rbiom is designed for microbiome researchers, providing visualizations
and statistical analyses from Biological Observation Matrix (BIOM)
files.
The latest stable version can be installed from CRAN.
install.packages('rbiom')The development version is available on GitHub.
install.packages('pak')
pak::pak('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')subset(biom, `Body Site` == 'Buccal mucosa') %>%
taxa_corrplot('Age', taxa = 2, layers = 'ptc', fit = 'lm', test = 'emtrends')taxa_heatmap(biom, taxa = 10, tracks = c('body', 'age'))taxa_stacked(biom, rank = 'Phylum')taxa_table(biom, 'Phylum')
#> # A tibble: 294 × 8
#> .rank .sample .taxa .abundance Age BMI `Body Site` Sex
#> <fct> <chr> <fct> <dbl> <dbl> <dbl> <fct> <fct>
#> 1 Phylum HMP01 Firmicutes 856 22 20 Buccal mucosa Female
#> 2 Phylum HMP01 Bacteroidetes 199 22 20 Buccal mucosa Female
#> 3 Phylum HMP01 Actinobacteria 16 22 20 Buccal mucosa Female
#> 4 Phylum HMP01 Proteobacteria 72 22 20 Buccal mucosa Female
#> 5 Phylum HMP01 Fusobacteria 32 22 20 Buccal mucosa Female
#> 6 Phylum HMP01 Tenericutes 0 22 20 Buccal mucosa Female
#> 7 Phylum HMP02 Firmicutes 803 24 23 Buccal mucosa Male
#> 8 Phylum HMP02 Bacteroidetes 192 24 23 Buccal mucosa Male
#> 9 Phylum HMP02 Actinobacteria 52 24 23 Buccal mucosa Male
#> 10 Phylum HMP02 Proteobacteria 96 24 23 Buccal mucosa Male
#> # ℹ 284 more rowsThe online manual for rbiom is available at
https://cmmr.github.io/rbiom/. It includes a getting started guide,
articles that explore specific use cases, and reference pages for each
function.
Bug reports, feature requests, and general questions can be submitted at https://github.com/cmmr/rbiom/issues.
Pull requests are welcome. Please ensure contributed code is covered by tests and documentation (add additional tests and documentation as needed) and that it passes all automated tests.
The following commands will check if rbiom passes the bundled testing
suite.
install.packages('testthat')
testthat::test_check('rbiom')