v2.0

DESCRIPTION

@@ -1,10 +1,12 @@
 Package: ggsci
 Type: Package
 Title: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
-Version: 1.5
+Version: 2.0
 Author: Nan Xiao <[email protected]>, Miaozhu Li <[email protected]>
 Maintainer: Nan Xiao <[email protected]>
-Description: A collection of 'ggplot2' color palettes inspired by scientific journals and science fiction TV shows.
+Description: A collection of 'ggplot2' color palettes inspired by
+    scientific journals, data visualization libraries, and
+    science fiction TV shows.
 License: GPL
 LazyData: TRUE
 VignetteBuilder: knitr
@@ -19,5 +21,6 @@ Imports:
 Suggests:
     knitr,
     rmarkdown,
-    gridExtra
+    gridExtra,
+    reshape2
 RoxygenNote: 5.0.1

NAMESPACE

@@ -1,14 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
 export(pal_aaas)
+export(pal_d3)
+export(pal_futurama)
+export(pal_gsea)
 export(pal_jco)
 export(pal_lancet)
 export(pal_npg)
 export(pal_rickandmorty)
 export(pal_simpsons)
 export(pal_uchicago)
 export(pal_ucscgb)
+export(rgb_gsea)
 export(scale_color_aaas)
+export(scale_color_d3)
+export(scale_color_futurama)
+export(scale_color_gsea)
 export(scale_color_jco)
 export(scale_color_lancet)
 export(scale_color_npg)
@@ -17,6 +24,9 @@ export(scale_color_simpsons)
 export(scale_color_uchicago)
 export(scale_color_ucscgb)
 export(scale_colour_aaas)
+export(scale_colour_d3)
+export(scale_colour_futurama)
+export(scale_colour_gsea)
 export(scale_colour_jco)
 export(scale_colour_lancet)
 export(scale_colour_npg)
@@ -25,6 +35,9 @@ export(scale_colour_simpsons)
 export(scale_colour_uchicago)
 export(scale_colour_ucscgb)
 export(scale_fill_aaas)
+export(scale_fill_d3)
+export(scale_fill_futurama)
+export(scale_fill_gsea)
 export(scale_fill_jco)
 export(scale_fill_lancet)
 export(scale_fill_npg)
@@ -33,6 +46,9 @@ export(scale_fill_simpsons)
 export(scale_fill_uchicago)
 export(scale_fill_ucscgb)
 importFrom(ggplot2,discrete_scale)
+importFrom(ggplot2,scale_color_gradientn)
+importFrom(ggplot2,scale_fill_gradientn)
 importFrom(grDevices,col2rgb)
+importFrom(grDevices,colorRamp)
 importFrom(grDevices,rgb)
 importFrom(scales,manual_pal)

NEWS.md

@@ -12,3 +12,13 @@
    * UChicago
    * Simpsons
    * Rick and Morty
+
+# CHANGES IN ggsci VERSION 2.0 (2016-11-20)
+
+## NEW FEATURES
+
+ * Two new discrete color palettes:
+   * D3 color palette
+   * Futurama color palette
+ * The first continuous color palette:
+   * GSEA GenePattern color palette

R/continuous.01.gsea.R

@@ -0,0 +1,127 @@
+#' The GSEA GenePattern Color Palettes
+#'
+#' Color palette inspired by the colors used in the
+#' heatmaps plotted by GSEA GenePattern.
+#'
+#' @param palette Palette type.
+#' Currently there is one available option: \code{"default"}
+#' (continuous palette with 12 base colors).
+#' @param n Number of individual colors to be generated.
+#' @param alpha Transparency level, a real number in (0, 1].
+#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
+#' @param reverse Logical. Should the order of the colors be reversed?
+#'
+#' @export rgb_gsea
+#'
+#' @importFrom grDevices colorRamp rgb
+#' @importFrom scales manual_pal
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{http://nanx.me}{http://nanx.me}>
+#'
+#' @note The 12 base colors used in this palette are derived from
+#' \href{ftp://ftp.broad.mit.edu/pub/genepattern/modules/HeatMapImage/broad.mit.edu:cancer.software.genepattern.module.analysis/00032/6/HeatMapImage.pdf}{this document}.
+#'
+#' @examples
+#' library("scales")
+#' show_col(pal_gsea("default")(12))
+#' show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30))
+rgb_gsea = function (palette = c('default'), n = 12,
+                     alpha = 1, reverse = FALSE) {
+
+  palette = match.arg(palette)
+
+  if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
+
+  raw_cols = ggsci_db$'gsea'[[palette]]
+  func_cols = colorRamp(raw_cols, space = 'Lab', interpolate = 'spline')
+  mat_cols = func_cols(seq(0L, 1L, length.out = n))
+  alpha_cols = rgb(mat_cols[, 1L], mat_cols[, 2L], mat_cols[, 3L],
+                   alpha = alpha * 255L, maxColorValue = 255L)
+
+  if (reverse) alpha_cols = rev(alpha_cols)
+
+  alpha_cols
+
+}
+
+#' The GSEA GenePattern Color Palettes
+#'
+#' Color palette inspired by the colors used in the
+#' heatmaps plotted by GSEA GenePattern.
+#'
+#' @inheritParams rgb_gsea
+#'
+#' @export pal_gsea
+#'
+#' @importFrom scales manual_pal
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{http://nanx.me}{http://nanx.me}>
+#'
+#' @examples
+#' library("scales")
+#' show_col(pal_gsea("default")(12))
+#' show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30))
+pal_gsea = function (palette = c('default'), n = 12,
+                     alpha = 1, reverse = FALSE) {
+
+  palette = match.arg(palette)
+
+  alpha_cols = rgb_gsea(palette, n, alpha, reverse)
+  manual_pal(unname(alpha_cols))
+
+}
+
+#' The GSEA GenePattern Color Scales
+#'
+#' See \code{\link{pal_gsea}} for details.
+#'
+#' @inheritParams pal_gsea
+#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
+#'
+#' @export scale_color_gsea
+#'
+#' @importFrom ggplot2 scale_color_gradientn
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{http://nanx.me}{http://nanx.me}>
+#'
+#' @rdname scale_gsea
+#'
+#' @examples
+#' library("ggplot2")
+#' library("reshape2")
+#' data("mtcars")
+#'
+#' cor = cor(mtcars)
+#' cor_melt = melt(cor)
+#'
+#' ggplot(cor_melt,
+#'        aes(x = Var1, y = Var2, fill = value)) +
+#'   geom_tile(colour = "black", size = 0.3) +
+#'   theme_bw() + scale_fill_gsea()
+scale_color_gsea = function (palette = c('default'),
+                             alpha = 1, reverse = FALSE, ...) {
+
+  palette = match.arg(palette)
+  scale_color_gradientn(colours = rgb_gsea(palette, n = 512, alpha = alpha,
+                                           reverse = reverse), ...)
+
+}
+
+#' @export scale_colour_gsea
+#' @rdname scale_gsea
+scale_colour_gsea = scale_color_gsea
+
+#' @export scale_fill_gsea
+#' @importFrom ggplot2 scale_fill_gradientn
+#' @rdname scale_gsea
+scale_fill_gsea = function (palette = c('default'), alpha = 1,
+                            reverse = FALSE, ...) {
+
+  palette = match.arg(palette)
+  scale_fill_gradientn(colours = rgb_gsea(palette, n = 512, alpha = alpha,
+                                          reverse = reverse), ...)
+
+}

R/01.npg.R → R/discrete.01.npg.R

@@ -60,7 +60,7 @@ pal_npg = function (palette = c('nrc'), alpha = 1) {
 #' ggplot(subset(diamonds, carat >= 2.2),
 #'        aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw() + scale_color_npg()
 #'
 #' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),

R/02.aaas.R → R/discrete.02.aaas.R

@@ -61,7 +61,7 @@ pal_aaas = function (palette = c('default'), alpha = 1) {
 #' ggplot(subset(diamonds, carat >= 2.2),
 #'        aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw() + scale_color_aaas()
 #'
 #' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),

R/03.lancet.R → R/discrete.03.lancet.R

@@ -60,7 +60,7 @@ pal_lancet = function (palette = c('lanonc'), alpha = 1) {
 #' ggplot(subset(diamonds, carat >= 2.2),
 #'        aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw() + scale_color_lancet()
 #'
 #' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),

R/04.jco.R → R/discrete.04.jco.R

@@ -59,7 +59,7 @@ pal_jco = function (palette = c('default'), alpha = 1) {
 #' ggplot(subset(diamonds, carat >= 2.2),
 #'        aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw() + scale_color_jco()
 #'
 #' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),

R/05.ucscgb.R → R/discrete.05.ucscgb.R

@@ -59,7 +59,7 @@ pal_ucscgb = function (palette = c('default'), alpha = 1) {
 #' ggplot(subset(diamonds, carat >= 2.2),
 #'        aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw() + scale_color_ucscgb()
 #'
 #' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),

R/discrete.06.d3.R

@@ -0,0 +1,114 @@
+#' D3.js Color Palettes
+#'
+#' Color palettes based on the colors used by D3.js.
+#'
+#' @param palette Palette type.
+#' There are 4 available options:
+#' \code{"category10"} (10-color palette);
+#' \code{"category20"} (20-color palette);
+#' \code{"category20b"} (20-color palette);
+#' \code{"category20c"} (20-color palette).
+#' @param alpha Transparency level, a real number in (0, 1].
+#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
+#'
+#' @export pal_d3
+#'
+#' @importFrom grDevices col2rgb rgb
+#' @importFrom scales manual_pal
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{http://nanx.me}{http://nanx.me}>
+#'
+#' @references \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md}
+#'
+#' @examples
+#' library("scales")
+#' show_col(pal_d3("category10")(10))
+#' show_col(pal_d3("category20")(20))
+#' show_col(pal_d3("category20b")(20))
+#' show_col(pal_d3("category20c")(20))
+pal_d3 = function (palette = c('category10', 'category20',
+                               'category20b', 'category20c'), alpha = 1) {
+
+  palette = match.arg(palette)
+
+  if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
+
+  raw_cols = ggsci_db$'d3'[[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))
+
+}
+
+#' D3.js Color Scales
+#'
+#' See \code{\link{pal_d3}} for details.
+#'
+#' @inheritParams pal_d3
+#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
+#'
+#' @export scale_color_d3
+#'
+#' @importFrom ggplot2 discrete_scale
+#'
+#' @author Nan Xiao <\email{me@@nanx.me}> |
+#' <\href{http://nanx.me}{http://nanx.me}>
+#'
+#' @references \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md}
+#'
+#' @rdname scale_d3
+#'
+#' @examples
+#' library("ggplot2")
+#' data("diamonds")
+#'
+#' p1 = 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()
+#'
+#' p2 = 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()
+#'
+#' p1 + scale_color_d3()
+#' p2 + scale_fill_d3()
+#'
+#' p1 + scale_color_d3(palette = "category20")
+#' p2 + scale_fill_d3(palette = "category20")
+#'
+#' p1 + scale_color_d3(palette = "category20b")
+#' p2 + scale_fill_d3(palette = "category20b")
+#'
+#' p1 + scale_color_d3(palette = "category20c")
+#' p2 + scale_fill_d3(palette = "category20c")
+scale_color_d3 = function (palette = c('category10', 'category20',
+                                       'category20b', 'category20c'),
+                           alpha = 1, ...) {
+
+  palette = match.arg(palette)
+  discrete_scale('colour', 'd3', pal_d3(palette, alpha), ...)
+
+}
+
+#' @export scale_colour_d3
+#' @rdname scale_d3
+scale_colour_d3 = scale_color_d3
+
+#' @export scale_fill_d3
+#' @importFrom ggplot2 discrete_scale
+#' @rdname scale_d3
+scale_fill_d3 = function (palette = c('category10', 'category20',
+                                      'category20b', 'category20c'),
+                          alpha = 1, ...) {
+
+  palette = match.arg(palette)
+  discrete_scale('fill', 'd3', pal_d3(palette, alpha), ...)
+
+}

R/06.uchicago.R → R/discrete.07.uchicago.R

@@ -66,7 +66,7 @@ pal_uchicago = function (palette = c('default', 'light', 'dark'), alpha = 1) {
 #' p1 = ggplot(subset(diamonds, carat >= 2.2),
 #'             aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw()
 #'
 #' p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),

R/07.simpsons.R → R/discrete.08.simpsons.R

@@ -59,7 +59,7 @@ pal_simpsons = function (palette = c('springfield'), alpha = 1) {
 #' ggplot(subset(diamonds, carat >= 2.2),
 #'        aes(x = table, y = price, colour = cut)) +
 #'   geom_point(alpha = 0.7) +
-#'   geom_smooth(alpha = 0.1, size = 1, span = 1) +
+#'   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
 #'   theme_bw() + scale_color_simpsons()
 #'
 #' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),