plot_nodes_phylo {nodiv}

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)