R: Plot tree with tips linked to geographic coordinates

phylo.to.map {phytools}

R Documentation

Plot tree with tips linked to geographic coordinates

Function plots a tree and tips pointing to coordinates on a global map.

phylo.to.map(tree, coords, rotate=TRUE, ...)
## S3 method for class 'phylo.to.map'
plot(x, type=c("phylogram","direct"), ...)

`tree`	an object of class "phylo".
`coords`	a matrix containing the latitude (in column 1) and the longitude of all tip species in the tree. The row names should be the same as `tree$tip.label`.
`rotate`	a logical value indicating whether or not to rotate nodes of the tree to better match longitudinal positions.
`x`	for `plot.phylo.to.map`, an object of class `"phylo.to.map"`.
`type`	a string indicating whether to map the tips of the tree onto a geographic map from a square phylogram (`type="phylogram"`) or to project the tree directly onto the map (`type="direct"`).
`...`	optional arguments. For `phylo.to.map`, which creates an object of class `"phylo.to.map"` and (optionally) plots that object, optional arguments include: `database` and `regions` (see `map`); `xlim` and `ylim`, which control the plot area for the map; `fsize` for the font size of plot labels; `split` which controls the proportion of vertical space for the tree (first) and map, in a vector; `psize` the size of the plotted points on the map; `mar` and `asp` (see `par`. For `plot.phylo.to.map`, the options are the same - excluding `database` and `regions`.

Plots a phylogeny and map and returns an object of class "phylo.to.map" invisibly.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

[Package phytools version 0.4-60 Index]