R/transformPhyloseq.R

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

#' Common Transformations
#'
#' @name transformation
#'
#' @details Common transformation in microbiome like proportions, clr.
#'
#' \code{getProportions} convert counts to relative abundance.
#'
#' \code{getCLR} convert counts to centred log transform 'clr'
#'
#' @param x \code{phyloseq} object
#'
#' @examples
#' library(biomeUtils)
#' data("FuentesIliGutData")
#' ps.rel <- getProportions(FuentesIliGutData)
#' ps.clr <- getCLR(FuentesIliGutData)
#'
#' @return Transformed phyloseq
#'
#' @author Sudarshan A. Shetty
#'
#' @references
#' Shetty SA (2020). Utilities for microbiome analytics.
#' \url{https://github.com/RIVM-IIV-Microbiome/biomeUtils}
#'
#'
NULL

#' @rdname transformation
#' @aliases getProportions
#' @importFrom microbiome abundances
#' @importFrom phyloseq otu_table
#' @export
getProportions <- function(x) {

  if (!is(x, "phyloseq")) {
    stop("Input is not an object of phyloseq class")
  }
  otu_table(x) <- otu_table(abundances(x, "compositional"), taxa_are_rows=T)
  return(x)

}

#' @rdname transformation
#' @aliases getCLR
#' @export
getCLR <- function(x){
  if (!is(x, "phyloseq")) {
    stop("Input is not an object of phyloseq class")
  }
  otu_table(x) <- otu_table(abundances(x, "clr"), taxa_are_rows=T)
  return(x)
}