subsetting data in ggtree

Subsetting is commonly used in ggtree as we would like to for example separating internal nodes from tips. We may also want to display annotation to specific node(s)/tip(s).

Some software may stored clade information (e.g. bootstrap value) as internal node labels. Indeed we want to manipulate such information and taxa labels separately.

In current ggplot2 (version=1.0.1, access date:2015-09-23), it support subset. For instance:

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library(ggplot2)
library(ggtree)
tree=read.tree(text="((A:2,B:2)95:2,(C:2,D:2)100:2);")
ggtree(tree) + geom_text(aes(label=label), subset=.(!isTip), hjust=-.2)

But this feature was removed in github version of ggplot2 and will not be available in next release.

In github version of ggtree, we implemented geom_text2, geom_point2, and geom_segment2, that works exactly like geom_text, geom_point and geom_segment respectively with subset supported. The syntax is slightly different.

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ggtree(tree) + geom_text2(aes(label=label, subset=!isTip), hjust=-.2) +
        geom_point2(aes(subset=!isTip), color="red", size=3)

Note: The example was from the discussion of github issue.

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