Integrated Analysis and Visualization of Microbiome Data

A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses.

rbiom

rbiom is designed for microbiome researchers, providing visualizations and statistical analyses from Biological Observation Matrix (BIOM) files.

Installation

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')

Usage

Import and rarefy abundance counts.

library(rbiom)

infile <- system.file(package = 'rbiom', 'extdata', 'hmp50.bz2')
biom   <- rarefy(infile)

Explore associations with metadata.

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')

Summarize counts by taxonomic rank.

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            866    22    20 Buccal mucosa Female
#>  2 Phylum HMP01   Bacteroidetes         202    22    20 Buccal mucosa Female
#>  3 Phylum HMP01   Actinobacteria         14    22    20 Buccal mucosa Female
#>  4 Phylum HMP01   Proteobacteria         60    22    20 Buccal mucosa Female
#>  5 Phylum HMP01   Fusobacteria           33    22    20 Buccal mucosa Female
#>  6 Phylum HMP01   Tenericutes             0    22    20 Buccal mucosa Female
#>  7 Phylum HMP02   Firmicutes            814    24    23 Buccal mucosa Male  
#>  8 Phylum HMP02   Bacteroidetes         181    24    23 Buccal mucosa Male  
#>  9 Phylum HMP02   Actinobacteria         49    24    23 Buccal mucosa Male  
#> 10 Phylum HMP02   Proteobacteria         97    24    23 Buccal mucosa Male  
#> # ℹ 284 more rows

Documentation

The 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.

Community guidelines

Support

Bug reports, feature requests, and general questions can be submitted at https://github.com/cmmr/rbiom/issues.

Contributing

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.

Automated tests

The following commands will check if rbiom passes the bundled testing suite.

install.packages('testthat')
testthat::test_check('rbiom')