Merge pull request #1 from jhrcook/add-cosmic-pal

Add two palettes for COSMIC

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(pal_aaas)
+export(pal_cosmic)
 export(pal_d3)
 export(pal_futurama)
 export(pal_gsea)
@@ -21,6 +22,7 @@ export(pal_ucscgb)
 export(rgb_gsea)
 export(rgb_material)
 export(scale_color_aaas)
+export(scale_color_cosmic)
 export(scale_color_d3)
 export(scale_color_futurama)
 export(scale_color_gsea)
@@ -39,6 +41,7 @@ export(scale_color_tron)
 export(scale_color_uchicago)
 export(scale_color_ucscgb)
 export(scale_colour_aaas)
+export(scale_colour_cosmic)
 export(scale_colour_d3)
 export(scale_colour_futurama)
 export(scale_colour_gsea)
@@ -57,6 +60,7 @@ export(scale_colour_tron)
 export(scale_colour_uchicago)
 export(scale_colour_ucscgb)
 export(scale_fill_aaas)
+export(scale_fill_cosmic)
 export(scale_fill_d3)
 export(scale_fill_futurama)
 export(scale_fill_gsea)

R/discrete-cosmic.R

@@ -0,0 +1,96 @@
+#' COSMIC Color Palettes
+#'
+#' Color palettes inspired by the colors used projects from the
+#' \href{https://cancer.sanger.ac.uk/cosmic}{Catalogue Of
+#' Somatic Mutations in Cancers (COSMIC)}
+#'
+#' @param palette Palette type.
+#' Currently there is two available options: \code{"signature_substitutions"}
+#' (6-color palette) and \code{"hallmarks"} (10-color palette).
+#' @param alpha Transparency level, a real number in (0, 1].
+#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
+#'
+#' @export pal_cosmic
+#'
+#' @importFrom grDevices col2rgb rgb
+#' @importFrom scales manual_pal
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{https://nanx.me}{https://nanx.me}>
+#' @author Joshua H. Cook <\email{joshuacook0023@@gmail.com}> |
+#' <\href{https://github.com/jhrcook}{GitHub/jhrcook}>
+#'
+#' @examples
+#' library("scales")
+#' show_col(pal_cosmic("hallmarks")(10))
+#' show_col(pal_cosmic("hallmarks", 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", "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 \code{\link{pal_cosmic}} for details.
+#'
+#' @inheritParams pal_cosmic
+#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
+#'
+#' @export scale_color_cosmic
+#'
+#' @importFrom ggplot2 discrete_scale
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{https://nanx.me}{https://nanx.me}>
+#' @author Joshua H. Cook <\email{joshuacook0023@@gmail.com}> |
+#' <\href{https://github.com/jhrcook}{GitHub/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"), alpha = 1, ...) {
+  palette <- match.arg(palette)
+  discrete_scale("colour", "cosmic", 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"), alpha = 1, ...) {
+  palette <- match.arg(palette)
+  discrete_scale("fill", "cosmic", pal_cosmic(palette, alpha), ...)
+}

data-raw/data-generator.R

@@ -184,6 +184,30 @@ ggsci_db$"uchicago"$"dark" <- c(
   "Violet" = "#350E20"
 )
 
+# Color palette inspired by COSMIC Hallmarks of Cancer
+ggsci_db$"cosmic"$"hallmarks" <- c(
+  "Invasion and Metastasis" = "#171717",
+  "Escaping Immunic Response to Cancer" = "#7D0226",
+  "Change of Cellular Energetics" = "#300049",
+  "Cell Replicative Immortality" = "#165459",
+  "Suppression of Growth" = "#3F2327",
+  "Genome Instability and Mutations" = "#0B1948",
+  "Angiogenesis" = "#E71012",
+  "Escaping Programmed Cell Death" = "#555555",
+  "Proliferative Signaling" = "#193006",
+  "Tumour Promoting Inflammation" = "#A8450C"
+)
+
+# Color palette inspired by COSMIC Hallmarks of Cancer
+ggsci_db$"cosmic"$"signature_substitutions" <- c(
+  "C>A" = "#5ABCEB",
+  "C>G" = "#050708",
+  "C>T" = "#D33C32",
+  "T>A" = "#CBCACB",
+  "T>C" = "#ABCD72",
+  "T>G" = "#E7C9C6"
+)
+
 # Color palette inspired by The Simpsons
 ggsci_db$"simpsons"$"springfield" <- c(
   "HomerYellow" = "#FED439", "HomerBlue" = "#709AE1",

vignettes/ggsci.Rmd

@@ -76,6 +76,9 @@ summarized in the table below.
 |                 | `scale_fill_uchicago()`      | `"light"`<br>                  |                      |
 |                 |                              | `"dark"`                       |                      |
 +-----------------+------------------------------+--------------------------------+----------------------+
+| COSMIC          | `scale_color_cosmic()`       | `"hallmarks"`                  | `pal_cosmic()`       |
+|                 | `scale_fill_cosmic()`        | `"signature_substitutions"`    |                      |
++-----------------+------------------------------+--------------------------------+----------------------+
 | Star Trek       | `scale_color_startrek()`     | `"uniform"`                    | `pal_startrek()`     |
 |                 | `scale_fill_startrek()`      |                                |                      |
 +-----------------+------------------------------+--------------------------------+----------------------+
@@ -263,6 +266,17 @@ p2_uchicago <- p2 + scale_fill_uchicago()
 grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
 ```
 
+## COSMIC
+
+# Color palette inspired by [COSMIC](https://cancer.sanger.ac.uk/cosmic) Hallmarks of Cancer (`"hallmarks"`) and the mutational signature substitution (`"signature_substitutions"`) colors.
+
+```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
+p1_cancer_hallmarks <- p1 + scale_color_cosmic()
+p2_cancer_hallmarks <- p2 + scale_fill_cosmic()
+grid.arrange(p1_cancer_hallmarks, p2_cancer_hallmarks, ncol = 2)
+```
+
+
 ## Star Trek
 
 This palette is inspired by the (uniform) colors in <emph>Star Trek</emph>: