fibre.plot: 'fibre.plot' (fibrously) plots a phylogeny

In pez: Phylogenetics for the Environmental Sciences

fibre.plot (fibrously) plots a phylogeny

Description

fibre.plot (fibrously) plots a phylogeny

Usage

fibre.plot(
  tree,
  gif,
  focal,
  frames = 60,
  colours = colorRampPalette(c("blue", "black", "red")),
  f.colours = colorRampPalette(c("darkgreen", "lightgreen")),
  pca = NULL,
  clade.mat = NULL,
  delay = 0.2,
  side.tree = TRUE,
  width = 600,
  height = 600
)

Arguments

tree	a phylogeny (of class phylo) you wish to plot
gif	name of GIF you would like to create. This should *not* including a folder name (this is due to the use of saveGIF); "plot.gif" would be fine, but "work/plot.gif" would not
focal	species numbers or clade numbers to plot differently (see examples). Note that specifying a clade will highlight the clade *before* it arises; this is by design. If not specified (the default) there will be no focal species; this is fine.
frames	number of frames for animation; this will also determine the time internals for the plot
colours	a function that will return a colour ramp for use in plotting of species on the fiber plot itself as well as the standard phylogeny to the right (e.g., rainbow)
f.colours	as colours but for the focal species
pca	PCA (of class prcomp) of phylogenetic dissimilarity matrix; NULL calculates one, I recommend you use the output from a previous run to speed things up
clade.mat	clade matrix (from clade.matrix$clade.matrix) of phylogeny; NULL calculates one, I recommend you use the output from a previous run to speed things up
delay	the delay between each slice's frame in the output GIF; default 0.2 seconds
side.tree	whether to plot a standard phylogeny to the right of the plot to aid with interpretation (default: TRUE). You almost certainly want this option
width	width of animation
height	height of animation

Details

Probably best to just plot it out and see what happens, to be honest.

Value

The data that were plotted last, the PCA and clade.matrix to speed later plots, and the colours used.

Note

I would be grateful if you could cite the article this code was released in when using this code. I maintain this code in the package "willeerd" on GitHub. I give an example of how to install this code from there below. Updates will be released through that, and I welcome code improvements!

Author(s)

Will Pearse

Examples

## Not run: 
fibre.plot(rlineage(0.1,0), "Yule_fibre.gif")

## End(Not run)

pez documentation built on Sept. 1, 2022, 1:09 a.m.