plotTreeHighlightBranches: Plot the provided tree, (optionally) rerooted, with specified...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Plot the provided tree, (optionally) rerooted, with specified branches highlighted

Description

Plot the provided tree, (optionally) rerooted, with specified branches highlighted

Usage

plotTreeHighlightBranches(
  tree,
  outgroup = NULL,
  hlspecies,
  hlcols = NULL,
  main = "",
  useGG = FALSE
)

Arguments

useGG	option to creat plot with ggtree. Improves plot readability for most data sets.
tree.	A tree object.
outgroup.	A vector of species to use to root the tree. If not provided, the tree remains unrooted.
hlspecies.	A vector of species whose terminal branches to highlight, or a vector of branch numbers within the tree.
hlcols.	Colors to use in highlighting the branches. If not specified, will use default R colors.
main.	Main text for plot.

Value

A plot of the the (optionally rerooted) tree, with branches highlighted.

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.