Sunday, December 2, 2012

Plot outline-only tree

I realized after posting yesterday that the same trick could be used to plot a pure "outline" tree (i.e., white edges outlined in black). Here's how, using the centrarchid tree of Near et al. (2005):

> # set line widths
> lwd.outer=9; lwd.inner=5
> par(col="white") # font color white
> plotTree(tree,lwd=lwd.outer,ftype="i")
> par(col="black") # reset
> # now the tricky part: create a "fake" mapping
> maps<-tree$edge.length
> maps<-as.list(maps)
> for(i in 1:length(maps)) names(maps[[i]])<-"1"
> cols<-"white"; names(cols)<-"1"
> tree$maps<-maps
> plotSimmap(tree,cols,lwd=lwd.inner,pts=F,add=T,ftype="i", offset=0.2*lwd.outer/3+0.2/3)

That's it.

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