Wednesday, May 8, 2013

Bug fix & update to phylomorphospace

Yesterday a phytools user identified a bug in the node-coloring of phylomorphospace. I thought that this was likely introduced when I recently did a major rewrite of the function (described here) and this seems to be correct. I have fixed this, and also added a new feature to the function that (for trees with a mapped discrete character) will automatically color nodes using the color of the mapped discrete character. The code of the updated function is here; and I have also posted a new phytools build (phytools 0.2-59).

Here's a demo of the fixed node coloring:

> require(phytools)
Loading required package: phytools
> packageVersion("phytools")
[1] ‘0.2.59’
> # first let's simulate a tree & data
> tree<-pbtree(n=30,scale=1)
> XX<-fastBM(tree,nsim=2)
> plotTree(tree,node.numbers=T)
> # now let's say we want to plot nodes
> # descended from "49" red:
> cols<-rep("black",length(tree$tip.label)+tree$Nnode)
> names(cols)<-1:length(cols)
> cols[getDescendants(tree,49)]<-"red"
> # and everything from "40" blue:
> cols[getDescendants(tree,40)]<-"blue"
> # finally, these can even be nested
> cols[getDescendants(tree,44)]<-"yellow"
> # and plot
> phylomorphospace(tree,XX,xlab="X1",ylab="X2", control=list(col.node=cols))
Cool. (This is basically the demo that I gave in an earlier post.)

Now, when I was doing this I realized that it might be cool to be able to color the nodes - as well as the edges - according to a mapped discrete character. To do this, we need to be able to compute the colors of all internal nodes on the tree from their states. Here is the code that I used to do that:

zz<-c(getStates(tree,type ="tips"), getStates(tree))
  function(x,y) which(y==x),y=tree$tip.label)
The first line just computes the states at all tip & internal nodes using getStates; the second is just a complicated way of translating tip labels in names(zz) into node numbers, which is what is need by phylomorphospace; finally, line three translates the node states to colors.

Here is a demo:

> # transition matrix
> Q<-matrix(c(-2,2,2,-2),2,2)
> colnames(Q)<-rownames(Q)<-letters[1:2]
> # simulate stochastic history
> tree<-sim.history(tree,Q)
> phylomorphospace(tree,XX,xlab="X1",ylab="X2", colors=setNames(c("blue","red"),letters[1:2]),

That's it.


  1. I tried your example and got the following:
    Error in setNames(sapply(tree$maps, function(x) names(x)[1]), tree$edge[, :
    'names' attribute [58] must be the same length as the vector [0]

    Dead stop from that point on.

    1. Can you post code to reproduce your error or email me code & data to produce the error? If not, it will be hard to solve this for you. Thanks! Liam