R/clean_taxa_names.R

In bryandmartin/corncob: Count Regression for Correlated Observations with the Beta-Binomial

#' Rename taxa
#'
#' Renames taxa to have short human-readable names
#'
#' @param x Object of class \code{phyloseq}
#' @param name Character, defaults to \code{"OTU"}. Optional. String to use in every taxa name.
#'
#' @details The original taxa names are saved as the \code{original_names} attribute. See the example for an example of how to access the original names.
#'
#' @return Object of class \code{phyloseq}, with taxa renamed (defaults to OTU1, OTU2, ...), with the original taxa names saved as an attribute.
#'
#' @export
clean_taxa_names <- function(x, name = "OTU") {
  if (requireNamespace("phyloseq", quietly = TRUE)) {
    if ("phyloseq" %in% class(x)) {
      attr(x, "original_names") <- phyloseq::taxa_names(x)
      phyloseq::taxa_names(x) <- paste0(name, seq(phyloseq::ntaxa(x)))
      return(x)
    } else {
      stop("clean_taxa_names is intended for phyloseq objects!")
    }
  } else {
    warn_phyloseq()
  }
}