R/gl.colors.R

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

# Set colors for plots

#' This is a helper function that supports the creation of color palettes for all plotting functions.
#' @param type the type of color or palette. Can be "2" [two colors], "2c" [two colors contrast], "3" [three colors], "4" [four colors], "pal" [need to be specify the palette type and the number of colors ]. A palette of colors can be specified via "div" [divergent], "dis" [discrete], "con" [convergent], "vir" [viridis]. Be aware a palette needs the number of colors specified as well. It returns a function and therefore the number of colors needs to be a part of the function call. Check the examples to see how this works. 
#' @export
#' @examples
#' gl.colors(2)
#' gl.colors("2")
#' gl.colors("2c")
#' #five discrete colors
#' gl.colors(type="dis")(5)
#' #seven divergent colors
#' gl.colors("div")(7)

gl.colors <- function(
    type=2) {
  
  #checks
  if (is.numeric(type))
    if (type<2 | type>4)
    {
      cat(error("No valid color option specified. Check ?gl.colors\n"))
      stop(-1)
    }
  
  check <- match(type, c("2","2c","3","4","structure","dis", "div", "vir","con"))
  
  if (is.na(check)) {
    cat(error("No valid color option specified. Check ?gl.colors\n"))
    stop(-1)
  }
  type <- as.character(type)
  cols <- NA
  # SET PLOTS COLORS
  if (type=="2")  cols <- c("#3B9AB2", "#78B7C5")
  if (type=="2c")  cols <- c("deeppink", "chartreuse3")
  if (type=="3")  cols <-  c("#3B9AB2", "deeppink", "lemonchiffon")
  if (type=="4")  cols <-  c("lemonchiffon", "deeppink", "dodgerblue", "chartreuse3")
  if (type=="structure")  cols<-  c( "#E4E1E3", "#F6222E", "#FE00FA", "#16FF32","#3283FE", "#FEAF16", "#B00068", "#1CFFCE", "#90AD1C","#2ED9FF", "#DEA0FD", "#AA0DFE", "#F8A19F", "#325A9B","#C4451C", "#1C8356", "#85660D", "#B10DA1", "#FBE426","#1CBE4F", "#FA0087", "#FC1CBF", "#F7E1A0", "#C075A6","#782AB6", "#AAF400", "#BDCDFF", "#822E1C", "#B5EFB5","#7ED7D1", "#1C7F93", "#D85FF7", "#683B79", "#66B0FF","#3B00FB")
  
  if (type=="div") cols <- colorRampPalette(c("#3B9AB2", "#78B7C5", "#EBCC2A", "#E1AF00", "#F21A00"))
  
  if (type=="dis") cols <- function(n) {
    hues <-seq(15, 375, length = n + 1)
    return(hcl(h = hues, l = 65, c = 100)[1:n])
  }
  if (type=="con") {
    cool <-
      rainbow(50, start = grDevices::rgb2hsv(col2rgb("cyan"))[1],
              end = grDevices::rgb2hsv(col2rgb("blue"))[1])
    warm <-
      rainbow(50, start = grDevices::rgb2hsv(col2rgb("red"))[1],
              end = grDevices::rgb2hsv(col2rgb("yellow"))[1])
    dummy <- c(rev(cool), rev(warm))
    cols <- colorRampPalette(dummy)
  }
  if (type=="vir")  {
    cols <- colorRampPalette(
      c(
        "#440154FF",
        "#482173FF",
        "#433E85FF",
        "#38598CFF",
        "#2D708EFF",
        "#25858EFF",
        "#1E9B8AFF",
        "#2BB07FFF",
        "#51C56AFF",
        "#85D54AFF",
        "#C2DF23FF",
        "#FDE725FF"
      ))
  }
  return(cols)  
}