R/aggregate_top_taxa2.R

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

#' @title Aggregate Top Taxa v2
#' @description Summarize phyloseq: combine other than the most abundant taxa.
#' @details Backup from microbiome R pkg. This function is replaced by
#' aggregate_rare function.
#' @param x \code{\link{phyloseq-class}} object
#' @param top Keep the top-n taxa, and merge the rest under the category
#' 'Other'. Instead of top-n numeric this can also be a character vector
#' listing the groups to combine.
#' @param level Summarization level (from \code{rank_names(pseq)})
#' @return \code{\link{phyloseq-class}} object
#' @examples
#' data(dietswap)
#' s <- aggregate_top_taxa2(dietswap, top = 3, "Phylum")
#' @export
#' @references See citation('microbiome')
#' @author Contact: Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities
aggregate_top_taxa2 <- function(x, top, level) {
  x <- aggregate_taxa(x, level)

  tops <- top_taxa(x, top)
  tax <- tax_table(x)

  inds <- which(!rownames(tax) %in% tops)

  tax[inds, level] <- "Other"

  tax_table(x) <- tax

  tt <- tax_table(x)[, level]
  tax_table(x) <- tax_table(tt)

  aggregate_taxa(x, level)
}