R help - Jan 2015 - Select subtree with vector of leaves using zoom function of the ape package

Dear all,
I am drawing a phylogenetic tree using the zoom() function of the ape package.
Since I have 476 sequences in my alignment, this allows me to have the outlook
of
the main tree and then highlight a portion of it, and this works fine.
At the moment I am using the approach of indicating the leaves (or tips) to
highlight by indicating their sequential number, for instance the zoom is based
on the
leaves 3:62.
In order to have more control on the tree I would like to use a vector with the
names of the sequences to highlight, but when I feed it to the "focus"
argument
I obtain the error:

Warning message:
In Ops.factor(focus[[i]]) : - not meaningful for factors

and the zoom is based on the whole tree rather than on the subtree.
The list of sequences is provided in the "leaf" vector in a column
names "tip" and this approach does not work if I provide neither
"leaf" nor "leaf$tip" as argument
for "focus".
Any tips?
Best regards
Luigi

Luigi Marongiu <marongiu.luigi <at> gmail.com> writes:

> I am drawing a phylogenetic tree using the zoom() function of the
> ape package. Since I have 476 sequences in my alignment, this allows
> me to have the outlook of the main tree and then highlight a portion
> of it, and this works fine.  At the moment I am using the approach
> of indicating the leaves (or tips) to highlight by indicating their
> sequential number, for instance the zoom is based on the leaves
> 3:62.  In order to have more control on the tree I would like to use
> a vector with the names of the sequences to highlight, but when I
> feed it to the "focus" argument I obtain the error:
 
> Warning message:
> In Ops.factor(focus[[i]]) : - not meaningful for factors
 
> and the zoom is based on the whole tree rather than on the subtree.
> The list of sequences is provided in the "leaf" vector in a
column
> names "tip" and this approach does not work if I provide neither
> "leaf" nor "leaf$tip" as argument for
"focus".
  This is not really answering your question, but I have a couple
of meta-suggestions for asking it:

  * you might be better off asking questions about ape, phylogenetic
analyses, etc., on the r-sig-phylo at r-project.org mailing list, which
focuses on these kinds of questions (it's a good idea *not* to post
in both places simultaneously, and to mention when you re-post there
that you previously posted here); more of the users there will be
familiar with these packages.

  * it would be really helpful, and greatly increase your odds
of getting an answer, if you can post a "minimum workable example",
that is a _small_ piece of data/code that people can use to replicate
your problem: see http://tinyurl.com/reproducible-000 ...

  Ben Bolker