plot_tree_pa: plot_tree_pa

In gtonkinhill/panstripe: Pangenome Plots

plot_tree_pa

Description

Plots a phylogeny alongside a presence/absence matrix of user selected genes.

Usage

plot_tree_pa(
  tree,
  pa,
  genes = colnames(pa),
  align = TRUE,
  order = TRUE,
  plot_titles = c("phylogeny", "gene presence/absence"),
  text_size = 14,
  label_genes = TRUE,
  label_tips = TRUE,
  cols = NULL
)

Arguments

tree	a phylogeny in 'phylo' format
pa	binary presence/absence matrix
genes	a vector of gene to include in the plot. Must be a subset of colnames(pa)
align	whether or not to align the tips of the phylogeny with the presence/absence matrix using dotted lines
order	whether to order the genes based upon their presence/absence pattern
plot_titles	the subplot titles (default=c('phylogeny', 'gene presence/absence'))
text_size	adjusts the size of text in the plot
label_genes	whether to print the gene labels in the presence/absence matrix
label_tips	whether to print the tree tip labels
cols	colours for the gene presence/absence matrix. These will be recycled if #genes > #colours.

Value

a patchwork object plotting the phylogeny alongside the gene presence/absence matrix

Examples

sim <- simulate_pan(rate=1e-3)
genes <- colnames(sim$pa)[which(apply(sim$pa, 2, sd)>0.2)]
plot_tree_pa(sim$tree, sim$pa, genes=genes, 
             label_genes=FALSE, label_tips=FALSE, cols='black')

gtonkinhill/panstripe documentation built on Feb. 27, 2025, 9:01 p.m.