Nothing
#' COSMIC color palettes
#'
#' Color palettes inspired by the colors used in projects from the
#' [Catalogue Of
#' Somatic Mutations in Cancers (COSMIC)](https://cancer.sanger.ac.uk/cosmic).
#'
#' @param palette Palette type. Currently there are three available options:
#' - `"signature_substitutions"` (6-color palette).
#' - `"hallmarks_light"` (10-color palette).
#' - `"hallmarks_dark"` (10-color palette).
#'
#' The `"hallmarks_light"` option is from
#' [Hanahan and Weinberg (2011)](https://pubmed.ncbi.nlm.nih.gov/21376230/).
#' @param alpha Transparency level, a real number in (0, 1].
#' See `alpha` in [grDevices::rgb()] for details.
#'
#' @export pal_cosmic
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Joshua H. Cook | \email{joshuacook0023@gmail.com} |
#' [@jhrcook](https://github.com/jhrcook)
#'
#' @examples
#' library("scales")
#' show_col(pal_cosmic("hallmarks_light")(10))
#' show_col(pal_cosmic("hallmarks_light", alpha = 0.6)(10))
#' show_col(pal_cosmic("hallmarks_dark")(10))
#' show_col(pal_cosmic("hallmarks_dark", alpha = 0.6)(10))
#' show_col(pal_cosmic("signature_substitutions")(6))
#' show_col(pal_cosmic("signature_substitutions", alpha = 0.6)(6))
pal_cosmic <- function(
palette = c("hallmarks_light", "hallmarks_dark", "signature_substitutions"),
alpha = 1) {
palette <- match.arg(palette)
if (alpha > 1L || alpha <= 0L) stop("alpha must be in (0, 1]")
raw_cols <- ggsci_db$"cosmic"[[palette]]
raw_cols_rgb <- col2rgb(raw_cols)
alpha_cols <- rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L
)
manual_pal(unname(alpha_cols))
}
#' COSMIC color scales
#'
#' See [pal_cosmic()] for details.
#'
#' @inheritParams pal_cosmic
#' @param ... Additional parameters for [ggplot2::discrete_scale()].
#'
#' @export scale_color_cosmic
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Joshua H. Cook | \email{joshuacook0023@gmail.com} |
#' [@jhrcook](https://github.com/jhrcook)
#'
#' @rdname scale_cosmic
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(
#' subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)
#' ) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() +
#' scale_color_cosmic()
#'
#' ggplot(
#' subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)
#' ) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() +
#' scale_fill_cosmic()
scale_color_cosmic <- function(
palette = c("hallmarks_light", "hallmarks_dark", "signature_substitutions"),
alpha = 1, ...) {
palette <- match.arg(palette)
if (is_ggplot2_350()) {
discrete_scale("colour", palette = pal_cosmic(palette, alpha), ...)
} else {
discrete_scale("colour", scale_name = "cosmic", palette = pal_cosmic(palette, alpha), ...)
}
}
#' @export scale_colour_cosmic
#' @rdname scale_cosmic
scale_colour_cosmic <- scale_color_cosmic
#' @export scale_fill_cosmic
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_cosmic
scale_fill_cosmic <- function(
palette = c("hallmarks_light", "hallmarks_dark", "signature_substitutions"),
alpha = 1, ...) {
palette <- match.arg(palette)
if (is_ggplot2_350()) {
discrete_scale("fill", palette = pal_cosmic(palette, alpha), ...)
} else {
discrete_scale("fill", scale_name = "cosmic", palette = pal_cosmic(palette, alpha), ...)
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.