R/cell_colors.R

In caleblareau/BuenColors: Plotting utils and colors for Buenrostrolab

#' @include plotHelp.R
NULL

#' List of maps between annotations and specified colors.
#'
#' Use \code{\link{jdb_color_map}} to map cell/feature to color hex.
#'
#' @export
jdb_color_maps <- c(
  "HSC" = "#00441B",
  "MPP" = "#46A040",
  "LMPP" = "#00AF99",
  "CMP" = "#FFC179",
  "CLP" = "#98D9E9",
  "MEP" = "#F6313E",
  "GMP"= "#FFA300",
  "pDC" = "#C390D4",
  "mono" = "#FF5A00",
  "GMP-A" = "#AFAFAF",
  "GMP-B" = "#7D7D7D",
  "GMP-C" =  "#4B4B4B",
  "Ery" = "#8F1336",
  "CD4" = "#0081C9",
  "CD8" = "#001588",
  "NK" = "#490C65",
  "B" = "#BA7FD0"
)

#' A mapping function to specific colors.
#'
#' This function maps a common feature/cell
#' type (e.g. "HSC") and returns the canonical
#' hex code associtated with it.
#'
#' color_map (no 's') is the function; color_maps
#' is a named character vector.
#'
#' @param name a character (vector) corresponding to a
#' name with a mappable color
#' @return a character (vector) of hex codes
#' @keywords colors
#' @examples
#' # See possible values
#' names(jdb_color_maps)
#'
#' # Get hex codes
#' jdb_color_map("HSC")
#' jdb_color_map(c("HSC", "LMPP", "HSC"))
#'
#' @export
jdb_color_map <- function(name) {
  stopifnot(all(name %in% names(jdb_color_maps)))
return(unname(jdb_color_maps[name]))
}


#' List of maps between annotations and specified colors for scHeme/UKBB
#' project
#'
#' Use ejc_color_map to map cell/feature to color hex.
#'
#' @export
ejc_color_maps <- c(
  "HSC" = "#00441B",
  "MPP" = "#46A040",
  "LMPP" = "#00AF99",
  "CMP" = "#FFC179",
  "CLP" = "#98D9E9",
  "MEP" = "#F6313E",
  "pDC" = "#CDA2DB",
  "Mono" = "#FF5A00",
  "GMP-A" = "#FFCE00",
  "GMP-B" = "#FFA300",
  "GMP-C" =  "#FF7900",
  "GMP" = "#FFA300",
  "Ery" = "#8F1336",
  "CD4" = "#0081C9",
  "CD8" = "#001588",
  "NK" = "#490C65",
  "B" = "#A65AC2",
  "Mega" = "#FF81AF",
  "mDC"= "#FFEC00"
)

#' A mapping function to specific colors for UKBB
#' single-cell heme paper.
#'
#' This function maps a common feature/cell
#' type (e.g. "HSC") and returns the canonical
#' hex code associtated with it.
#'
#' color_map (no 's') is the function; color_maps
#' is a named character vector.
#'
#' @param name a character (vector) corresponding to a
#' name with a mappable color
#' @return a character (vector) of hex codes
#' @keywords colors
#' @examples
#' # See possible values
#' names(ejc_color_maps)
#'
#' # Get hex codes
#' ejc_color_map("HSC")
#' ejc_color_map(c("HSC", "LMPP", "HSC"))
#'
#' @export
ejc_color_map <- function(name) {
  stopifnot(all(name %in% names(ejc_color_maps)))
return(unname(ejc_color_maps[name]))
}

#' List of maps between annotations and specified colors
#' for the TF1 phylogeny analyses.
#'
#' Use tf1_color_map to map cell/feature to color hex.
#'
#' @export
tf1_color_maps <- c(
  "C9" = "#F6313E",
  "D6" = "#46A040",
  "G10" = "#0081C9",

  "G11" = "#A65AC2", # 21
  "B3" = "#FFA300", # 13
  "D2" = "#FFFF32", # 5
  "B5" = "#89774A", #5
  "B11" = "#FF6A80", #5
  "F4" = "#999999", #5
  "A9" = "#0DB2AA", #3

  "bulk" = "#001588",
  "mix"= "#00441B",

  "B9" = "#CDA2DB",
  "C10" = "#98D9E9",
  "C4" = "#FF9999",
  "C7" =  "#FFC966",
  "D3" = "#A9FBA9"
)

#' A mapping function to specific colors for the
#' TF1 clone paper
#'
#' This function maps a common feature/cell
#' type (e.g. "B9") and returns the canonical
#' hex code associtated with it.
#'
#' color_map (no 's') is the function; color_maps
#' is a named character vector.
#'
#' @param name a character (vector) corresponding to a
#' name with a mappable color
#' @return a character (vector) of hex codes
#' @keywords colors
#' @examples
#' # See possible values
#' names(tf1_color_maps)
#'
#' # Get hex codes
#' tf1_color_map("B9")
#' tf1_color_map(c("C9", "D6", "G10"))
#'
#' @export
tf1_color_map <- function(name) {
  stopifnot(all(name %in% names(tf1_color_maps)))
return(unname(tf1_color_maps[name]))
}