If you're comfortable with solid colors, rather than semi-transparent as
in geo.legend, you could do something like this:
plotTree(tree)
obj<-geo.legend() ## this is just to get the colors
plotTree(tree,type="fan",lwd=1)
for(i in nrow(obj$leg):1){
color<-paste(strsplit(obj$colors[i],"")[[1]][1:7],collapse="")
draw.circle(0,0,radius=obj$leg[i,1],col=color,border="transparent")
}
par(fg="transparent")
plotTree(tree,type="fan",add=TRUE,lwd=1)
par(fg="black")
Otherwise you need to plot 'donuts' rather than circles. Let me figure
that one out & get back to you.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/3/2018 10:17 AM, Jacob Berv wrote:
Hi all,
Does anyone know of a function to plot a geologic time scale as a series of
concentric circles on a circularly plotted tree?
As far as I can tell there are three available functions that can do this on a
regular cladogram:
axisGeo (phyloch)
geoscale.Phylo (strap)
geo.legend (phytools)
But none of these works with a circular tree, as far as I can tell. It
shouldn’t be too hard to code this manually as a series of concentric circles
(going try that now), but I figured I’d ask here in case someone has already
done this.
Cheers,
Jake Berv
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