## Saturday, December 1, 2012

### Plotting an outline around a stochastic character mapped tree

In the functions contMap and densityMap I introduced the option of "outlining" the plotted edges with a fine black line (e.g., described here). It is also now possible to do this with typical stochastic mapped trees using plotSimmap, although not as a built-in option. Here's a quick demo (illustrated with simulated data):
> # first simulate tree & data
> Q<-matrix(c(-2,1,1,1,-2,1,1,1,-2),3,3)
> tree<-sim.history(pbtree(n=30,scale=1),Q,anc=1)
> # now plot (modify as desired
> cols<-c("blue","red","green"); names(cols)<-1:3
> lwd.outer=9; lwd.inner=5
> par(col="white") # font color white
> plotTree(tree,lwd=lwd.outer,ftype="i")
> par(col="black") # reset

What we're doing here is not complicated. Basically, the option plotSimmap(...,add=TRUE) (new only in the latest versions of phytools) lets us first create a tree with the edges plotted in plain black; onto which we overlay the slightly finer lines of our plotted stochastic character mapped tree. A neat thing about this technique is that we use white as a mapping color and it doesn't look ridiculous, for instance, using the same tree as before:
> cols<-c("white","red","green"); names(cols)<-1:3
> lwd.outer=9; lwd.inner=5
> par(col="white") # font color white
> plotTree(tree,lwd=lwd.outer,ftype="i")
> par(col="black") # reset

Finally, readers might notice that to specify the outer line widths, I have added a specifically even number to the inner line width (here, 4 - but it could be 2 or 6). This results in the appearance of a line of equal thickness on either side of the plotted tree. If we use an odd number instead, the appearance is a slight shadow. For instance - readers can try the code below:
> cols<-c("blue","red","green"); names(cols)<-1:3
> lwd.outer=9; lwd.inner=6
> par(col="white") # font color white
> plotTree(tree,lwd=lwd.outer,ftype="i")
> par(col="black") # reset