R/brain_palettes.R

In LCBC-UiO/ggbrain: Plotting Tool for Brain Atlases

#' Generate palettes from the ggseg atlases
#'
#' \code{brain_pal} return HEX colours for the different ggseg atlases.
#'
#' @param name String name of atlas
#' @param n Number of colours to return (or "all" [default])
#' @param package package to get brain_pals data from (ggseg or ggsegExtra)
#' @param direction Direction of  HEX, -1 reverses order
#' Necessary if applying palette to other data than the brain atlas it comes from.
#' @param unname return unnamed vector (default = FALSE)
#' @return vector of colours
#' @export
#' @examples
#' brain_pal("dk")
#' brain_pal("aseg")
brain_pal <- function(name, n="all", direction=1, unname=FALSE,
                      package="ggseg"){

  brain_pals <- get_pals(package)

  info <- brain_pals_info(package = package)

  if(!(name %in% info$atlas)){
    stop(paste(name,"is not a valid palette name for brain_pal\n"))
  }

  if(length(n)>1){
    n = n
  }else if(n == "all"){
    n = seq(1,info[info$atlas %in% name,"maxcol"])
  }else if(n < 3){
    warning("minimal value for n is 3, returning requested palette with 3 different levels\n")
    n = seq(1:3)
  }else if(n > info[info$atlas %in% name,"maxcol"]){
    warning(paste("n too large, allowed maximum for palette",name,"is",
                  info[info$atlas %in% name,"maxcol"],
                  "\nReturning the palette you asked for with that many colors\n"))
    n = seq(1,info[info$atlas %in% name,"maxcol"])
  }else{
    n = seq(1,n)
  }

  pal = brain_pals[[name]]

  if (direction == -1) {
    pal <- rev(pal)
  }

  if(unname){
    pal = unname(pal)
  }

  pal[n]
}

#' Get info on brain palettes
#'
#' @inheritParams brain_pal
#' @return data.frame with palette information
#' @export
#'
#' @examples
#' brain_pals_info()
brain_pals_info <- function(package="ggseg"){

  brain_pals <- get_pals(package)

  data.frame(
    atlas=names(unlist(lapply(brain_pals,length))),
    maxcol=unname(unlist(lapply(brain_pals,length))),
    category="qual",
    colorblind=FALSE,
    stringsAsFactors = FALSE)
}


#' Get colours from brain palettes
#'
#' Needed to display the colours, and inspect
#' the number of colours of each palette
#'
#' @inheritParams brain_pal
#' @keywords internal
#' @noRd
get_colours <- function(name, n, unname, package){
  data.frame(atlas = name,
             colour = brain_pal(name=name, n=n, unname=unname,
                                package = package),
             stringsAsFactors = FALSE)
}

#' Get brain palettes
#'
#' Brain palettes can be found in either ggseg
#' or ggsegExtra. This functions is a helper
#' to choose which package to get the palette
#' from.
#'
#' @inheritParams brain_pal
#' @keywords internal
#' @noRd
get_pals <- function(package = "ggseg"){
  eval(parse(text=paste(package, "brain_pals", sep=":::")))
}

## quiets concerns of R CMD check
if(getRversion() >= "2.15.1"){
  utils::globalVariables(c("info","brain_pals"))
}