plot.phyloExtra: Extra Fuctions to Plot and Annotate Phylogenies

In ape: Analyses of Phylogenetics and Evolution

Extra Fuctions to Plot and Annotate Phylogenies

Description

These are extra functions to plot and annotate phylogenies, mostly calling basic graphical functions in ape.

Usage

plotBreakLongEdges(phy, n = 1, ...)
drawSupportOnEdges(value, ...)

Arguments

phy	an object of class "phylo".
n	the numner of long branches to be broken.
value	the values to be printed on the internal branches of the tree.
...	further arguments to be passed to plot.phylo or to edgelabels.

Details

drawSupportOnEdges assumes the tree is unrooted, so the vector value should have as many values than the number of internal branches (= number of nodes - 1). If there is one additional value, it is assumed that it relates to the root node and is dropped (see examples).

Value

NULL

Author(s)

Emmanuel Paradis

See Also

plot.phylo, edgelabels, boot.phylo, plotTreeTime

Examples

tr <- rtree(10)
tr$edge.length[c(1, 18)] <- 100
op <- par(mfcol = 1:2)
plot(tr); axisPhylo()
plotBreakLongEdges(tr, 2); axisPhylo()

## from ?boot.phylo:
f <- function(x) nj(dist.dna(x))
data(woodmouse)
tw <- f(woodmouse) # NJ tree with K80 distance
set.seed(1)
## bootstrap with 100 replications:
(bp <- boot.phylo(tw, woodmouse, f, quiet = TRUE))
## the first value relates to the root node and is always 100
## it is ignored below:
plot(tw, "u")
drawSupportOnEdges(bp)
## more readable but the tree is really unrooted:
plot(tw)
drawSupportOnEdges(bp)
par(op)

ape documentation built on May 29, 2024, 10:50 a.m.