R/ColorPalettes.R

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

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# Plot Aesthetics Objects and Methods
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#' List of color palettes that can be used in plots
#' 
#' A collection of some original and some borrowed color palettes to provide appealing color aesthetics for plots in ArchR
#' 
#' @export
ArchRPalettes <- list(

  #DISCLOSURE: This is a collection of palettes that includes some original palettes and some palettes originally
  #implemented by others in other packages.
  #They are included here for convenience because they help improve plot aesthetics.

  #NOTE: all palettes included in the "Primarily Continuous Palettes" section should also work for discrete usage but not vice versa.
  #Each continuous palette has been ordered by color to generate a visually appealing discrete palette.
  
  #---------------------------------------------------------------
  # Primarily Discrete Palettes
  #---------------------------------------------------------------
  
  #20-colors
  stallion = c("1"="#D51F26","2"="#272E6A","3"="#208A42","4"="#89288F","5"="#F47D2B", "6"="#FEE500","7"="#8A9FD1","8"="#C06CAB","19"="#E6C2DC",
               "10"="#90D5E4", "11"="#89C75F","12"="#F37B7D","13"="#9983BD","14"="#D24B27","15"="#3BBCA8", "16"="#6E4B9E","17"="#0C727C", "18"="#7E1416","9"="#D8A767","20"="#3D3D3D"),

  stallion2 = c("1"="#D51F26","2"="#272E6A","3"="#208A42","4"="#89288F","5"="#F47D2B", "6"="#FEE500","7"="#8A9FD1","8"="#C06CAB","19"="#E6C2DC",
               "10"="#90D5E4", "11"="#89C75F","12"="#F37B7D","13"="#9983BD","14"="#D24B27","15"="#3BBCA8", "16"="#6E4B9E","17"="#0C727C", "18"="#7E1416","9"="#D8A767"),

  calm = c("1"="#7DD06F", "2"="#844081", "3"="#688EC1", "4"="#C17E73", "5"="#484125", "6"="#6CD3A7", "7"="#597873","8"="#7B6FD0", "9"="#CF4A31", "10"="#D0CD47",
          "11"="#722A2D", "12"="#CBC594", "13"="#D19EC4", "14"="#5A7E36", "15"="#D4477D", "16"="#403552", "17"="#76D73C", "18"="#96CED5", "19"="#CE54D1", "20"="#C48736"),

  kelly = c("1"="#FFB300", "2"="#803E75", "3"="#FF6800", "4"="#A6BDD7", "5"="#C10020", "6"="#CEA262", "7"="#817066", "8"="#007D34", "9"="#F6768E", "10"="#00538A",
          "11"="#FF7A5C", "12"="#53377A", "13"="#FF8E00", "14"="#B32851", "15"="#F4C800", "16"="#7F180D", "17"="#93AA00", "18"="#593315", "19"="#F13A13", "20"="#232C16"),

  #16-colors
  bear = c("1"="#faa818", "2"="#41a30d","3"="#fbdf72", "4"="#367d7d",  "5"="#d33502", "6"="#6ebcbc", "7"="#37526d",
           "8"="#916848", "9"="#f5b390", "10"="#342739", "11"="#bed678","12"="#a6d9ee", "13"="#0d74b6",
           "14"="#60824f","15"="#725ca5", "16"="#e0598b"),
  
  #15-colors
  ironMan = c("9"='#371377',"3"='#7700FF',"2"='#9E0142',"10"='#FF0080', "14"='#DC494C',"12"="#F88D51","1"="#FAD510","8"="#FFFF5F","4"='#88CFA4',
           "13"='#238B45',"5"="#02401B", "7"="#0AD7D3","11"="#046C9A", "6"="#A2A475", "15"='grey35'),
  
  circus = c("1"="#D52126", "2"="#88CCEE", "3"="#FEE52C", "4"="#117733", "5"="#CC61B0", "6"="#99C945", "7"="#2F8AC4", "8"="#332288",
             "9"="#E68316", "10"="#661101", "11"="#F97B72", "12"="#DDCC77", "13"="#11A579", "14"="#89288F", "15"="#E73F74"),

  #12-colors
  paired = c("9"="#A6CDE2","1"="#1E78B4","3"="#74C476","12"="#34A047","11"="#F59899","2"="#E11E26",
               "10"="#FCBF6E","4"="#F47E1F","5"="#CAB2D6","8"="#6A3E98","6"="#FAF39B","7"="#B15928"),
  
  #11-colors
  grove = c("11"="#1a1334","9"="#01545a","1"="#017351","6"="#03c383","8"="#aad962","2"="#fbbf45","10"="#ef6a32","3"="#ed0345","7"="#a12a5e","5"="#710162","4"="#3B9AB2"),
  
  #7-colors
  summerNight = c("1"="#2a7185", "2"="#a64027", "3"="#fbdf72","4"="#60824f","5"="#9cdff0","6"="#022336","7"="#725ca5"),
  
  #5-colors
  zissou = c("1"="#3B9AB2", "4"="#78B7C5", "3"="#EBCC2A", "5"="#E1AF00", "2"="#F21A00"), #wesanderson
  darjeeling = c("1"="#FF0000", "2"="#00A08A", "3"="#F2AD00", "4"="#F98400", "5"="#5BBCD6"), #wesanderson
  rushmore = c("1"="#E1BD6D", "5"="#EABE94", "2"="#0B775E", "4"="#35274A" , "3"="#F2300F"), #wesanderson
  captain = c("1"="grey","2"="#A1CDE1","3"="#12477C","4"="#EC9274","5"="#67001E"),

  #---------------------------------------------------------------
  # Primarily Continuous Palettes
  #---------------------------------------------------------------
  
  #10-colors
  horizon = c("1"='#000075',"4"='#2E00FF', "6"='#9408F7', "10"='#C729D6', "8"='#FA4AB5', "3"='#FF6A95', "7"='#FF8B74', "5"='#FFAC53', "9"='#FFCD32', "2"='#FFFF60'),
  
  #9-colors
  horizonExtra =c("1"="#000436","4"="#021EA9","6"="#1632FB","8"="#6E34FC","3"="#C732D5","9"="#FD619D","7"="#FF9965","5"="#FFD32B","2"="#FFFC5A"),
  blueYellow = c("1"="#352A86","2"="#343DAE","3"="#0262E0","4"="#1389D2","5"="#2DB7A3","6"="#A5BE6A","7"="#F8BA43","8"="#F6DA23","9"="#F8FA0D"),
  sambaNight = c("6"='#1873CC',"2"='#1798E5',"8"='#00BFFF',"5"='#4AC596',"1"='#00CC00',"4"='#A2E700',"9"='#FFFF00',"7"='#FFD200',"3"='#FFA500'), #buencolors
  solarExtra = c("5"='#3361A5', "7"='#248AF3', "1"='#14B3FF', "8"='#88CEEF', "9"='#C1D5DC', "4"='#EAD397', "3"='#FDB31A',"2"= '#E42A2A', "6"='#A31D1D'),  #buencolors
  whitePurple = c("9"='#f7fcfd',"6"='#e0ecf4',"8"='#bfd3e6',"5"='#9ebcda',"2"='#8c96c6',"4"='#8c6bb1',"7"='#88419d',"3"='#810f7c',"1"='#4d004b'),
  whiteBlue = c("9"='#fff7fb',"6"='#ece7f2',"8"='#d0d1e6',"5"='#a6bddb',"2"='#74a9cf',"4"='#3690c0',"7"='#0570b0',"3"='#045a8d',"1"='#023858'),
  whiteRed = c("1"="white", "2"="red"),
  comet = c("1"="#E6E7E8","2"="#3A97FF","3"="#8816A7","4"="black"),

  #7-colors
  greenBlue = c("4"='#e0f3db',"7"='#ccebc5',"2"='#a8ddb5',"5"='#4eb3d3',"3"='#2b8cbe',"6"='#0868ac',"1"='#084081'),
  
  #6-colors
  beach = c("4"="#87D2DB","1"="#5BB1CB","6"="#4F66AF","3"="#F15F30","5"="#F7962E","2"="#FCEE2B"),
  
  #5-colors
  coolwarm = c("1"="#4858A7", "4"="#788FC8", "5"="#D6DAE1", "3"="#F49B7C", "2"="#B51F29"),
  fireworks = c("5"="white","2"="#2488F0","4"="#7F3F98","3"="#E22929","1"="#FCB31A"),
  greyMagma = c("2"="grey", "4"="#FB8861FF", "5"="#B63679FF", "3"="#51127CFF", "1"="#000004FF"),
  fireworks2 = c("5"="black", "2"="#2488F0","4"="#7F3F98","3"="#E22929","1"="#FCB31A"),
  purpleOrange = c("5"="#581845", "2"="#900C3F", "4"="#C70039", "3"="#FF5744", "1"="#FFC30F")
)

#' Optimized discrete color palette generation
#'
#' This function assesses the number of inputs and returns a discrete color palette that is tailored to provide the most
#' possible color contrast from the designated color set.
#'
#' @param values A character vector containing the sample names that will be used. Each entry in this character vector will be
#' given a unique color from the designated palette set.
#' @param set The name of a color palette provided in the `ArchRPalettes` list object.
#' @param reverse A boolean variable that indicates whether to return the palette colors in reverse order.
#' @export
paletteDiscrete <- function(
  values = NULL,
  set = "stallion",  
  reverse = FALSE
  ){

  .validInput(input = set, name = "set", valid = c("character"))
  .validInput(input = values, name = "values", valid = c("character", "factor"))
  .validInput(input = reverse, name = "reverse", valid = c("boolean"))
  
  values <- unique(values)
  values <- gtools::mixedsort(values)
  n <- length(unique(values))
  pal <- ArchRPalettes[[set]]
  palOrdered <- pal[gtools::mixedsort(names(pal))] #mixed sort gets 1,2,3,4..10,11,12

  if(n > length(palOrdered)){
    message("Length of unique values greater than palette, interpolating..")
    palOut <- colorRampPalette(pal)(n)
  }else{
    palOut <- palOrdered[seq_len(n)]
  }
  
  if(reverse){
    palOut <- rev(palOut)
  }

  names(palOut) <- unique(values)

  return(palOut)
  
}

#' Continuous Color Palette
#'
#' @param set The name of a color palette provided in the `ArchRPalettes` list object.
#' @param n The number of unique colors to generate as part of this continuous color palette.
#' @param reverse A boolean variable that indicates whether to return the palette colors in reverse order.
#' @export
paletteContinuous <- function(
  set = "solarExtra", 
  n = 256, 
  reverse = FALSE
  ){

  .validInput(input = set, name = "set", valid = c("character"))
  .validInput(input = n, name = "n", valid = c("integer"))
  .validInput(input = reverse, name = "reverse", valid = c("boolean"))
  
  pal <- ArchRPalettes[[set]]
  palOut <- colorRampPalette(pal)(n)
  
  if(reverse){
    palOut <- rev(palOut)
  }

  return(palOut)
  
}