Tuesday, August 28, 2012

Trick to name the edges of a "phylo" object (for reference)

In my response to a recent R-sig-phylo message, I posted a trick for assigning the "names" attribute of the vector of edge lengths in a "phylo" object in R such that the name of each edge is given by the formula "parent node #,daughter node #" or, if the daughter node is a tip, then "parent node #,daughter tip label". I'll repeat this hear for the future reference of me & the readers of this blog (if there are any left by the end of this entry):

> library(ape)
> set.seed(100)
> tree<-rtree(10) # simulate random tree
> X<-tree$edge # store tree$edge in a matrix
> # replace all node numbers for tips with their labels
> X[X[,2]%in%1:length(tree$tip),2]<-
tree$tip[X[X[,2]%in%1:length(tree$tip),2]]
> # substitute the names of tree$edge.length for the rows of X
> names(tree$edge.length)<-paste(X[,1],X[,2],sep=",")
> round(tree$edge.length,2)
11,12  12,t9  12,13  13,t4  13,t5  11,14  14,15  15,t2  15,16
  0.20   0.36   0.36   0.69   0.54   0.71   0.54   0.75   0.42
16,t10  16,17  17,t8  17,t7  14,18  18,t6  18,19  19,t3  19,t1
  0.17   0.77   0.88   0.55   0.28   0.49   0.93   0.35   0.95
> plot(tree,no.margin=T)
> edgelabels(round(tree$edge.length,2))
> nodelabels()


(We can see that the branch lengths of the tree, plotted as edge labels, line up exactly with the branch names in tree$edge.length. Cool.)

That's it.

2 comments:

  1. I should add to this that we can pull out the lengths of specific branches of the tree as follows:
    > tree$edge.length["18,19"]
    18,19
    0.9285051

    or

    > tree$edge.length["15,t2"]
    15,t2
    0.7489722

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