Specifying node colors with phylomorphospace()

A user recently made the following request:

I was just wondering if you would mind posting a short example of the code and data format used to specify colours in the phylomorphospace function (e.g., to create the figure form the paper describing the packages)?

Ok, just for reference, a screen grab of that figure is here:

What this figure shows is a projection of the phylogeny of Caribbean Anolis ecomorph species into a two dimensional morphospace defined by PC 1 & PC 2 from the morphological dataset and tree of Mahler et al. (2010). The tip nodes are colored by ecomorph category; and the internal nodes are black.

All right, for simplicity I'll assume that we want to replicate this general plot in a hypothetical case. First, let's simulate a tree and data for two characters:

> require(phytools)
> tree<-pbtree(n=21)
> X<-cbind(fastBM(tree),fastBM(tree))

Here, I have just simulated the tree & data; normally we would probably read these from file using functions like read.tree or read.nexus and read.csv. Here is a visualization of our simulated tree:

> plotTree(tree,pts=F)

Next, let's say we want to color (for simplicity) every third tip red, blue, or green. (I.e., the series t1, t4, t7, etc. is red.) Normally, we would probably read this from a file as well. For instance, in the ecomorph example, above, we would read a data file containing the ecomorph identification of each of the species from the tree. We could then settle on a color scheme for translation and convert our ecomorph codes to colors. In our example here, we can just do:

> tip.cols<-rep(c("red","blue","green"),7)
> names(tip.cols)<-tree$tip.label
> cols<-c(tip.cols[tree$tip.label],rep("black",tree$Nnode))
> names(cols)<-1:(length(tree$tip)+tree$Nnode)
> phylomorphospace(tree,X,control=list(col.node=cols))

If you examine this figure closely, you'll see that (as intended) everything third numbered tip node is colored red, blue, and green. Obviously, with a real (rather than simulated) tree and dataset we would read in the states for the tip nodes from a file (and they would most likely mean something). It is important to both reorder the color vector by tree$tip.label and re-number it by node number. Don't forget to add elements for internal nodes, even if they are to be colored black (for now at least: perhaps I will fix this in a future version). If we just want to color tip nodes, this is not difficult because the node numbers of the tips are 1 through N (for N species) in the order given by tree$tip.label. It is also probably a good idea to provide X as a matrix & control$col.node as a named vector, just to be safe.

I hope this helps!