Friday, February 15, 2013

Function to get the sister(s) of a node or tip

I just posted a new utility function, getSisters, that takes as input a tree and a node or tip number or label, and returns the sister node or tip numbers or labels. It has two modes: mode="number", which returns node or tip numbers as an integer or vector; and mode="label" which returns a list with up to two components - one component for node labels (if available) or numbers, and the other component with tip labels.

The code for the function is here, but it also in the most recent build of phytools: phytools 0.2-18.

Here's a quick demo:
> require(phytools)
> tree<-rtree(n=12)
> plotTree(tree,node.numbers=TRUE)
> getSisters(tree,19)
[1] 23
> getSisters(tree,18,mode="label")
$tips
[1] "t10"

You get the idea. We can also collapse some branches so that some tips or nodes have multiple sister tips or nodes:
> tree$edge.length[which(tree$edge[,2]==18)]<-0
> tree$edge.length[which(tree$edge[,2]==23)]<-0
> tree$edge.length[which(tree$edge[,2]==20)]<-0
> tree$edge.length[which(tree$edge[,2]==21)]<-0
> tree<-di2multi(tree)
> plotTree(tree,node.numbers=T)
> getSisters(tree,18,mode="label")
$tips
[1] "t8" "t2" "t10"

> getSisters(tree,"t4",mode="label")
$nodes
[1] 19

$tips
[1] "t3" "t11"

That's it.
Posted by at

4 comments:

  1. Emma SherrattAugust 15, 2016 at 12:05 AM

    A useful little utility function, thanks Liam!

    Thought I'd just post a little code I use with this utility function to find all of the sister species pairs in a tree (Only works for fully resolved, but can be easily modified for polytomies)

    # find only sister-species pairs
    sisters <- matrix(NA, ncol=2, nrow=length(tree$tip.label)) # empty matrix
    sisters[,1] <- tree$tip.label # populate first column with tip.labels
    for(i in 1:length(tree$tip.label)){
    tmp <- phytools::getSisters(tree, tree$tip.label[i], mode="label")
    if(!is.null(tmp$tips)){sisters[i,2] <- tmp$tips}
    }
    sisters <- sisters[-which(is.na(sisters[,2])),] # prune away tips that do not have a labelled tip as sister

    ReplyDelete
    Replies
    1. Liam RevellAugust 15, 2016 at 11:21 AM

      Hi Emma. sisters is redundant with functions in phangorn, which are probably faster.

      You might get a table with all pairs of sister species in a bifurcating tree using phangorn & apply family functions as follows:

      dd<-lapply(1:tree$Nnode+Ntip(tree),function(n,t)
      Descendants(t,n)[[1]],t=tree)
      nodes<-c(1:tree$Nnode+Ntip(tree))[which(sapply(dd,length)==2)]
      sisters<-t(sapply(nodes,function(n,t)
      t$tip.label[Descendants(t,n)[[1]]],t=tree))

      - Liam

      Delete
  2. Andreia MiraldoNovember 30, 2016 at 6:33 AM

    Hi Liam,

    This is really useful. Is it possible to get all the sister species from a multiphylo object?

    ReplyDelete
  3. Jens C. KruseMay 3, 2017 at 5:53 AM

    good

    ReplyDelete

Note: due to the very large amount of spam, all comments are now automatically submitted for moderation.

Subscribe to: Post Comments (Atom)