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taxonomy.R
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taxonomy.R
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#' @title Retrieving Taxonomic Information of a Query Organism
#' @description This function takes the scientific name of a query organism
#' and returns selected output formats of taxonomic information for the corresponding organism.
#' @param organism a character string specifying the scientific name of a query organism.
#' @param db a character string specifying the database to query, e.g. \code{db} = \code{"itis"} or \code{"ncbi"}.
#' @param output a character string specifying the taxonomic information that shall be returned.
#' Implemented are: \code{output} = \code{"classification"}, \code{"taxid"}, or \code{"children"}.
#' @details This function is based on the powerful package \pkg{taxize} and implements
#' the customized retrieval of taxonomic information for a query organism.
#'
#' The following data bases can be selected to retrieve taxonomic information:
#'
#' \itemize{
#' \item \code{db = "itis"} : Integrated Taxonomic Information Service
#' \item \code{db = "ncbi"} : National Center for Biotechnology Information
#' }
#'
#'
#'
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' # retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
#' # from NCBI Taxonomy
#' taxonomy("Arabidopsis thaliana",db = "ncbi")
#'
#' # the same can be applied to database : "itis"
#' taxonomy("Arabidopsis thaliana",db = "itis")
#'
#' # retrieving the taxonomic hierarchy of "Arabidopsis"
#' taxonomy("Arabidopsis",db = "ncbi") # analogous : db = "ncbi" or "itis"
#'
#' # or just "Arabidopsis"
#' taxonomy("Arabidopsis",db = "ncbi")
#'
#' # retrieving the taxonomy id of the query organism and in the correspondning database
#' # taxonomy("Arabidopsis thaliana",db = "ncbi", output = "taxid")
#'
#' # the same can be applied to databases : "ncbi" and "itis"
#' taxonomy("Arabidopsis thaliana",db = "ncbi", output = "taxid")
#' taxonomy("Arabidopsis thaliana",db = "itis", output = "taxid")
#'
#'
#' # retrieve children taxa of the query organism stored in the correspondning database
#' taxonomy("Arabidopsis",db = "ncbi", output = "children")
#'
#' # the same can be applied to databases : "ncbi" and "itis"
#' taxonomy("Arabidopsis thaliana",db = "ncbi", output = "children")
#' taxonomy("Arabidopsis thaliana",db = "itis", output = "children")
#'
#' }
#' @references
#'
#' Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search and retrieval in R. F1000Research,
#' 2:191. URL: http://f1000research.com/articles/2-191/v2.
#'
#' Scott Chamberlain, Eduard Szocs, Carl Boettiger, Karthik Ram, Ignasi Bartomeus, and John Baumgartner
#' (2014) taxize: Taxonomic information from around the web. R package version 0.3.0.
#' https://github.com/ropensci/taxize
#' @export
taxonomy <- function(organism, db = "ncbi", output = "classification"){
if (!is.element(output,c("classification","taxid","children")))
stop ("The output '",output,"' is not supported by this function.")
if (!is.element(db,c("ncbi","itis")))
stop ("Database '",db,"' is not supported by this function.")
name <- id <- NULL
if (db == "ncbi")
tax_hierarchy <- as.data.frame(taxize::classification(taxize::get_uid(organism), db = "ncbi")[[1]])
else if (db == "itis")
tax_hierarchy <- as.data.frame(taxize::classification(taxize::get_tsn(organism), db = "itis")[[1]])
# tryCatch({colnames(tax_hierarchy) <- c("name","rank","id")},stop("The connection to ",db," did not work properly. Please check your internet connection or maybe the API did change.", call. = FALSE))
if(output == "classification"){
return(tax_hierarchy)
}
if(output == "taxid"){
return(dplyr::select(dplyr::filter(tax_hierarchy, name == organism),id))
}
if(output == "children"){
return(as.data.frame(taxize::children(organism, db = db)[[1]]))
}
}