plotTrees: 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,
  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
)

Value

a grob containing a tree plotted by ggtree.

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)
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: strecth 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

Details

Function uses ggtree functions to plot tree topologlies 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.

Examples

Run this code

data(ExampleClones)
trees <- getTrees(ExampleClones[10,])
plotTrees(trees)[[1]]