highlight_clades: Highlight monophyletic clades on a tree plot
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

highlight_clades

R Documentation

Highlight monophyletic clades on a tree plot

Description

Adds colored highlighting for specified taxonomic groups. Only monophyletic groups are highlighted; non-monophyletic groups trigger a warning. Supports special identifiers LUCA, LACA, LBCA for ancestral nodes.

Usage

highlight_clades(
  p,
  tree,
  groups,
  rank,
  format = "auto",
  colors = NULL,
  alpha = 0.2,
  custom_patterns = NULL,
  delimiter_mode = "reverse",
  taxonomy_levels = NULL
)

Arguments

`p`	A `ggplot` object (from `plot_timetree()`).
`tree`	A `phylo` object.
`groups`	Character vector of group names to highlight. Can include special identifiers: `"LUCA"`, `"LACA"`, `"LBCA"`.
`rank`	Character. Taxonomic rank of the groups (ignored for special identifiers).
`format`	Character. Taxonomy label format. Default: `"auto"`.
`colors`	Named character vector of colors for each group. If `NULL`, colors are auto-generated.
`alpha`	Numeric. Transparency of the highlight. Default: `0.2`.
`custom_patterns`	Named list of regex patterns for custom format.
`taxonomy_levels`	Custom taxonomy level configuration (list with codes and names). Default: `NULL`.