plotTrees {dowser}

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
)

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.

Value

a grob containing a tree plotted by ggtree.

See Also

getTrees, findSwitches

Examples

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