R/genusLookup.R

In microcontax: The ConTax Data Package

#' @name genusLookup
#' @aliases genusLookup
#' @title Taxonomy lookup
#' 
#' @description Extracting taxonomic information from the \code{\link{taxonomy.table}}.
#' 
#' @usage genusLookup(genera, rank = "Phylum")
#' 
#' @param genera A vector of texts, the genera names to look up.
#' @param rank A single text, the level of the taxonomy to look up.
#' 
#' @details Function for looking up higher-level taxonomy of specified genera.
#' 
#' The argument \code{genera} must consist of names in the \code{Genus} column of the data
#' set \code{\link{taxonomy.table}}.
#' 
#  The \code{rank} text must be either "Domain", "Phylum", "Class", "Order" or "Family".
#' 
#' @return A character vector containing the taxonomy information. Names in \code{genera} not recognized will 
#' return \code{NA}. Please note that there are some cases of un-assigned taxonomy at some ranks 
#' (Class, Order or Family), this is returned as "unknown".
#' 
#' @author Hilde Vinje, Lars Snipen.
#' 
#' @seealso \code{\link{taxonomy.table}}.
#' 
#' @examples 
#' genus <-  c("Acidilobus","Nitrosopumilus","Hyphomonas") 
#' genusLookup(genus, rank = "Phylum")
#' genusLookup(genus, rank = "Class")
#' 
#' 
#' @export genusLookup
#' 
genusLookup <- function(genera, rank = "Phylum"){
  ranks <- c("DOMAIN", "PHYLUM", "CLASS", "ORDER", "FAMILY")
  col <- match(toupper(rank), ranks)
  if(is.na(col)) stop("Unknown rank, must be: Domain, Phylum, Class, Order or Family")
  taxonomy.table <- NULL
  load(paste0(path.package("microcontax"), "/data/taxonomy.table.rda"))
  vec <- match(genera, taxonomy.table$Genus)
  ret <- taxonomy.table[vec,col]
  return(ret)
}



#' @name fullTaxonomy
#' @title The full taxonomy of a genus
#' 
#' @description Converts a genus to a string containing the full taxonomy.
#' 
#' @usage fullTaxonomy(genera)
#' 
#' @param genera A vector of texts, the genera names to look up.
#' 
#' @details The argument \code{genera} must consist of names in the \code{Genus} column of the data
#' set \code{\link{taxonomy.table}}.
#' 
#  Each genus is converted to a string with the following format:
#'
#' "k__<...>;p__<...>;c__<...>;o__<...>;f__<...>;g__<...>;"
#' 
#' where <...> is some proper text.
#' 
#' @return A character vector containing the taxonomy information. 
#' 
#' @author Lars Snipen.
#' 
#' @seealso \code{\link{taxonomy.table}}, \code{\link{genusLookup}}.
#' 
#' @examples 
#' genera <-  c("Bacillus","Clostridium","Hyphomonas") 
#' fullTaxonomy(genera)
#' 
#' 
#' @export fullTaxonomy
#' 
fullTaxonomy <- function(genera){
  taxonomy.table <- NULL
  load(paste0(path.package("microcontax"), "/data/taxonomy.table.rda"))
  qiime.heads <- paste0("k__", taxonomy.table$Domain,
                        ";p__", taxonomy.table$Phylum,
                        ";c__", taxonomy.table$Class,
                        ";o__", taxonomy.table$Order,
                        ";f__", taxonomy.table$Family,
                        ";g__", taxonomy.table$Genus)
  vec <- match(genera, taxonomy.table$Genus)
  return(qiime.heads[vec])
}