edges: Draw Additional Edges on a Plotted Tree

In ape: Analyses of Phylogenetics and Evolution

Draw Additional Edges on a Plotted Tree

Description

edges draws edges on a plotted tree. fancyarrows enhances arrows with triangle and harpoon heads; it can be called from edges.

Usage

edges(nodes0, nodes1, arrows = 0, type = "classical", ...)
fancyarrows(x0, y0, x1, y1, length = 0.25, angle = 30, code = 2,
            col = par("fg"), lty = par("lty"), lwd = par("lwd"),
            type = "triangle", ...)

Arguments

nodes0, nodes1	vectors of integers giving the tip and/or node numbers where to start and to end the edges (eventually recycled).
arrows	an integer between 0 and 3; 0: lines (the default); 1: an arrow head is drawn at nodes0; 2: at nodes1; 3: both.
type	if the previous argument is not 0, the type of arrow head: "classical" (just lines, the default), "triangle", "harpoon", or any unambiguous abbreviations of these. For fancyarrows only the last two are available.
x0, y0, x1, y1	the coordinates of the start and end points for fancyarrows (these are not recycled and so should be vectors of the same length).
length, angle, code, col, lty, lwd	default options similar to those of arrows.
...	further arguments passed to segments.

Details

The first function is helpful when drawing reticulations on a phylogeny, especially if computed from the edge matrix.

fancyarrows does not work with log-transformed scale(s).

Author(s)

Emmanuel Paradis

See Also

plot.phylo, nodelabels

Examples

set.seed(2)
tr <- rcoal(6)
plot(tr, "c")
edges(10, 9, col = "red", lty = 2)
edges(10:11, 8, col = c("blue", "green")) # recycling of 'nodes1'
edges(1, 2, lwd = 2, type = "h", arrows = 3, col = "green")
nodelabels()

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