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:

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.

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.


G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12628.