R/get_children.R

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

#' Get child nodes from NCBI taxonomy
#'
#' This function will utilize an organism classification table to obtain all
#' children species and/or strains with available NCBI reference sequences given
#' a parent taxon and its rank.
#'
#' @param input_taxon The parent taxon.
#' @param input_rank The taxonomic rank of the input taxon.
#' @param tax_dat A dataframe of organism classification information.
#' At minimum, should have a column indicating "strain", and and all others
#' should be taxonomic ranks. Each row should be a taxonomic relationship.
#' This defaults to \code{NULL}, which calls the `taxonomy_table` object.
#'
#' @return Returns a vector of all the child species and/or strains of the
#' input taxon.
#'
#' @export
#'
#' @examples
#' ## Get all child species and strains in bacteria superkingdom
#' get_children('Bacteria','superkingdom')
#'
#' ## Get all child species and strains in fungi kingdom
#' get_children('Fungi', 'kingdom')
#'
#' ## Get all child species in primate order
#' get_children('Primates', 'order')
#'

get_children <- function(input_taxon, input_rank, tax_dat = NULL) {
  if (is.null(tax_dat)) tax_dat <- taxonomy_table
  # Get child strains
  ind <- tolower(tax_dat[, input_rank]) %in% tolower(input_taxon)
  strain_list <- unique(tax_dat[, "strain"][ind])
  strain_list <- strain_list[!is.na(strain_list)]
  ## Delete rows with child strains
  new_table <- tax_dat[!(tax_dat[, "strain"] %in% strain_list), ]
  ind <- tolower(new_table[, input_rank]) %in% tolower(input_taxon)
  species_list <- unique(new_table[, "species"][ind])
  species_list <- species_list[!is.na(species_list)]
  children_list <- c(strain_list, species_list)
  return(children_list)
}