In GuangchuangYu/ggtreeghost:

ggtree ghost

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.

GuangchuangYu/ggtreeghost documentation built on May 6, 2019, 9:01 p.m.