Get Overview of Taxa Abundances

Source: R/getTaxaOverview.R

Get Overview of Taxa Abundances

getTaxaOverview(x, rank = NULL)

Arguments

x

A phyloseq object

rank

Default is NULL and returns overview matching taxa_names. Else user can provide one of the ranks available in 'rank_names' of phyloseq object.

Value

A tibble

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

See also

getTaxaSummary

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
getProportions(FuentesIliGutData) |>
   filterSampleData(ILI == "C") |>
   getTaxaOverview(rank="Phylum")
#> # A tibble: 10 × 9
#>    taxa          mean_…¹ media…² min_a…³ max_a…⁴ stdev…⁵ cv_ab…⁶ decte…⁷ preva…⁸
#>    <chr>           <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#>  1 Firmicutes    7.83e-1 0.803   3.60e-1 0.976   1.10e-1   0.140     184   100  
#>  2 Bacteroidetes 1.42e-1 0.125   1.42e-3 0.624   1.00e-1   0.706     184   100  
#>  3 Verrucomicro… 2.16e-2 0.00177 0       0.425   5.24e-2   2.43      130    70.7
#>  4 Actinobacter… 2.07e-2 0.00955 5.34e-5 0.189   2.91e-2   1.40      184   100  
#>  5 Proteobacter… 1.57e-2 0.00609 2.78e-5 0.380   3.69e-2   2.35      184   100  
#>  6 Euryarchaeota 1.52e-2 0.00237 0       0.168   2.68e-2   1.76      123    66.8
#>  7 Tenericutes   1.35e-3 0       0       0.0383  4.13e-3   3.06       82    44.6
#>  8 Lentisphaerae 1.31e-4 0       0       0.00541 5.07e-4   3.87       50    27.2
#>  9 Cyanobacteria 1.26e-4 0       0       0.00481 4.90e-4   3.90       38    20.7
#> 10 Synergistetes 5.69e-5 0       0       0.00318 3.43e-4   6.04       21    11.4
#> # … with abbreviated variable names ¹​mean_abund, ²​median_abund, ³​min_abund,
#> #   ⁴​max_abund, ⁵​stdev_abund, ⁶​cv_abund, ⁷​dectected_samples, ⁸​prevalence