This is an R package for interactive visualization of counts and time series arranged along trees. Motivated by the problem of describing abundances of evolutionarily related microbes, we designed representations inspired by literature in the Data Visualization community.
First, install the
devtools package. Then you can get
devtools::install_github( "krisrs1128/treelapse", dependencies = TRUE )
The dependencies argument installs the packages that treelapse depends on
DESCRIPTION file for the list) if these aren’t already available.
To view vignettes, add the argument
build_vignettes = TRUE to the
installation command above and then run
It might take some time to build each of the vignettes.
Examples of the compiled vignettes are available at,
treelapse currently supports four kinds displays
It also includes a few utilities for structuring data into the required form.
tree_sum(): Aggregate counts from leaves to internal nodes, given a tree structure.
tree_mean(): Average counts from leaves to internal nodes, given a tree structure.
taxa_edgelist(): Create an edgelist from a taxonomic tables whose columns are different levels in the hierarchy and rows are leaves. The
ijth element is leaf
i’s ancestors at level
To get a sense of how to navigate treelapse visualizations, click the demo video linked below.
The essential ideas behind the visualizations in this package come from these papers.
The implementation hinges heavily on these (very nice) tools,
We need your help to improve this package. For bug reports and feature requests, either create an issue on github or email me.