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 ______________________________________________ [email protected] 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.
