Description Usage Arguments Examples
View source: R/plot_sub_cluster.R
Creates a zoom plot using ggtree focusing on a cluster.
1 | plot_sub_cluster(hb.object, tree, level, sub.cluster)
|
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. |
1 2 3 4 5 | 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)
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