_sub_cluster

Description

Creates a zoom plot using ggtree focusing on a cluster.

Usage

plot_sub_cluster(hb.object, tree, level, sub.cluster)

Arguments

hb.object	The resulting object from running hierBAPS
tree	A phylo tree object to plot
level	The level of the subcluster to be considered.
sub.cluster	An integer representing the subcluster to be considered.

Examples

snp.matrix <- load_fasta(system.file("extdata", "seqs.fa", package = "rhierbaps"))
newick.file.name <- system.file("extdata", "seqs.fa.treefile", package = "rhierbaps")
tree <- phytools::read.newick(newick.file.name)
hb.result <- hierBAPS(snp.matrix, max.depth=2, n.pops=20)
plot_sub_cluster(hb.result, tree, level = 1, sub.cluster = 9)

rhierbaps documentation built on Nov. 18, 2022, 5:06 p.m.