phytools (version 2.1-1)

plot.backbonePhylo: Plots backbone tree with triangles as clades

Description

Plots a backbone tree (stored as an object of class "backbonePhylo") with triangles as subtrees.

Usage

# S3 method for backbonePhylo
plot(x, ...)

Value

Plots a tree.

Arguments

x

an object of class "backbonePhylo".

...

optional arguments. Includes vscale (to rescale the vertical dimension in plotting), fixed.height (logical value to fix the plotted height of subtree triangles), print.clade.size (logical), fixed.n1 (logical value indicating whether or not to use the fixed triangle height for subtrees containing only one taxon, or to plot as a leaf - defaults to FALSE), and col (a single value, or a vector with names, giving the clade colors), as well as xlim, ylim, and lwd (as well as perhaps other standard plotting arguments).

Author

Liam Revell

References

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

See Also

phylo.toBackbone

Examples

## first create our backbone tree with
## random subtree diversities
tree<-phytools:::lambdaTree(pbtree(n=10),lambda=0.5)
## create a translation table
## leaving a couple of single-taxon clades for fun
tip.label<-sample(tree$tip.label,8)
clade.label<-LETTERS[1:8]
N<-ceiling(runif(n=8,min=1,max=20))
## set crown node depth to 1/2 the maximum depth
depth<-sapply(tip.label,function(x,y) 
    0.5*y$edge.length[which(tree$edge[,2]==
    which(y$tip.label==x))],y=tree)
trans<-data.frame(tip.label,clade.label,N,depth)
rownames(trans)<-NULL
## here's what trans looks like
print(trans)
## convert
obj<-phylo.toBackbone(tree,trans)
## plot
plot(obj)
par(mar=c(5.1,4.1,4.1,2.1)) ## reset par