Taxa abundance summary by group — get_group_abundances • microbiomeutilities

Taxa abundance summary by group. Useful for description of microbiome.

get_group_abundances(x, level, group, transform = "compositional")

Arguments

x: phyloseq-class object
level: Taxonomic level uses microbiome::aggregate_taxa, if NULL with return OTU/ASVs level stats.
group: Provide overview by groups. Default=NULL and will return values for entire dataset, akin to taxa_summary.
transform: Either "compositional" or "counts". Default= compositional

Value

A data frames/ grouped tibble

Examples

if (FALSE) {
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
get_group_abundances(p0, level = "Phylum", group = "DiseaseState")
}