R/pstoveg_otu.R

In sw1/theseus: Analysis and Visualization Tools for Microbial Community Data

#' converts the otu_table slot of a phyloseq object to a vegan-compatible matrix
#'
#' physeq2veg_otu is a helper function intended to convert the species/taxa
#' count slot of a phyloseq object to a vegan-friendly matrix. This function
#' ensures that sites/samples are rows and species are columns.
#'
#' @param PS (required) a phyloseq object
#'
#' @return A matrix containing a phyloseq object's otu_table slot.
#'
#' @seealso \code{\link[phyloseq]{phyloseq-class}}
#'   \code{\link[phyloseq]{otu_table-class}}
#'   \code{\link[phyloseq]{otu_table}}
#'
#' @examples
#' \dontrun{
#' library(theseus)
#' library(phyloseq)
#' data(WWTP_Impact, package='theseus')
#' dim(otu_table(WWTP_Impact))
#' taxa_are_rows(WWTP_Impact)
#' otu <- pstoveg_otu(WWTP_Impact)
#' dim(otu)
#'
#' data(GlobalPatterns, package='phyloseq')
#' dim(otu_table(GlobalPatterns))
#' taxa_are_rows(GlobalPatterns)
#' otu.gp <-pstoveg_otu(GlobalPatterns)
#' dim(otu.gp)
#'
#' # move transformed OTU table back to phyloseq
#' wwtp <- WWTP_Impact
#' otu.ra <- vegan::decostand(otu, method='total')
#' otu_table(wwtp) <- otu_table(otu.ra,
#'                              taxa_are_rows = taxa_are_rows(WWTP_Impact))
#' }
#'
#' @export

pstoveg_otu <- function(PS) {
  OTU <- phyloseq::otu_table(PS)
  if (phyloseq::taxa_are_rows(OTU)) {
    OTU <- t(OTU)
  }
  return(as(OTU,'matrix'))
}