R/tax_names2rank.R

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

#' Add taxa_names as last column in phyloseq tax_table
#'
#' The taxa names in your phyloseq may specify a further unique classification
#' of your taxa, e.g. ASVs, that is not otherwise represented in the tax_table itself.
#' This function fixes that, and allows you to include this level in taxatree_plots for example.
#'
#' @param data phyloseq object, or psExtra or tax_table (taxonomyTable)
#' @param colname name of new rank to add at right side of tax_table
#'
#' @return same class object as passed in to data
#' @export
tax_names2rank <- function(data, colname = "unique") {
  # get tt
  tt <- tt_get(data)

  # return data unchanged if already last column matches colname
  if (identical(colname, rev(phyloseq::rank_names(tt))[[1]])) {
    return(data)
  }

  # modify tt
  new <- matrix(data = rownames(tt), ncol = 1, dimnames = list(NULL, colname))
  tt <- cbind(tt, new)
  tt <- phyloseq::tax_table(tt)

  # return object
  if (is(data, "taxonomyTable")) {
    return(tt)
  }
  if (is(data, "phyloseq")) {
    data@tax_table <- tt
  } else {
    stop("Bad data - should never reach this line")
  }
  return(data)
}