knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", fig.height = 4, fig.width = 8, dev="ragg_png" )
This package is a toolkit for working with Biological Observation Matrix (BIOM) files. Features include reading/writing all 'BIOM' formats, rarefaction, alpha diversity, beta diversity (including 'UniFrac'), summarizing counts by taxonomic level, subsetting, visualizations, and statistical analysis. All CPU intensive operations are written in C.
Reference material is available online at https://cmmr.github.io/rbiom/index.html
Source code can be found at https://github.com/cmmr/rbiom
The latest stable version can be installed from CRAN.
install.packages("rbiom")
The development version is available on GitHub.
install.packages("remotes") remotes::install_github("cmmr/rbiom")
library(rbiom) infile <- system.file(package = "rbiom", "extdata", "hmp50.bz2") biom <- rarefy(infile)
# bdiv_ord_plot(biom, stat.by = "Body Site", facet.by = "Sex") adiv_boxplot(biom, x = "Sex", adiv = c("otu", "shan"), stat.by = "Body Site") taxa_corrplot(biom, x = "Age", layers = "ptc", taxa = 2, stat.by = "bod")
taxa_heatmap(biom, taxa = 30, color.by = c("body", "age")) taxa_stacked(biom, rank = "Phylum") taxa_table(biom, 'Phylum')
Computation of beta diversity metrics (UniFrac, Bray-Curtis, etc) will use all available CPU cores by default. To limit the number of cores used, you can set the numThreads option:
RcppParallel::setThreadOptions(numThreads = 4)
rbiom requires the following system libraries which can be installed through your operating system's package manager.
libudunits2-dev libssl-dev libxml2-dev libcurl4-openssl-dev libgdal-dev
udunits2-devel openssl-devel libxml2-devel libcurl-devel gdal-devel
libssl_dev openssl@1.1 libxml2_dev gdal_dev
udunits
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