plotTrees: Plot a tree with colored internal node labels using ggtree

In dowser: B Cell Receptor Phylogenetics Toolkit

Plot a tree with colored internal node labels using ggtree

Description

plotTrees plots a tree or group of trees

Usage

plotTrees(
  trees,
  nodes = FALSE,
  tips = NULL,
  tipsize = NULL,
  scale = 0.01,
  palette = "Dark2",
  base = FALSE,
  show_occupancy = FALSE,
  layout = "rectangular",
  node_nums = FALSE,
  tip_nums = FALSE,
  title = TRUE,
  labelsize = NULL,
  common_scale = FALSE,
  ambig = "grey",
  bootstrap_scores = FALSE,
  tip_palette = NULL,
  node_palette = NULL,
  guide_title = NULL,
  branch_lengths = NULL,
  pch = 16,
  densitree = FALSE,
  alpha = 1
)

Arguments

trees	A tibble containing phylo and airrClone objects
nodes	color internal nodes if possible?
tips	color tips if possible?
tipsize	size of tip shape objects
scale	width of branch length scale bar
palette	color palette for tips and/or nodes. Can supply a named vector for all tip states, or a palette named passed to ggplot2::scale_color_brewer (e.g. "Dark2", "Paired", "Set1") or ggplot2::scale_color_distiller (e.g. RdYlBu) or
base	recursion base case (don't edit)
show_occupancy	if plotting trees from an expectedOccupancy model in TyCHE, will color branch lengths by expected occupancy in the first state if true. Requires palette to be specified as a named vector in order of: c(state1=color1, state2+state1=color2, state2=color3).
layout	rectangular or circular tree layout?
node_nums	plot internal node numbers?
tip_nums	plot tip numbers?
title	use clone id as title?
labelsize	text size
common_scale	stretch plots so branches are on same scale? determined by sequence with highest divergence
ambig	How to color ambiguous node reconstructions? (grey or blend)
bootstrap_scores	Show bootstrap scores for internal nodes? See getBootstraps.
tip_palette	deprecated, use palette
node_palette	deprecated, use palette
guide_title	Title of color guide. Defaults to tips variable if specified.
branch_lengths	Use branch lenghts? Use "none" if not.
pch	Numeric tip/node shape. If >20 will use "fill" instead of "color"
densitree	Use densitree visualization? Requires trees_with_traits/trees posterior to be loaded in (see posterior options in readBEAST).
alpha	Alpha value for ggtree. Lower makes the tree more transparent.

Details

Function uses ggtree functions to plot tree topologies estimated by getTrees, and findSwitches. Object can be further modified with ggtree functions. Please check out https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html and cite ggtree in addition to dowser if you use this function.

Value

a grob containing a tree plotted by ggtree.

See Also

getTrees, findSwitches

Examples

## Not run: 
data(ExampleClones)
trees <- getTrees(ExampleClones[10,])
plotTrees(trees)[[1]]

## End(Not run)

dowser documentation built on Aug. 20, 2026, 5:06 p.m.