R/EcdcColors.R
In EU-ECDC/EpiReport: Epidemiological Report
Defines functions
EcdcColors
Documented in
EcdcColors
#' Colour palettes following the March 2018 ECDC guidelines for presentation of surveillance data
#'
#' Full document: European Centre for Disease Prevention and Control. Guidelines for presentation of surveillance data.
#' Stockholm: ECDC; 2018. Available from: \href{https://www.ecdc.europa.eu/en/publications-data/guidelines-presentation-surveillance-data}{Guidelines for presentation of surveillance data}
#'
#' @param col_scale Selected colour scale, defaults to 'green'. Select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'
#' @param n Number of colours from each colour scale, apart from grey, in order indicated in the guidelines. Defaults to one colour, apart from two colours for the hotcold scale,
#' max 7-8 colours for each scale. To select grey shades, use the argument grey_shade; to select number of hot (warm) colours in the hotcold scale, use the argument hot_cols.
#' @param grey_shade (Optional: use only for 'grey') Selected shade(s) of grey in selected order; c('light', 'mediumlight','medium','mediumdark','dark'). Overrides given number of colours (n). Defaults to 'medium'.
#' @param hot_cols (Optional: use only for 'hotcold') Selected number of hot (warm) colours in the hotcold colour scale. Must be smaller than the total number of colours (n).
#' Defaults to floored half of total hotcold colours.
#' @author Tommi Karki
#' @keywords colourscales
#' @importFrom "grDevices" "rgb"
#' @export
#' @examples
#' # Select three first green colours
#' EcdcColors("green", n=3)
#'
#' # Select two first qualitative colours
#' EcdcColors("qual", n=2)
#'
#' # Select seven red colours
#' EcdcColors("red", n=7)
#'
#' EcdcColors("grey", grey_shade = c("mediumlight", "dark"))
#'
#' # Use in a graph
#' # Dummy data
#' mydat <- data.frame(ID = c(seq(1,10,1)),
#' Gender = c(rep(c("F", "M"),5)))
#' barplot(table(mydat$Gender),
#' col = EcdcColors(col_scale = "qual", n=2))
#'
#' # Hot-cold colour scale
#' barplot(c(1:4),
#' col = EcdcColors(col_scale = "hotcold", n = 4, hot_cols = 2))
#'
EcdcColors <- function(col_scale = "green", n = NULL, grey_shade = NULL,
hot_cols = NULL){
if(grepl("gray", col_scale)){
col_scale <- "grey"
}
if(grepl("qual", col_scale)){
col_scale <- "qualitative"
}
if(grepl("hot", col_scale)){
col_scale <- "hotcold"
}
if (is.null(n) & col_scale == "hotcold"){
n <- 2
}else if(is.null(n)){
n <- 1
}else{
n <- n
}
if(n < 2 & col_scale == "hotcold"){
n <- 2
}
if(is.null(hot_cols)){
hot_cols <- floor(n/2)
}
if(!is.null(n)){
if(n>7 & !col_scale %in% c("qualitative", "hotcold")){
stop("Maximum number of colours (n) for selected colour scale is 7!")
}else if(n>8 & col_scale %in% c("qualitative", "hotcold")){
stop("Maximum number of colours (n) for selected colour scale is 8!")
}}
if(col_scale=="green"){
# greens
gscale1 <- rgb(101,179,46, maxColorValue = 255)
gscale2 <- rev(c(rgb(32,119,50, maxColorValue = 255), #--- We reverse the initial order from EcdcColor package
rgb(178,207,110, maxColorValue = 255)))
gscale3 <- rev(c(rgb(26,110,49, maxColorValue = 255),
rgb(101,179,46, maxColorValue = 255),
rgb(201,217,113, maxColorValue = 255)))
gscale4 <- rev(c(rgb(26,110,49, maxColorValue = 255),
rgb(40,147,55, maxColorValue = 255),
rgb(156,198,90, maxColorValue = 255),
rgb(201,217,113, maxColorValue = 255)))
gscale5 <- rev(c(rgb(12,72,40, maxColorValue = 255),
rgb(32,129,53, maxColorValue = 255),
rgb(101,179,46, maxColorValue = 255),
rgb(178,207,110, maxColorValue = 255),
rgb(231,231,185, maxColorValue = 255)))
gscale6 <- rev(c(rgb(12,72,40, maxColorValue = 255),
rgb(32,119,50, maxColorValue = 255),
rgb(66,158,53, maxColorValue = 255),
rgb(137,190,71, maxColorValue = 255),
rgb(192,212,122, maxColorValue = 255),
rgb(231,231,185, maxColorValue = 255)))
gscale7 <- rev(c(rgb(12,72,40, maxColorValue = 255),
rgb(26,110,49, maxColorValue = 255),
rgb(40,147,55, maxColorValue = 255),
rgb(101,179,46, maxColorValue = 255),
rgb(156,198,90, maxColorValue = 255),
rgb(201,217,113, maxColorValue = 255),
rgb(231,231,185, maxColorValue = 255)))
cols <- get(paste0("gscale", n))
}
if(col_scale%in%c("blue", "hotcold")){
# blues
bscale1 <- rgb(124,189,196, maxColorValue = 255)
bscale2 <- c(rgb(60,142,162, maxColorValue = 255),
rgb(173,210,221, maxColorValue = 255))
bscale3 <- c(rgb(26,107,133, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(194,218,232, maxColorValue = 255))
bscale4 <- c(rgb(26,107,133, maxColorValue = 255),
rgb(73,153,171, maxColorValue = 255),
rgb(165,206,215, maxColorValue = 255),
rgb(194,218,232, maxColorValue = 255))
bscale5 <- c(rgb(0,60,80, maxColorValue = 255),
rgb(60,142,162, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(173,210,221, maxColorValue = 255),
rgb(227,232,240, maxColorValue = 255))
bscale6 <- c(rgb(0,60,80, maxColorValue = 255),
rgb(39,117,142, maxColorValue = 255),
rgb(95,167,181, maxColorValue = 255),
rgb(147,199,207, maxColorValue = 255),
rgb(187,216,229, maxColorValue = 255),
rgb(227,232,240, maxColorValue = 255))
bscale7 <- c(rgb(0,60,80, maxColorValue = 255),
rgb(26,107,133, maxColorValue = 255),
rgb(73,153,171, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(165,206,215, maxColorValue = 255),
rgb(194,218,232, maxColorValue = 255),
rgb(227,232,240, maxColorValue = 255))
if(col_scale=="blue"){
cols <- get(paste0("bscale", n))}
}
if(col_scale%in%c("red", "hotcold")){
# reds
rscale1 <- rgb(168,45,23, maxColorValue = 255)
rscale2 <- c(rgb(168,45,23, maxColorValue = 255),
rgb(225,167,68, maxColorValue = 255))
rscale3 <- c(rgb(168,45,23, maxColorValue = 255),
rgb(204,107,33, maxColorValue = 255),
rgb(233,184,85, maxColorValue = 255))
rscale4 <- c(rgb(168,45,23, maxColorValue = 255),
rgb(195,74,23, maxColorValue = 255),
rgb(220,150,53, maxColorValue = 255),
rgb(233,184,85, maxColorValue = 255))
rscale5 <- c(rgb(124,23,15, maxColorValue = 255),
rgb(182,61,23, maxColorValue = 255),
rgb(204,107,33, maxColorValue = 255),
rgb(225,167,68, maxColorValue = 255),
rgb(241,214,118, maxColorValue = 255))
rscale6 <- c(rgb(124,23,15, maxColorValue = 255),
rgb(174,52,23, maxColorValue = 255),
rgb(199,79,27, maxColorValue = 255),
rgb(214,133,43, maxColorValue = 255),
rgb(230,176,77, maxColorValue = 255),
rgb(241,214,118, maxColorValue = 255))
rscale7 <- c(rgb(124,23,15, maxColorValue = 255),
rgb(168,45,23, maxColorValue = 255),
rgb(195,74,23, maxColorValue = 255),
rgb(204,107,33, maxColorValue = 255),
rgb(220,150,53, maxColorValue = 255),
rgb(233,184,85, maxColorValue = 255),
rgb(241,214,118, maxColorValue = 255))
if(col_scale=="red"){
cols <- get(paste0("rscale", n))}
}
# greyscale
if(col_scale == "grey"){
if(is.null(grey_shade)){
message("Greyzone - number of colours defined by shades of grey, defaults to 'medium'. If you want specific grey shade(s) in specific order, please insert the grey_shade(s): c('light', 'mediumlight','medium','mediumdark','dark')")
grey_shade <- "medium"
}
shades <- c("light",
"mediumlight",
"medium",
"mediumdark",
"dark")
cols <- c(rgb(229,229,229, maxColorValue = 255),
rgb(199,199,199, maxColorValue = 255),
rgb(128,128,128, maxColorValue = 255),
rgb(113,113,113, maxColorValue = 255),
rgb(63,63,63, maxColorValue = 255))
cols <- cols[shades %in% grey_shade]
shades <- shades[shades %in% grey_shade]
cols <- cols[order(match(shades, grey_shade))]
}
if(col_scale=="qualitative"){
# qualitative colours
cols <- c(rgb(101,179,46, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(192,210,54, maxColorValue = 255),
rgb(62,91,132, maxColorValue = 255),
rgb(0,140,117, maxColorValue = 255),
rgb(130,66,141, maxColorValue = 255),
rgb(232,104,63, maxColorValue = 255),
rgb(184,26,93, maxColorValue = 255))
cols <- cols[1:n]
}
if(col_scale=="hotcold"){
if(n<=hot_cols){
stop("Total number (n) of colours must be greater than n of hot colours (hot_cols)!")
}
cold_cols <- n-hot_cols
cols <- get(paste0("rscale", hot_cols))
cols <- c(cols, rev(get(paste0("bscale", cold_cols))))
}
if(!col_scale%in%c("green", "blue", "red", "grey", "qualitative", "hotcold")){
stop("col_scale is not among the currently defined colour palettes,
please select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'")
}
return(cols)
}
EU-ECDC/EpiReport documentation built on Feb. 11, 2021, 6:30 p.m.
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Defines functions EcdcColors
Documented in EcdcColors
#' Colour palettes following the March 2018 ECDC guidelines for presentation of surveillance data
#'
#' Full document: European Centre for Disease Prevention and Control. Guidelines for presentation of surveillance data.
#' Stockholm: ECDC; 2018. Available from: \href{https://www.ecdc.europa.eu/en/publications-data/guidelines-presentation-surveillance-data}{Guidelines for presentation of surveillance data}
#'
#' @param col_scale Selected colour scale, defaults to 'green'. Select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'
#' @param n Number of colours from each colour scale, apart from grey, in order indicated in the guidelines. Defaults to one colour, apart from two colours for the hotcold scale,
#' max 7-8 colours for each scale. To select grey shades, use the argument grey_shade; to select number of hot (warm) colours in the hotcold scale, use the argument hot_cols.
#' @param grey_shade (Optional: use only for 'grey') Selected shade(s) of grey in selected order; c('light', 'mediumlight','medium','mediumdark','dark'). Overrides given number of colours (n). Defaults to 'medium'.
#' @param hot_cols (Optional: use only for 'hotcold') Selected number of hot (warm) colours in the hotcold colour scale. Must be smaller than the total number of colours (n).
#' Defaults to floored half of total hotcold colours.
#' @author Tommi Karki
#' @keywords colourscales
#' @importFrom "grDevices" "rgb"
#' @export
#' @examples
#' # Select three first green colours
#' EcdcColors("green", n=3)
#'
#' # Select two first qualitative colours
#' EcdcColors("qual", n=2)
#'
#' # Select seven red colours
#' EcdcColors("red", n=7)
#'
#' EcdcColors("grey", grey_shade = c("mediumlight", "dark"))
#'
#' # Use in a graph
#' # Dummy data
#' mydat <- data.frame(ID = c(seq(1,10,1)),
#' Gender = c(rep(c("F", "M"),5)))
#' barplot(table(mydat$Gender),
#' col = EcdcColors(col_scale = "qual", n=2))
#'
#' # Hot-cold colour scale
#' barplot(c(1:4),
#' col = EcdcColors(col_scale = "hotcold", n = 4, hot_cols = 2))
#'
EcdcColors <- function(col_scale = "green", n = NULL, grey_shade = NULL,
hot_cols = NULL){
if(grepl("gray", col_scale)){
col_scale <- "grey"
}
if(grepl("qual", col_scale)){
col_scale <- "qualitative"
}
if(grepl("hot", col_scale)){
col_scale <- "hotcold"
}
if (is.null(n) & col_scale == "hotcold"){
n <- 2
}else if(is.null(n)){
n <- 1
}else{
n <- n
}
if(n < 2 & col_scale == "hotcold"){
n <- 2
}
if(is.null(hot_cols)){
hot_cols <- floor(n/2)
}
if(!is.null(n)){
if(n>7 & !col_scale %in% c("qualitative", "hotcold")){
stop("Maximum number of colours (n) for selected colour scale is 7!")
}else if(n>8 & col_scale %in% c("qualitative", "hotcold")){
stop("Maximum number of colours (n) for selected colour scale is 8!")
}}
if(col_scale=="green"){
# greens
gscale1 <- rgb(101,179,46, maxColorValue = 255)
gscale2 <- rev(c(rgb(32,119,50, maxColorValue = 255), #--- We reverse the initial order from EcdcColor package
rgb(178,207,110, maxColorValue = 255)))
gscale3 <- rev(c(rgb(26,110,49, maxColorValue = 255),
rgb(101,179,46, maxColorValue = 255),
rgb(201,217,113, maxColorValue = 255)))
gscale4 <- rev(c(rgb(26,110,49, maxColorValue = 255),
rgb(40,147,55, maxColorValue = 255),
rgb(156,198,90, maxColorValue = 255),
rgb(201,217,113, maxColorValue = 255)))
gscale5 <- rev(c(rgb(12,72,40, maxColorValue = 255),
rgb(32,129,53, maxColorValue = 255),
rgb(101,179,46, maxColorValue = 255),
rgb(178,207,110, maxColorValue = 255),
rgb(231,231,185, maxColorValue = 255)))
gscale6 <- rev(c(rgb(12,72,40, maxColorValue = 255),
rgb(32,119,50, maxColorValue = 255),
rgb(66,158,53, maxColorValue = 255),
rgb(137,190,71, maxColorValue = 255),
rgb(192,212,122, maxColorValue = 255),
rgb(231,231,185, maxColorValue = 255)))
gscale7 <- rev(c(rgb(12,72,40, maxColorValue = 255),
rgb(26,110,49, maxColorValue = 255),
rgb(40,147,55, maxColorValue = 255),
rgb(101,179,46, maxColorValue = 255),
rgb(156,198,90, maxColorValue = 255),
rgb(201,217,113, maxColorValue = 255),
rgb(231,231,185, maxColorValue = 255)))
cols <- get(paste0("gscale", n))
}
if(col_scale%in%c("blue", "hotcold")){
# blues
bscale1 <- rgb(124,189,196, maxColorValue = 255)
bscale2 <- c(rgb(60,142,162, maxColorValue = 255),
rgb(173,210,221, maxColorValue = 255))
bscale3 <- c(rgb(26,107,133, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(194,218,232, maxColorValue = 255))
bscale4 <- c(rgb(26,107,133, maxColorValue = 255),
rgb(73,153,171, maxColorValue = 255),
rgb(165,206,215, maxColorValue = 255),
rgb(194,218,232, maxColorValue = 255))
bscale5 <- c(rgb(0,60,80, maxColorValue = 255),
rgb(60,142,162, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(173,210,221, maxColorValue = 255),
rgb(227,232,240, maxColorValue = 255))
bscale6 <- c(rgb(0,60,80, maxColorValue = 255),
rgb(39,117,142, maxColorValue = 255),
rgb(95,167,181, maxColorValue = 255),
rgb(147,199,207, maxColorValue = 255),
rgb(187,216,229, maxColorValue = 255),
rgb(227,232,240, maxColorValue = 255))
bscale7 <- c(rgb(0,60,80, maxColorValue = 255),
rgb(26,107,133, maxColorValue = 255),
rgb(73,153,171, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(165,206,215, maxColorValue = 255),
rgb(194,218,232, maxColorValue = 255),
rgb(227,232,240, maxColorValue = 255))
if(col_scale=="blue"){
cols <- get(paste0("bscale", n))}
}
if(col_scale%in%c("red", "hotcold")){
# reds
rscale1 <- rgb(168,45,23, maxColorValue = 255)
rscale2 <- c(rgb(168,45,23, maxColorValue = 255),
rgb(225,167,68, maxColorValue = 255))
rscale3 <- c(rgb(168,45,23, maxColorValue = 255),
rgb(204,107,33, maxColorValue = 255),
rgb(233,184,85, maxColorValue = 255))
rscale4 <- c(rgb(168,45,23, maxColorValue = 255),
rgb(195,74,23, maxColorValue = 255),
rgb(220,150,53, maxColorValue = 255),
rgb(233,184,85, maxColorValue = 255))
rscale5 <- c(rgb(124,23,15, maxColorValue = 255),
rgb(182,61,23, maxColorValue = 255),
rgb(204,107,33, maxColorValue = 255),
rgb(225,167,68, maxColorValue = 255),
rgb(241,214,118, maxColorValue = 255))
rscale6 <- c(rgb(124,23,15, maxColorValue = 255),
rgb(174,52,23, maxColorValue = 255),
rgb(199,79,27, maxColorValue = 255),
rgb(214,133,43, maxColorValue = 255),
rgb(230,176,77, maxColorValue = 255),
rgb(241,214,118, maxColorValue = 255))
rscale7 <- c(rgb(124,23,15, maxColorValue = 255),
rgb(168,45,23, maxColorValue = 255),
rgb(195,74,23, maxColorValue = 255),
rgb(204,107,33, maxColorValue = 255),
rgb(220,150,53, maxColorValue = 255),
rgb(233,184,85, maxColorValue = 255),
rgb(241,214,118, maxColorValue = 255))
if(col_scale=="red"){
cols <- get(paste0("rscale", n))}
}
# greyscale
if(col_scale == "grey"){
if(is.null(grey_shade)){
message("Greyzone - number of colours defined by shades of grey, defaults to 'medium'. If you want specific grey shade(s) in specific order, please insert the grey_shade(s): c('light', 'mediumlight','medium','mediumdark','dark')")
grey_shade <- "medium"
}
shades <- c("light",
"mediumlight",
"medium",
"mediumdark",
"dark")
cols <- c(rgb(229,229,229, maxColorValue = 255),
rgb(199,199,199, maxColorValue = 255),
rgb(128,128,128, maxColorValue = 255),
rgb(113,113,113, maxColorValue = 255),
rgb(63,63,63, maxColorValue = 255))
cols <- cols[shades %in% grey_shade]
shades <- shades[shades %in% grey_shade]
cols <- cols[order(match(shades, grey_shade))]
}
if(col_scale=="qualitative"){
# qualitative colours
cols <- c(rgb(101,179,46, maxColorValue = 255),
rgb(124,189,196, maxColorValue = 255),
rgb(192,210,54, maxColorValue = 255),
rgb(62,91,132, maxColorValue = 255),
rgb(0,140,117, maxColorValue = 255),
rgb(130,66,141, maxColorValue = 255),
rgb(232,104,63, maxColorValue = 255),
rgb(184,26,93, maxColorValue = 255))
cols <- cols[1:n]
}
if(col_scale=="hotcold"){
if(n<=hot_cols){
stop("Total number (n) of colours must be greater than n of hot colours (hot_cols)!")
}
cold_cols <- n-hot_cols
cols <- get(paste0("rscale", hot_cols))
cols <- c(cols, rev(get(paste0("bscale", cold_cols))))
}
if(!col_scale%in%c("green", "blue", "red", "grey", "qualitative", "hotcold")){
stop("col_scale is not among the currently defined colour palettes,
please select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'")
}
return(cols)
}
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