roundPhylogram: Plot a round, sigmoidal, or spline phylogram or cladogram

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Plot a round, sigmoidal, or spline phylogram or cladogram

Description

Plots one or multiple round phylograms, a sigmoidal phylogram or cladogram, or a phylogram draw using cubic splines through the nodes.

Usage

roundPhylogram(tree, fsize=1.0, ftype="reg", lwd=2, mar=NULL, offset=NULL, 
   direction="rightwards", type="phylogram", xlim=NULL, ylim=NULL, ...)
sigmoidPhylogram(tree, ...)
splinePhylogram(tree, ...)

Arguments

tree	an object of class "phylo" or "multiPhylo" containing one or multiple phylogenies.
fsize	relative font size for tip labels.
ftype	font type - options are "reg", "i" (italics), "b" (bold), or "bi" (bold-italics).
lwd	line width for plotting.
mar	vector containing the margins for the plot to be passed to par. If not specified, the default margins are [0.1,0.1,0.1,0.1].
offset	offset for the tip labels.
direction	plotting direction. Only the option direction="rightwards" is presently supported.
type	plot type. Can be "phylogram" or "cladogram". If type="cladogram" then the branch lengths are not necessary (and, indeed, are not used).
xlim	x-limits for the plot.
ylim	y-limits for the plot.
...	optional arguments. In the case of roundPhylogram, these are mostly as in plotTree and plotSimmap.

Details

The underscore character "_" is automatically swapped for a space in tip labels, as in plotSimmap.

Value

Plots a tree.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

plotSimmap, plotTree

Examples

## load mammal.tree
data(mammal.tree)
## plot using roundPhylogram
roundPhylogram(compute.brlen(mammal.tree),
    fsize=0.8,ftype="i")
## load anoletree
data(anoletree)
## plot using sigmoidPhylogram
sigmoidPhylogram(anoletree,fsize=0.6,
    ftype="i",direction="upwards")
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margin to default

phytools documentation built on June 22, 2024, 10:39 a.m.