fibre.plot
(fibrously) plots a phylogenyfibre.plot
(fibrously) plots a phylogeny
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)
a phylogeny (of class phylo) you wish to plot
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
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.
number of frames for animation; this will also determine the time internals for the plot
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
)
as colours
but for the focal
species
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 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
the delay between each slice's frame in the output GIF; default 0.2 seconds
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 of animation
height of animation
The data that were plotted last, the PCA and clade.matrix to speed later plots, and the colours used.
Probably best to just plot it out and see what happens, to be honest.
# NOT RUN {
fibre.plot(rlineage(0.1,0), "Yule_fibre.gif")
# }
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