plot_sub_cluster {rhierbaps} | R Documentation |
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)
[Package rhierbaps version 1.1.4 Index]