Monday, December 17, 2018

A phylogenetic Christmas tree in R (adapted from Gustavo Ballen)

Today, a colleague Gustavo Ballen shared an cleverly decorated phylogenetic Christmas tree that he created using the phylogenetic visualization software, FigTree.

I hope that he doesn't mind that I'm sharing a script to recreate his plot in R:

library(phytools)
library(plotrix)
library(phangorn)
tree<-stree(20,"left")
tree$tip.label<-paste("taxon_",1:20,sep="")
for(i in 1:tree$Nnode) if(i%%2==1) tree<-rotate(tree,Ntip(tree)+i)
tree$edge.length<-c(0,rep(1,nrow(tree$edge)-1))
tree<-di2multi(tree)
plot.new()
par(mar=rep(0.1,4))
plot.window(xlim=c(0.5,20.5),ylim=c(-1,20))
lines(c(10.5,10.5),c(-1,-0.2),lwd=15,col="brown",lend=2)
plotTree(tree,direction="upwards",ftype="i",fsize=0.7,offset=0.5,
    ylim=c(-1,20),color="black",lwd=7,add=TRUE)
plotTree(tree,direction="upwards",ftype="i",fsize=0.7,offset=0.5,
    ylim=c(-1,20),color="darkgreen",lwd=5,add=TRUE)
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
for(i in 1:tree$Nnode){
    node<-i+Ntip(tree)
    daughters<-Children(tree,node)
    daughters<-daughters[c(1,length(daughters))]
    xx<-lastPP$xx[daughters]
    yy<-rep(lastPP$yy[node],2)
    cols<-if(i%in%c(2,5,6,9,10,13,14,17,18)) c("red","yellow") else
        c("yellow","red")
    draw.circle(xx[1]-0.1,yy[2]-0.25,0.25,col=cols[1])
    draw.circle(xx[2]+0.1,yy[2]-0.25,0.25,col=cols[2])
    length.out<-floor(diff(xx)/4)+2
    if(length.out>2){
        xx<-seq(xx[1],xx[2],length.out=length.out)
        if(length(xx)==3) xx[2]<-if(xx[2]>mean(range(lastPP$xx))) 
            xx[2]+0.25*(xx[3]-xx[2]) else xx[2]-0.25*(xx[3]-xx[2])
        xx<-xx[2:(length(xx)-1)]
        cols<-if(i%in%c(2,5,6,9,10,13,14,17,18)) rep(c("yellow","red"),
            ceiling(length(xx)/2)) else rep(c("red","yellow"),
            ceiling(length(xx)/2))
        for(j in 1:length(xx)) draw.circle(xx[j],yy[1]-0.25,0.25,
            col=cols[j])
    }
}

plot of chunk unnamed-chunk-1

Happy holidays!

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