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-ph...@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 ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
