plotTrees

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,
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.

Value¶

a grob containing a tree plotted by ggtree.

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.

Examples¶

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

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