Wednesday, January 3, 2018

Adding a geological legend to a fan-style tree using concentric circles

Today an R-sig-phylo subscriber asked:

“Does anyone know of a function to plot a geologic time scale as a series of concentric circles on a circularly plotted tree?”

Here is a demo using solid, rather than semi-transparent (as in geo.legend colors. This avoids the problem of having to plot 'donuts' rather than filled circles. The former scenario I will consider later.

Note that in the following tree - though a genuine empirical phylogeny - has been arbitrarily rescaled to have a total depth of 100 my for illustrative purposes only!

library(phytools)
## Loading required package: ape
## Loading required package: maps
library(plotrix)
tree
## 
## Phylogenetic tree with 82 tips and 81 internal nodes.
## 
## Tip labels:
##  Anolis_ahli, Anolis_allogus, Anolis_rubribarbus, Anolis_imias, Anolis_sagrei, Anolis_bremeri, ...
## 
## Rooted; includes branch lengths.
plotTree(tree,ftype="off",ylim=c(-0.2*Ntip(tree),Ntip(tree)),lwd=1,
    xlim=c(max(nodeHeights(tree)),0),direction="leftwards")
obj<-geo.legend() ## this is just to get the colors

plot of chunk unnamed-chunk-1

r<-max(obj$leg[,1])-obj$leg[,2]

plotTree(tree,type="fan",fsize=0.7,lwd=1,ftype="i")
for(i in 1:nrow(obj$leg)){
    color<-paste(strsplit(obj$colors[i],"")[[1]][1:7],collapse="")
    draw.circle(0,0,radius=r[i],col=color,border="transparent")
}
par(fg="transparent")
plotTree(tree,type="fan",add=TRUE,fsize=0.7,lwd=1,ftype="i")
par(fg="black")

add.simmap.legend(colors=sapply(obj$colors[rownames(obj$leg)],
    function(x) paste(strsplit(x,"")[[1]][1:7],collapse="")),
    prompt=FALSE,x=0.95*par()$usr[1],y=0.7*par()$usr[3])

plot of chunk unnamed-chunk-1

Neat.

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