Phylomorphospace with time since the root projected using a color gradient

Two different people (Marcio Pie and a student whose name has somehow slipped my mind - please identify yourself!) independently suggested to me recently that I could use a similar approach to that employed when overlaying a posterior density map from stochastic mapping on a phylomorphospace to project time since the root of the tree onto a phylomorphospace. In theory, this would help overcome the difficulty that all temporal information about the phylogeny is lost when it is projected into morphospace.

Well, this is quite easy** (**that is, easy only because I've already programmed all the pieces in phytools) to do. Here's a hack using simulated data.

First let's load phytools & simulate tree & data:

> require(phytools)
Loading required package: phytools
> packageVersion("phytools")
[1] ‘0.2.93’
> # simulate tree & data
> tree<-pbtree(n=30,scale=100)
> X<-fastBM(tree,nsim=2)

Next, we're going to create an object of class "contMap". This is just a placeholder into which we'll slot our temporal data:

# unfortunately, there's no way to prevent this from plotting
AA<-contMap(tree,X[,1])

Now, we'll swap our color palette (although we don't need to - this is just an arbitrary decision); and then we'll substitute information about the height from the root for our trait data mapped onto the tree:

> AA$cols[]<-rainbow(1001,start=0.7,end=0)
> H<-nodeHeights(tree)
> h<-max(H)
> for(i in 1:nrow(H)) names(AA$tree$maps[[i]])<- round((H[i,1]+cumsum(AA$tree$maps[[i]]))/h*1000)
> # check to verify that temporal information is correct
> plot(AA,legend=FALSE)

Finally, let's plot our phylomorphospace with color as a temporal axis:

> phylomorphospace(AA$tree,X,colors=AA$cols,lwd=3, node.by.map=TRUE,xlab="trait 1",ylab="trait 2")
> add.color.bar(2,AA$cols,title="time from the root", lims=c(0,h),digits=1)
Click where you want to draw the bar

(Click here for full size.)

The final step (add.color.bar(...)) is the biggest hack of all as it only works because I artfully positioned it close enough to the x axis so that the bottom legend text is hidden!

Try it out!