phytools (version 2.1-1)

add.arrow: Add an arrow pointing to a tip or node on the tree

Description

Adds an arrow or a set of arrows to a plotted tree.

Usage

add.arrow(tree=NULL, tip, ...)

Arguments

tree

an object of class "phylo", "contMap", or "densityMap". If not supplied, the function will obtain the last plotted phylogeny from the environmental variable last_plot.phylo.

tip

label of tip or tip or node number; or vector of such values. If tree=NULL then the tip label(s) or node number(s) must be supplied.

...

optional arguments to control the shape and size of the arrow including: its length (arrl) in the units of the plot; the length of the arrowhead (hedl); the total angle between the wings in the arrowhead (angle); the line width for the plotted lines (lwd); the offset from the tip or end of tip label, in character widths (offset); and the color (col).

Author

Liam Revell

Details

Trees can be plotted using phytools function plotTree, plotSimmap, contMap, densityMap, and ape S3 method plot.phylo.

References

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

See Also

nodelabels

Examples

## show arrows with a black outline
data(anoletree)
plotTree(anoletree,type="fan",fsize=0.7,ftype="i")
add.arrow(anoletree,tip=c("cuvieri","krugi",
    "pulchellus","poncensis","stratulus",
    "evermanni","cooki","cristatellus",
    "gundlachi","occultus"),lwd=5,arrl=1)
add.arrow(anoletree,tip="cuvieri",col="green",
    lwd=3,arrl=1)
add.arrow(anoletree,tip=c("krugi","pulchellus",
    "poncensis"),col="#E4D96F",lwd=3,arrl=1)
add.arrow(anoletree,tip=c("stratulus","evermanni"),
    col="darkgreen",lwd=3,arrl=1)
add.arrow(anoletree,tip=c("cooki","cristatellus",
    "gundlachi"),col="brown",lwd=3,arrl=1)
add.arrow(anoletree,tip="occultus",col="darkgrey",
    lwd=3,arrl=1)
legend(x="topleft",c("crown-giant","grass-bush","trunk-crown","trunk-ground",
    "twig"),pch=22,pt.bg=c("green","#E4D96F","darkgreen",
    "brown","darkgrey"),cex=0.9,
    pt.cex=2,title="PR ecomorphs",bty="n")
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margins to default