plot_tree: Plot phylogenetic tree panel

In phylepic: Combined Visualisation of Phylogenetic and Epidemiological Data

Plot phylogenetic tree panel

Description

The tree is drawn using ggraph with its dendrogram layout. When customising it, you may wish to add layers such as ggraph::geom_node_point(). The metadata table is joined onto the tree, so all its column names are available for use in the various ggraph geoms.

Usage

plot_tree(phylepic, label = .data$name, bootstrap = TRUE)

Arguments

phylepic	object of class "phylepic".
label	variable in metadata table corresponding to the tip labels (tidy-eval).
bootstrap	when TRUE, draw bootstrap vaues on the tree. These are only drawn if they are detected from the node labels having the form "a/b" where both "a" and "b" are numbers. Currently, the bootstrap values are displayed as a percentage, suppressing zero values and values for very short branches. To customise the appearance or details instead use bootstrap = FALSE and add your own layer with ggraph::geom_edge_elbow.

Value

If phylepic is specified returns a ggplot, otherwise a function that when passed a "phylepic" object produces a ggplot for use with plot.phylepic().

See Also

Other phylepic plots: plot.phylepic(), plot_bars(), plot_calendar(), plot_epicurve()

phylepic documentation built on June 22, 2024, 9:46 a.m.