I recently discovered the R package speedyseq
by Michael McLaren. It includes much faster implementations of some phyloseq
functions : tax_glom()
, tip_glom()
, and the plotting functions that make use of psmelt()
: plot_bar()
, plot_heatmap()
, and 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")
Or:
if (!requireNamespace("devtools", quietly =TRUE))
install.packages("devtools")
devtools::install_github("mikemc/speedyseq"