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,
node_palette = "Dark2",
tip_palette = node_palette,
base = FALSE,
layout = "rectangular",
node_nums = FALSE,
tip_nums = FALSE,
title = TRUE,
labelsize = NULL,
common_scale = FALSE
)

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
node_palette
color palette for nodes
tip_palette
color palette for tips
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

Value

a grob containing a tree plotted by ggtree.

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

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

2

See also

getTrees, findSwitches