edges: 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.

Author

Emmanuel Paradis

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).

Examples

Run this code

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()