plot_nodes_phylo: Plot a phylogeny with colored node labels

In mkborregaard/nodiv: Compares the Distribution of Sister Clades Through a Phylogeny

Plot a phylogeny with colored node labels

Description

A wrapper for the plot.phylo function defined in package ape, which is useful for plotting the values at each node

Usage

plot_nodes_phylo(variable, tree, label = variable, main = deparse(substitute(variable)),
  zlim = NULL, col, show.legend = TRUE, sig.cutoff, nodes, 
  roundoff = TRUE, show.tip.label = NULL, cex = NULL, ...)

Arguments

variable	The variable to be plotted
label	The text to write in each node label
tree	The phylogeny to plot, in the ape phylo format
main	The title text
zlim	The values to use for the most extreme colors of the color scale
col	The color palette used to create the color scale
show.legend	Should a legend for the color scale be plotted?
sig.cutoff	The minimum value for nodes to be plotted on the tree, useful for trees with many nodes
nodes	The nodes to be plotted on the tree
roundoff	Whether to round values when writing them as nodelabel text
show.tip.label	Show tip labels on the tree
cex	Controls the size of the node symbols
...	Further arguments to pass to plot.phylo

Author(s)

Michael Krabbe Borregaard

Examples

data(coquettes)
Clade_occupancy <- Node_occupancy(coquettes)
plot_nodes_phylo(Clade_occupancy, coquettes$phylo, cex = 0.7)

mkborregaard/nodiv documentation built on April 7, 2023, 9:52 a.m.