I recently discovered the R package
speedyseq by Michael McLaren. It includes much faster implementations of some
phyloseq functions :
tip_glom(), and the plotting functions that make use of
plot_tree(). There are also lots of convenience functions including ones for extracting the otu, sample data and taxonomy tables, and even the entire
phyloseq object, as tibbles.
For further information, check out the Readme file on GitHub at https://github.com/mikemc/speedyseq.
speedyseq can be installed in R using either of the following methods:
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("mikemc/speedyseq")
if (!requireNamespace("devtools", quietly =TRUE)) install.packages("devtools") devtools::install_github("mikemc/speedyseq"