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("pak")
pak::pak("rbiom")The development version is available on GitHub.
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")
taxa_corrplot(biom, x = "Age", layers = "ptc", taxa = 2, stat.by = "bod")
taxa_heatmap(biom, taxa = 30, 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 850 22 20 Buccal mucosa Female
#> 2 Phylum HMP01 Bacteroidetes 201 22 20 Buccal mucosa Female
#> 3 Phylum HMP01 Actinobacteria 14 22 20 Buccal mucosa Female
#> 4 Phylum HMP01 Proteobacteria 78 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 804 24 23 Buccal mucosa Male
#> 8 Phylum HMP02 Bacteroidetes 183 24 23 Buccal mucosa Male
#> 9 Phylum HMP02 Actinobacteria 56 24 23 Buccal mucosa Male
#> 10 Phylum HMP02 Proteobacteria 97 24 23 Buccal mucosa Male
#> # ℹ 284 more rows