pt_step5_render_and_collapse: Step 5: Render base tree and collapse clades

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Step 5: Render base tree and collapse clades

Description

Builds the ggplot tree, binds taxonomy data, collapses clades, handles circular layout rescaling, and colors collapse branches.

Usage

pt_step5_render_and_collapse(
  tree,
  group_vec,
  mrca_map,
  colors,
  layout,
  angle,
  line_width,
  branch_length_mode,
  triangle_mode,
  space_mode,
  low_memory,
  color_group_vec = NULL
)

Value

A named list with:

p	ggplot object
actual_ntips	displayed tip count after collapse (or NULL)

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.