R/map_edit_names.R

In Racmacs: Antigenic Cartography Macros

#' Edit antigen names in an acmap
#'
#' @param map The map data object to be updated
#' @param old_names Old names to be replaced
#' @param new_names Replacement for old names
#'
#' @returns Returns the acmap object with antigen names updated.
#'
#' @family functions for working with map data
#' @export
#'
edit_agNames <- function(
  map,
  old_names,
  new_names
  ) {

  # Check the length of the old and new names are the same
  if (length(old_names) != length(new_names)) {
    stop("The lengths of old names and new names must match")
  }

  # Match the names
  ag_indices <- get_ag_indices(old_names, map, TRUE)

  # Replace the names
  agNames(map)[ag_indices[!is.na(ag_indices)]] <- new_names[!is.na(ag_indices)]

  # Return the updated map data
  map

}


#' Edit sera names in an acmap
#'
#' @param map The map data object to be updated
#' @param old_names Old names to be replaced
#' @param new_names Replacement for old names
#'
#' @returns Returns the acmap object with sera names updated.
#'
#' @family functions for working with map data
#' @export
#'
edit_srNames <- function(
  map,
  old_names,
  new_names
  ) {

  # Check the length of the old and new names are the same
  if (length(old_names) != length(new_names)) {
    stop("The lengths of old names and new names must match")
  }

  # Match the names
  sr_indices <- get_sr_indices(old_names, map, TRUE)

  # Replace the names
  srNames(map)[sr_indices[!is.na(sr_indices)]] <- new_names[!is.na(sr_indices)]

  # Return the updated map data
  map

}


#' Update the ferret serum names to match antigens
#'
#' @param map The map data object
#' @param dictionary_file The path to the dictionary file you want to use
#'   (should be .csv). If not supplied then the default dictionary that comes
#'   with Racmacs will be used.
#'
#' @returns Returns the updated map data object
#' @export
#' @keywords internal
#'
update_ferret_seraNames <- function(
  map,
  dictionary_file = NULL
  ) {

  # Read from default dictionary if not supplied
  if (is.null(dictionary_file)) {
    dictionary_file <- system.file(
      "extdata/ferret_ag_dictionary.csv",
      package = "Racmacs"
    )
  }

  # Read in csv file
  dictionary <- utils::read.csv(
    file   = dictionary_file,
    header = FALSE,
    stringsAsFactors = FALSE
  )

  # Update the map file
  edit_srNames(
    map       = map,
    old_names = dictionary[, 1],
    new_names = dictionary[, 2]
  )

}