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Tommi Karki
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Added equivalent wrappers for 'SurvColors'
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-184
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‎EcdcColors.Rproj

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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export(EcdcColors)
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export(EcdcCols)
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export(SurvColors)
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export(SurvCols)
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importFrom("grDevices","rgb")

‎R/EcdcColors.R

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#' Colour palettes following the March 2018 ECDC guidelines for presentation of surveillance data
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#'
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#' Full document: European Centre for Disease Prevention and Control. Guidelines for presentation of surveillance data.
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#' Stockholm: ECDC; 2018. Available from: \href{https://ecdc.europa.eu/en/publications-data/guidelines-presentation-surveillance-data}{Guidelines for presentation of surveillance data}
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#'
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#' @param col_scale Selected colour scale, defaults to 'green'. Select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'
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#' @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,
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#' 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.
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#' @param grey_shade Only used with grey colours, defaults to 'medium'. Selected shade(s) of grey in selected order; c('light', 'mediumlight','medium','mediumdark','dark'). Overrides given number of colours (n).
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#' @param hot_cols Selected number of hot (warm) colours in the hotcold colour scale, use only for hotcold. Must be smaller than the total number of colours (n).
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#' Defaults to floored half of total hotcold colours.
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#' @author Tommi Karki
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#' @keywords colourscales
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#' @importFrom "grDevices" "rgb"
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#' @export
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#' @examples
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#' # Select three first green colours
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#' EcdcColors("green", n=3)
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#'
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#' # Select two first qualitative colours
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#' EcdcColors("qual", n=2)
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#'
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#' # Select seven red colours
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#' EcdcColors("red", n=7)
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#'
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#' EcdcColors("grey", grey_shade = c("mediumlight", "dark"))
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#'
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#' # Use in a graph
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#' # Dummy data
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#' mydat <- data.frame(ID = c(seq(1,10,1)),
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#' Gender = c(rep(c("F", "M"),5)))
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#' barplot(table(mydat$Gender), col = EcdcColors(col_scale = "qual", n=2))
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#'
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#' # Hot-cold colour scale
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#' barplot(c(1:4), col = EcdcColors(col_scale = "hotcold", n = 4, hot_cols = 2))
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EcdcColors <- function(col_scale = "green", n = NULL, grey_shade = NULL,
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hot_cols = NULL){
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return(SurvColors(col_scale = col_scale, n = n, grey_shade = grey_shade,
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hot_cols = hot_cols))
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}

‎R/EcdcCols.R

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#' Colour palettes following the March 2018 ECDC guidelines for presentation of surveillance data
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#'
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#' Full document: European Centre for Disease Prevention and Control. Guidelines for presentation of surveillance data.
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#' Stockholm: ECDC; 2018. Available from: \href{https://ecdc.europa.eu/en/publications-data/guidelines-presentation-surveillance-data}{Guidelines for presentation of surveillance data}
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#'
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#' @param col_scale Selected colour scale, defaults to 'green'. Select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'
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#' @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,
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#' 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.
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#' @param grey_shade Only used with grey colours, defaults to 'medium'. Selected shade(s) of grey in selected order; c('light', 'mediumlight','medium','mediumdark','dark'). Overrides given number of colours (n).
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#' @param hot_cols Selected number of hot (warm) colours in the hotcold colour scale, use only for hotcold. Must be smaller than the total number of colours (n).
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#' Defaults to floored half of total hotcold colours.
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#' @author Tommi Karki
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#' @keywords colourscales
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#' @importFrom "grDevices" "rgb"
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#' @export
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#' @examples
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#' # Select three first green colours
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#' EcdcCols("green", n=3)
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#'
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#' # Select two first qualitative colours
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#' EcdcCols("qual", n=2)
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#'
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#' # Select seven red colours
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#' EcdcCols("red", n=7)
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#'
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#' EcdcCols("grey", grey_shade = c("mediumlight", "dark"))
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#'
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#' # Use in a graph
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#' # Dummy data
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#' mydat <- data.frame(ID = c(seq(1,10,1)),
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#' Gender = c(rep(c("F", "M"),5)))
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#' barplot(table(mydat$Gender), col = EcdcCols(col_scale = "qual", n=2))
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#'
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#' # Hot-cold colour scale
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#' barplot(c(1:4), col = EcdcCols(col_scale = "hotcold", n = 4, hot_cols = 2))
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EcdcCols <- function(col_scale = "green", n = NULL, grey_shade = NULL,
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hot_cols = NULL){
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return(SurvColors(col_scale = col_scale, n = n, grey_shade = grey_shade,
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hot_cols = hot_cols))
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}

‎R/SurvCols.R

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SurvCols <- function(col_scale = "green", n = NULL, grey_shade = NULL,
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hot_cols = NULL){
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if(grepl("gray", col_scale)){
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col_scale <- "grey"
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}
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if(grepl("qual", col_scale)){
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col_scale <- "qualitative"
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}
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if(grepl("hot", col_scale)){
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col_scale <- "hotcold"
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}
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if (is.null(n) & col_scale == "hotcold"){
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n <- 2
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}else if(is.null(n)){
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n <- 1
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}else{
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n <- n
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}
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if(n < 2 & col_scale == "hotcold"){
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n <- 2
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}
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if(is.null(hot_cols)){
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hot_cols <- floor(n/2)
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}
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if(!is.null(n)){
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if(n>7 & col_scale != "qualitative"){
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stop("Maximum number of colours (n) for selected colour scale is 7!")
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}else if(n>8 & col_scale == "qualitative"){
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stop("Maximum number of colours (n) for selected colour scale is 8!")
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}}
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if(col_scale=="green"){
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# greens
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gscale1 <- rgb(101,179,46, maxColorValue = 255)
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gscale2 <- c(rgb(32,119,50, maxColorValue = 255),
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rgb(178,207,110, maxColorValue = 255))
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gscale3 <- c(rgb(26,110,49, maxColorValue = 255),
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rgb(101,179,46, maxColorValue = 255),
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rgb(201,217,113, maxColorValue = 255))
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gscale4 <- c(rgb(26,110,49, maxColorValue = 255),
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rgb(40,147,55, maxColorValue = 255),
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rgb(156,198,90, maxColorValue = 255),
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rgb(201,217,113, maxColorValue = 255))
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gscale5 <- c(rgb(12,72,40, maxColorValue = 255),
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rgb(32,129,53, maxColorValue = 255),
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rgb(101,179,46, maxColorValue = 255),
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rgb(178,207,110, maxColorValue = 255),
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rgb(231,231,185, maxColorValue = 255))
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gscale6 <- c(rgb(12,72,40, maxColorValue = 255),
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rgb(32,119,50, maxColorValue = 255),
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rgb(66,158,53, maxColorValue = 255),
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rgb(137,190,71, maxColorValue = 255),
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rgb(192,212,122, maxColorValue = 255),
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rgb(231,231,185, maxColorValue = 255))
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gscale7 <- c(rgb(12,72,40, maxColorValue = 255),
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rgb(26,110,49, maxColorValue = 255),
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rgb(40,147,55, maxColorValue = 255),
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rgb(101,179,46, maxColorValue = 255),
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rgb(156,198,90, maxColorValue = 255),
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rgb(201,217,113, maxColorValue = 255),
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rgb(231,231,185, maxColorValue = 255))
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cols <- get(paste0("gscale", n))
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}
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if(col_scale%in%c("blue", "hotcold")){
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# blues
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bscale1 <- rgb(124,189,196, maxColorValue = 255)
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bscale2 <- c(rgb(60,142,162, maxColorValue = 255),
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rgb(173,210,221, maxColorValue = 255))
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bscale3 <- c(rgb(26,107,133, maxColorValue = 255),
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rgb(124,189,196, maxColorValue = 255),
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rgb(194,218,232, maxColorValue = 255))
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bscale4 <- c(rgb(26,107,133, maxColorValue = 255),
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rgb(73,153,171, maxColorValue = 255),
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rgb(165,206,215, maxColorValue = 255),
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rgb(194,218,232, maxColorValue = 255))
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bscale5 <- c(rgb(0,60,80, maxColorValue = 255),
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rgb(60,142,162, maxColorValue = 255),
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rgb(124,189,196, maxColorValue = 255),
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rgb(173,210,221, maxColorValue = 255),
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rgb(227,232,240, maxColorValue = 255))
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bscale6 <- c(rgb(0,60,80, maxColorValue = 255),
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rgb(39,117,142, maxColorValue = 255),
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rgb(95,167,181, maxColorValue = 255),
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rgb(147,199,207, maxColorValue = 255),
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rgb(187,216,229, maxColorValue = 255),
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rgb(227,232,240, maxColorValue = 255))
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bscale7 <- c(rgb(0,60,80, maxColorValue = 255),
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rgb(26,107,133, maxColorValue = 255),
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rgb(73,153,171, maxColorValue = 255),
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rgb(124,189,196, maxColorValue = 255),
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rgb(165,206,215, maxColorValue = 255),
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rgb(194,218,232, maxColorValue = 255),
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rgb(227,232,240, maxColorValue = 255))
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if(col_scale=="blue"){
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cols <- get(paste0("bscale", n))}
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}
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if(col_scale%in%c("red", "hotcold")){
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# reds
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rscale1 <- rgb(168,45,23, maxColorValue = 255)
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rscale2 <- c(rgb(168,45,23, maxColorValue = 255),
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rgb(225,167,68, maxColorValue = 255))
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rscale3 <- c(rgb(168,45,23, maxColorValue = 255),
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rgb(204,107,33, maxColorValue = 255),
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rgb(233,184,85, maxColorValue = 255))
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rscale4 <- c(rgb(168,45,23, maxColorValue = 255),
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rgb(195,74,23, maxColorValue = 255),
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rgb(220,150,53, maxColorValue = 255),
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rgb(233,184,85, maxColorValue = 255))
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rscale5 <- c(rgb(124,23,15, maxColorValue = 255),
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rgb(182,61,23, maxColorValue = 255),
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rgb(204,107,33, maxColorValue = 255),
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rgb(225,167,68, maxColorValue = 255),
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rgb(241,214,118, maxColorValue = 255))
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rscale6 <- c(rgb(124,23,15, maxColorValue = 255),
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rgb(174,52,23, maxColorValue = 255),
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rgb(199,79,27, maxColorValue = 255),
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rgb(214,133,43, maxColorValue = 255),
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rgb(230,176,77, maxColorValue = 255),
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rgb(241,214,118, maxColorValue = 255))
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rscale7 <- c(rgb(124,23,15, maxColorValue = 255),
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rgb(168,45,23, maxColorValue = 255),
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rgb(195,74,23, maxColorValue = 255),
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rgb(204,107,33, maxColorValue = 255),
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rgb(220,150,53, maxColorValue = 255),
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rgb(233,184,85, maxColorValue = 255),
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rgb(241,214,118, maxColorValue = 255))
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if(col_scale=="red"){
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cols <- get(paste0("rscale", n))}
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}
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# greyscale
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if(col_scale == "grey"){
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if(is.null(grey_shade)){
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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')")
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grey_shade <- "medium"
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}
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shades <- c("light",
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"mediumlight",
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"medium",
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"mediumdark",
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"dark")
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cols <- c(rgb(229,229,229, maxColorValue = 255),
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rgb(199,199,199, maxColorValue = 255),
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rgb(128,128,128, maxColorValue = 255),
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rgb(113,113,113, maxColorValue = 255),
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rgb(63,63,63, maxColorValue = 255))
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cols <- cols[shades %in% grey_shade]
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shades <- shades[shades %in% grey_shade]
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cols <- cols[order(match(shades, grey_shade))]
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}
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if(col_scale=="qualitative"){
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# qualitative colours
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cols <- c(rgb(101,179,46, maxColorValue = 255),
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rgb(124,189,196, maxColorValue = 255),
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rgb(192,210,54, maxColorValue = 255),
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rgb(62,91,132, maxColorValue = 255),
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rgb(0,140,117, maxColorValue = 255),
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rgb(130,66,141, maxColorValue = 255),
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rgb(232,104,63, maxColorValue = 255),
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rgb(184,26,93, maxColorValue = 255))
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cols <- cols[1:n]
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}
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if(col_scale=="hotcold"){
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if(n<=hot_cols){
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stop("Total number (n) of colours must be greater than n of hot colours (hot_cols)!")
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}
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cold_cols <- n-hot_cols
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cols <- get(paste0("rscale", hot_cols))
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cols <- c(cols, rev(get(paste0("bscale", cold_cols))))
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}
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if(!col_scale%in%c("green", "blue", "red", "grey", "qualitative", "hotcold")){
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stop("col_scale is not among the currently defined colour palettes,
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please select from 'green', 'blue', 'red', 'grey', 'qual(itative)' or 'hot(cold)'")
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}
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return(cols)
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return(SurvColors(col_scale = col_scale, n = n, grey_shade = grey_shade,
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hot_cols = hot_cols))
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}

‎man/EcdcColors.Rd

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