R/pstoveg_sample.R

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

#' Converts sample_data slot of a phyloseq object to 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.
#'
#' @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(phyloseq)
#' data("GlobalPatterns")
#' # inspect otu_table()
#' dim(otu_table(GlobalPatterns))
#' str(otu_table(GlobalPatterns))
#' taxa_are_rows(GlobalPatterns)
#' gp.otu <- physeq2veg_otu(GlobalPatterns)
#' dim(gp.otu)
#' str(gp.otu)
#' }
#'
#' @export

pstoveg_sample <- function(PS) {

  SAMP <- phyloseq::sample_data(PS)

  return(as(SAMP,'data.frame'))

}