R/ps_reorder.R

In david-barnett/microViz: Microbiome Data Analysis and Visualization

#' Set order of samples in phyloseq object
#'
#' @description
#' Manually set order of samples by specifying samples names in desired order.
#'
#' @details
#' Ordering of samples in a phyloseq is controlled from the otu_table slot!
#'
#' @param ps phyloseq
#' @param sample_order names or current numerical indices of samples in desired order
#'
#' @return phyloseq
#' @export
#'
#' @seealso \code{\link{ps_arrange}} for arranging samples by sample_data variables (or otu_table)
#' @seealso \code{\link{ps_seriate}} for arranging samples by microbiome similarity
#' @seealso \code{\link{ps_filter}} for keeping only some samples, based on sample_data
#'
#' @examples
#' library(phyloseq)
#' data("dietswap", package = "microbiome")
#'
#' dietswap %>%
#'   sample_data() %>%
#'   head(8)
#'
#' new_order <- rev(sample_names(dietswap))
#' dietswap %>%
#'   ps_reorder(new_order) %>%
#'   sample_data() %>%
#'   head(8)
#'
#' # random ordering with numbers
#' set.seed(1000)
#' random_order <- sample(1:nsamples(dietswap))
#' dietswap %>%
#'   ps_reorder(random_order) %>%
#'   sample_data() %>%
#'   head(8)
ps_reorder <- function(ps, sample_order) {
  ps <- ps_get(ps)
  otu <- phyloseq::otu_table(ps)
  if (phyloseq::taxa_are_rows(ps)) {
    otu <- otu[, sample_order]
  } else {
    otu <- otu[sample_order, ]
  }
  phyloseq::otu_table(ps) <- otu

  return(ps)
}