phylo.to.map | R Documentation |
Project a phylogeny on a geographic 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 |
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 |
rotate |
a logical value indicating whether or not to rotate nodes of the tree to better match longitudinal positions. |
x |
for |
type |
a string indicating whether to map the tips of the tree onto a geographic map from a square phylogram ( |
... |
various optional arguments. For the function |
phylo.to.map
creates an object of class "phylo.to.map"
and (optionally) plots that object.
plot.phylo.to.map
plots an object of class "phylo.to.map"
in which the tips of the tree point to coordinates on a geographic map.
phylo.to.map
creates an object of class "phylo.to.map"
and (if plot=TRUE
) plots a phylogeny projected onto a geographic map.
plot.phylo.to.map
plots on object of class "phylo.to.map"
.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2014) Graphical methods for visualizing comparative data on phylogenies. Chapter 4 in Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice (L. Z. Garamszegi ed.), pp. 77-103.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
## generally recommend using higher resolution map
## e.g., from mapdata package
data(tortoise.tree)
data(tortoise.geog)
tortoise.phymap<-phylo.to.map(tortoise.tree,
tortoise.geog,plot=FALSE,direction="rightwards",
regions="Ecuador")
plot(tortoise.phymap,direction="rightwards",pts=FALSE,
xlim=c(-92.25,-89.25),ylim=c(-1.8,0.75),ftype="i",
fsize=0.8,lty="dashed",map.bg="lightgreen",
colors="slategrey")
## reset margins
par(mar=c(5.1,4.1,4.1,2.1))
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