Dear Kamila,
plotBS checks if trees are rooted or not and if not midpoint roots the tree
nrooted <- root(nj(dist),outgroup=x)
is.rooted(nrooted) # returns FALSE
however the ape function does not pick up that the tree is rooted.
Add the argument resolve.root=TRUE:
nrooted <- root(nj(dist),outgroup=x, resolve.root=TRUE)
is.rooted(nrooted) # returns TRUE
This should solve your problem.
Regards,
Klaus
On Mon, Aug 31, 2015 at 8:56 AM, Kamila Naxerova <knaxer...@partners.org>
wrote:
> Hi all,
>
> I have a (almost certainly trivial) question about plotting a rooted tree
> with bootstrap values using ape and phangorn. I am using a simple script
> that looks like this:
>
> dist <- daisy(matrix,metric="gower")
> nrooted <- root(nj(dist),outgroup=x)
>
> plot(nrooted) ## this plots the tree with the correct root, just the way I
> want it
>
> # now I would like to put some bootstrap values on this tree
> f <- function (xx) root(nj(daisy(xx,metric="gower")),outgroup=x)
> b <- boot.phylo(nrooted,matrix,FUN = f, B=1000, trees=T)
> tree <- plotBS(nrooted,b$trees,type="phylogram”)
>
> The tree that is produced by plotBS has lost the root I assigned it. I
> would be really grateful is somebody could point out to me how to do this
> right!
>
> Thanks so much.
> Kamila
>
>
> The information in this e-mail is intended only for th...{{dropped:28}}
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