[R] Select subtree with vector of leaves using zoom function of the ape package
marongiu.luigi at gmail.com
Thu Jan 1 20:01:58 CET 2015
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
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:
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
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