Get Taxa Summary at Specific Taxonomic Level

Get Taxa Summary at Specific Taxonomic Level

getTaxaSummary(x, rank = "Phylum")

Arguments

x

A phyloseq object

rank

Taxonomic rank for which abundance summaries are required.

Details

Get a summary of total abundances of taxa at specific taxonomic level.

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)
library(dplyr)
data("SprockettTHData")
x <- subset_samples(SprockettTHData,
                    Delivery_Mode=="Vaginal" & Cohort == "Tsimane")
x <- removeZeros(x)
getTaxaSummary(x, rank="Phylum")
#> # A tibble: 19 × 3
#>    Phylum              Counts   Percent
#>    <chr>                <dbl>     <dbl>
#>  1 Firmicutes         8108793 45.0     
#>  2 Bacteroidetes      3380191 18.7     
#>  3 Actinobacteria     3320636 18.4     
#>  4 Proteobacteria     2391621 13.3     
#>  5 Spirochaetes        235598  1.31    
#>  6 Fusobacteria        215503  1.19    
#>  7 Tenericutes         127683  0.708   
#>  8 Epsilonbacteraeota  100020  0.555   
#>  9 Euryarchaeota        64367  0.357   
#> 10 Verrucomicrobia      59628  0.331   
#> 11 Cyanobacteria        15267  0.0846  
#> 12 NA                    9909  0.0549  
#> 13 Elusimicrobia         3779  0.0210  
#> 14 Kiritimatiellaeota    2115  0.0117  
#> 15 Lentisphaerae          758  0.00420 
#> 16 Patescibacteria        732  0.00406 
#> 17 Planctomycetes         505  0.00280 
#> 18 Synergistetes          294  0.00163 
#> 19 Fibrobacteres           35  0.000194