plotnj: Plot an Unrooted Trees.

In snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

Plot an Unrooted Trees.

Description

This is a enhanced version of plot.phylo in ape which can plot trees in Class phylo including neighbor-joining trees, unrooted trees, trees with star shapes, ... etc.

Usage

plotnj(unrooted.tree, X.class = NULL, type = "u", main = NULL,
   show.tip.label = FALSE, show.node.label = FALSE,
   edge.width = 1, edge.width.class = edge.width, ...)

Arguments

unrooted.tree	an unrooted tree in Class phylo.
X.class	class ids indicated for all tips.
type	plot types, see plot.phylo in ape for details.
main	main label.
show.tip.label	show tip label if available.
show.node.label	show node label if available.
edge.width	edge width for all internal branches if X.class is set.
edge.width.class	edge width for tip branches if X.class is set.
...	other options passed to plot.phylo.

Details

This function is built to plot unrooted trees, but it may also apply for other trees in Class phylo.

type can be "u", "p", "c", "f", "r" as in plot.phylo.

If X.class is set, then the tip branches will be drawn with colors by class ids, and the colors are controlled by .color. The width of branches is controlled by edge.width for all internal branches and by edge.width.class for tip branches.

Value

Return a tree plot.

Author(s)

Wei-Chen Chen [e-mail]

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

plot.phylo, .Color.

Examples

## Not run: 
library(phyclust, quiet = TRUE)

set.seed(1234)
ret.ms <- ms(nsam = 24, opts = "-T -G 0.5")
tree.anc <- read.tree(text = ret.ms[3])

is.rooted(tree.anc)
tree.new <- as.star.tree(tree.anc)
X.class <- rep(1:6, each = 4)

par(mfrow = c(2, 2))
plotnj(tree.anc, X.class, type = "u", edge.width.class = 2,
       main = "unrooted tree")
plotnj(tree.new, X.class, type = "u", edge.width.class = 2,
       main = "star tree")
plotnj(tree.anc, X.class, type = "c", edge.width.class = 2,
       main = "unrooted tree in cladogram")
plotnj(tree.new, X.class, type = "r", edge.width.class = 2,
       main = "star tree in radial")

## End(Not run)

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.