Dear Romain,
the small function below returns the out group. I define he outgroup as the
clade with less taxa from the root. If both clades have the same number of
taxa in it one clades is chosen randomly.
library(phangorn)
getOutgroup <- function(tree){
tree = midpoint(tree) # you probably have done this beforehand
tmp = Descendants(tree)
kids = Children(tree, getRoot(tree))
tmp = tmp[kids]
x = sapply(tmp, length)
tree$tip.label[tmp[[which.min(x)]]]
}
# example
trees = rmtree(10, 5)
outGroups <- lapply(trees, getOutgroup)
res = sapply(outGroups , function(x, y)any(y %in% x), y="t1")
sum(res) # number of outgroups which contain "t1"
which(res) # which trees have "t1" in the outgroup
which(res & (sapply(outGroups, length)==1)) # which trees have only "t1" in
the outgroup
trees = lapply(trees, midpoint)
class(trees) = "multiPhylo"
plot(trees)
Cheers,
Klaus
PS: midpoint is now part of the phangorn package and much faster for larger
trees.
On Thu, Oct 23, 2014 at 5:57 AM, romain <[email protected]> wrote:
> Dear Klauss,
>
> Following the topic below, I was wondering if there is function to get the
> name of the outgroup after having rooted the tree with the midpoint
> function.
> I can plot the tree and just check it by eyes. However I got > 1000 trees
> and I want to count how many times on particular species is placed as
> outgroup.
>
> Thank you for your help.
>
> Romain Blanc-Mathieu
> PhD INRA-CNRS-UNS Agrobiotech sophia Antipolis
> 06160 Antibes
> FRANCE
>
>
> Dear Robin,
>
> here is a function, that does midpoint rooting, you have to attach the
> phangorn package. It is likely to appear in one of the next ape
> versions.
>
> Cheers,
> Klaus
>
>
>
>
> midpoint <- function(tree){
> dm = cophenetic(tree)
> tree = unroot(tree)
> rn = max(tree$edge)+1
> maxdm = max(dm)
> ind = which(dm==maxdm,arr=TRUE)[1,]
> tmproot = Ancestors(tree, ind[1], "parent")
> tree = phangorn:::reroot(tree, tmproot)
> edge = tree$edge
> el = tree$edge.length
> children = tree$edge[,2]
> left = match(ind[1], children)
> tmp = Ancestors(tree, ind[2], "all")
> tmp= c(ind[2], tmp[-length(tmp)])
> right = match(tmp, children)
> if(el[left]>= (maxdm/2)){
> edge = rbind(edge, c(rn, ind[1]))
> edge[left,2] = rn
> el[left] = el[left] - (maxdm/2)
> el = c(el, maxdm/2)
> }
> else{
> sel = cumsum(el[right])
> i = which(sel>(maxdm/2))[1]
> edge = rbind(edge, c(rn, tmp[i]))
> edge[right[i],2] = rn
> eltmp = sel[i] - (maxdm/2)
> # el = c(el, sel[i] - (maxdm/2))
> el = c(el, el[right[i]] - eltmp)
> el[right[i]] = eltmp
> }
> tree$edge.length = el
> tree$edge=edge
> tree$Nnode = tree$Nnode+1
> phangorn:::reorderPruning(phangorn:::reroot(tree, rn))
> }
>
>
>
>
> On 9/2/10, Velzen, Robin van <Robin.vanVelzen at wur.nl <
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>> wrote:
> >/ Dear Ape authors and mailing list members,
> />/
> />/ I am new to R. and to Ape and very much impressed by the
> functionality the
> />/ platform offers. I have used Ape to construct distance-based trees
> using the
> />/ 'read.dna', 'dist.dna' and 'nj' functions. Now I wish to root the
> resulting
> />/ Neighbor Joining tree using midpoint rooting, but have not been able
> to find
> />/ the right function.
> />/
> />/ Does anyone know if there is a function for midpoint rooting in Ape or
> />/ similar R. package, or if there is a smart way to define a midpoint
> root
> />/ outgroup that can be used with the 'root' function in Ape?
> />/
> />/ Any help or suggestion will be much appreciated!
> />/
> />/ Thanks,
> />/
> />/ Robin
> />/
> />/ Robin van Velzen
> />/ PhD student
> />/ Biosystematics Group
> />/ Wageningen University
> />/
> />/ Wageningen Campus, Radix building 107, Room W4.Aa.095
> />/ Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
> />/ PO Box 647, 6700 AP Wageningen, The Netherlands
> />/ Tel. +31 (0)317 483425
> />/ http://www.bis.wur.nl
> />/
> />/
> />/
> />/ [[alternative HTML version deleted]]
> />/
> />/ _______________________________________________
> />/ R-sig-phylo mailing list
> />/ R-sig-phylo at r-project.org <
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>
> />/ https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> />/
> /
>
> --
> Klaus Schliep
> Universit� Paris 6 (Pierre et Marie Curie)
> 9, Quai Saint-Bernard, 75005 Paris
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
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