R/asPhyloseq.R

In gheysenemma/microsimR: A Simulator Package with a collection of basic community models that outputs count data of microbial communities

#' @title Microbiome Phyloseq wrapper for community samples
#'
#' @description Takes in samples in vector or matrix format
#' and merges them to a microbiome phyloseq class object.
#'
#' @param S Each parameter given to the function is a sample vector or matrix to be merged
#' into one phyloseq object of samples.
#' The vectors/matrices must all contain the same number of species in order to be merged.
#' A phyloseq object requires at least a matrix of min. 2 columns,
#' therefore an error is thrown if only a vector is given without additional vector/matrix objects.
#' @param ... vector(s)/matrice(s): see description of S
#' @return A microbiome phyloseq class object with species/OTUs as rows and samples as columns.
#' @details Requires phyloseq package (Bioconductor). Function will install package when not installed yet.
#' @examples
#' \dontrun{
#' A = powerlawA(n = 80, alpha = 1.6),
#' glv_timeseries <- glv(N = 80, A = A, tend = 100)
#' soi_sample <- rmse_sample(soi(N = 80, I = 1000, A = A, tend = 1000))
#' physeq <- asPhyloseq(glv_timeseries, soi_sample)
#' }
#' @export

asPhyloseq <- function(S, ...){
  param=c(as.list(environment()), list(...))
  names(param)=1:length(param)
  merge = as.matrix(param[[1]])
  if(length(param)>1){
    for(i in 2:length(param)){
      param[[i]] <- as.matrix(param[[i]])
      if(nrow(merge) != nrow(param[[i]])){
        stop("Samples must contain the same number of species.")
      }
      if(ncol(param[[i]]) == sum(colSums(param[[i]]))){
        stop("Samples should consist of absolute count data (no relative abundances)")
      }
      merge = cbind(merge, param[[i]])
    }
  } else {
    if(ncol(param[[1]])==1){
      stop("Need more samples.")
    }
  }
  rownames(merge) <- paste0("OTU", 1:nrow(merge))
  colnames(merge) <- paste0("Sample", 1:ncol(merge))

  physeq = phyloseq(otu_table(merge, taxa_are_rows = TRUE))
  return(physeq)
}