Plotting continuous traits on the tree using varied dot sizes at the tips

There may be code in another package to automate this more easily, but in response to a user question I thought I'd give a quick demo on one way that we can plot circles to represent the phenotypic trait values of species at the tips of a tree.

This example uses draw.circle in the plotrix library, and it might be necessary to modify it in various ways for your own purposes.

I have written a custom function for this - called dotTree. The kinks probably still need to be ironed out. Here is a demo.

First load libraries & simulate some data

## load libraries
library(plotrix)
library(phytools)
## to simulate data
tip.labels<-paste(LETTERS,replicate(26,
    paste(sample(letters,round(runif(1,4,8))),collapse="")),
    sep="._") ## realistic looking tip labels
tree<-pbtree(n=26,tip.label=tip.labels,scale=1)
x<-fastBM(tree,sig2=1)

Now the functions themselves:

dotTree<-function(tree,x,...){
    ## plot tree
    tree<-reorder(tree,"cladewise")
    plotTree(tree,offset=1.7,ylim=c(-1/25*Ntip(tree),
        Ntip(tree)),...)
    ## get last phylo plot parameters
    obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
    x.tip<-obj$xx[1:obj$Ntip]
    y.tip<-obj$yy[1:obj$Ntip]
    ## in case any x<0
    min.x<-min(x)
    max.x<-max(x)
    if(any(x<0)) x<-x-min(x)
    ## plot points
    x<-x[tree$tip.label]
    draw.circle(x.tip+1.2*strwidth("W"),y.tip,nv=200,
        radius=(0.8*x/max(x)+0.1)/2*diff(par()$usr[1:2])/
        diff(par()$usr[3:4]),col="blue")
    ## add legend
    circle.legend(x=par()$usr[1]+0.1*max(nodeHeights(tree)),
        y=0.1*(1+par()$usr[3]),min.x,max.x,length=5,...)
}

circle.legend<-function(x,y,min,max,length=4,prompt=FALSE,...){
    if(hasArg(cex)) cex<-list(...)$cex
    else cex<-1
    if(prompt){
        obj<-locator(1)
        x<-obj$x
        y<-obj$y
    }
    text(x,y-0.5,round(min,2),pos=1,cex=cex)
    s<-(0.8*max(min,0)/min(max,max+min)+0.1)/2*diff(par()$usr[1:2])/
        diff(par()$usr[3:4])
    e<-(0.8/2*diff(par()$usr[1:2])+0.1)/diff(par()$usr[3:4])
    rr<-seq(s,e,length.out=length)
    temp<-c(0,cumsum(1.1*rep(2*max(rr),length-1)))
    draw.circle(x+temp,rep(y,length),nv=200,radius=rr,col="blue")
    text(max(x+temp),y-0.5,round(max,2),pos=1,cex=cex)
    y1<-0.1/25*Ntip(tree)
    lines(c(x,max(x+temp)),rep(y-0.5-y1,2))
    lines(c(x,x),y-c(y1+0.5,2*y1+0.5))
    lines(c(max(x+temp),max(x+temp)),y-c(y1+0.5,2*y1+0.5))  
}

Now let's try it:

dotTree(tree,x,ftype="i")

The visualization seems to work OK in this sized plotting device up to about 60 or 70 tips - after that a different method (or a bigger plotting device) is needed. For instance:

tree<-pbtree(n=60,scale=1)
x<-fastBM(tree,a=10,sig2=2)
dotTree(tree,x,lwd=1,fsize=0.6,cex=0.6)

That's it.