Plots backbone tree with triangles as clades
Function plots a backbone tree (stored as an object of class "backbonePhylo"
) with triangles as subtrees.
## S3 method for class 'backbonePhylo' plot(x, ...)
x |
an object of class |
... |
optional arguments. Includes |
Plots a tree.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
## 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 rm(tip.label,clade.label,N,depth) ## here's what trans looks like trans ## convert obj<-phylo.toBackbone(tree,trans) ## plot plot(obj)
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