just an idea of using ggghost
to work with ggtree
.
> tree Phylogenetic tree with 30 tips and 29 internal nodes. Tip labels: t4, t18, t20, t10, t8, t12, ... Rooted; includes branch lengths. > p <- ggtreeghost(tree) + geom_hilight(40) > code = summary(p, combine=TRUE) > code [1] "ggplot(tr, mapping = mapping, layout = layout, mrsd = mrsd, as.Date = as.Date, yscale = yscale, yscale_mapping = yscale_mapping, ladderize = ladderize, right = right, branch.length = branch.length, ndigits = ndigits) + geom_tree(layout = layout, multiPhylo = multiPhylo) + theme_tree() + geom_hilight(40)" ## reproduce the *plot* by running the code text > eval(parse(text=code))
The tree
will be stored in attr(p, "data")$data
and with the
summary(p, combine=TRUE)
, we can output tree and source code to
visualize the tree (in GGTREE
block) into a NEXSUS
file.
Then by parsing the output NEXUS
, we have the tree
object and the
source code to reproduce tree visualization.
Just
similar to Figtree which can save the plot to NEXUS
tree file. Figtree
introduce a figtree
block in NEXUS file to store visualization
setting. The idea here is similar.
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