R/default.grin.colors.R

In GRIN2: Genomic Random Interval (GRIN)

#' Assign Default GRIN Colors
#'
#' @description
#' Assigns a default set of colors to lesion types for use in GRIN plots.
#'
#' @usage
#' default.grin.colors(
#'   lsn.types
#' )
#'
#' @param lsn.types A character vector of lesion types, typically obtained from
#' the \code{"lsn.type"} column of lesion data. Duplicate lesion types are
#' automatically removed and the remaining lesion types are sorted before
#' colors are assigned.
#'
#' @details
#' This function assigns colors from a predefined palette of up to 10 colors.
#' Colors are assigned to unique lesion types in alphabetical order. If more
#' than 10 unique lesion types are provided, custom colors must be specified
#' manually in the plotting function.
#'
#' @return
#' A named character vector in which names correspond to the unique lesion types
#' and values correspond to their assigned colors.
#'
#' @importFrom stats setNames
#'
#' @export
#'
#' @author
#' Abdelrahman Elsayed \email{abdelrahman.elsayed@stjude.org},
#' Stanley Pounds \email{stanley.pounds@stjude.org}
#'
#' @examples
#' data(lesion_data)
#'
#' # Extract unique lesion types
#' lsn.types <- unique(lesion_data$lsn.type)
#'
#' # Assign default colors to lesion types
#' default.grin.colors(lsn.types)
default.grin.colors=function(lsn.types) # Unique lesion types as specified in the lesion data file
{
  message("Computationally assigning lesion type colors for GRIN plots.")
  uniq.types=sort(unique(lsn.types))
  n.types=length(uniq.types)
  default.colors=c("black", "red","blue",
                   "olivedrab", "purple",
                   "cyan", "brown", "gold",
                   "orange","steelblue")

  if (n.types==0)
    return(setNames(character(0),character(0)))

  if (n.types>length(default.colors))
    stop(paste0("Too many lesion types for default GRIN colors; please assign colors manually."))

  res=default.colors[1:n.types]
  names(res)=uniq.types
  return(res)
}