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

fibre.plot {pez}

R Documentation

`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)

[Package pez version 1.2-4 Index]

fibre.plot (fibrously) plots a phylogeny