diff --git a/DESCRIPTION b/DESCRIPTION index 5bb4c75..41c2015 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,3 +31,4 @@ Suggests: VignetteBuilder: knitr Encoding: UTF-8 RoxygenNote: 7.3.1 +Roxygen: list(markdown = TRUE) diff --git a/R/continuous-gsea.R b/R/continuous-gsea.R index 5cf6640..446b639 100644 --- a/R/continuous-gsea.R +++ b/R/continuous-gsea.R @@ -1,14 +1,14 @@ -#' The GSEA GenePattern Color Palettes +#' 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). +#' Currently there is one available option: `"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. +#' See `alpha` in [grDevices::rgb()] for details. #' @param reverse Logical. Should the order of the colors be reversed? #' #' @export rgb_gsea @@ -16,11 +16,10 @@ #' @importFrom grDevices colorRamp rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @note The 12 base colors used in this palette are derived from the -#' \href{https://modulerepository.genepattern.org/gpModuleRepository/download/prod/module/?file=/HeatMapImage/broad.mit.edu:cancer.software.genepattern.module.analysis/00032/6/HeatMapImage.pdf}{HeatMapImage documentation}. +#' [HeatMapImage documentation](https://modulerepository.genepattern.org/gpModuleRepository/download/prod/module/?file=/HeatMapImage/broad.mit.edu:cancer.software.genepattern.module.analysis/00032/6/HeatMapImage.pdf). #' #' @examples #' library("scales") @@ -44,7 +43,7 @@ rgb_gsea <- function(palette = c("default"), n = 12, alpha = 1, reverse = FALSE) alpha_cols } -#' The GSEA GenePattern Color Palettes +#' The GSEA GenePattern color palettes #' #' Color palette inspired by the colors used in the #' heatmaps plotted by GSEA GenePattern. @@ -55,8 +54,7 @@ rgb_gsea <- function(palette = c("default"), n = 12, alpha = 1, reverse = FALSE) #' #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -68,19 +66,18 @@ pal_gsea <- function(palette = c("default"), n = 12, alpha = 1, reverse = FALSE) manual_pal(unname(alpha_cols)) } -#' The GSEA GenePattern Color Scales +#' The GSEA GenePattern color scales #' -#' See \code{\link{pal_gsea}} for details. +#' See [pal_gsea()] for details. #' #' @inheritParams pal_gsea -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_gsea #' #' @importFrom ggplot2 scale_color_gradientn #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_gsea #' diff --git a/R/continuous-material.R b/R/continuous-material.R index 7557e4c..bc8dab7 100644 --- a/R/continuous-material.R +++ b/R/continuous-material.R @@ -1,34 +1,34 @@ -#' Material Design Color Palettes -#' -#' The Material Design color palettes. -#' -#' @param palette Palette type. -#' There are 19 available options: -#' \itemize{ -#' \item \code{"red"} -#' \item \code{"pink"} -#' \item \code{"purple"} -#' \item \code{"deep-purple"} -#' \item \code{"indigo"} -#' \item \code{"blue"} -#' \item \code{"light-blue"} -#' \item \code{"cyan"} -#' \item \code{"teal"} -#' \item \code{"green"} -#' \item \code{"light-green"} -#' \item \code{"lime"} -#' \item \code{"yellow"} -#' \item \code{"amber"} -#' \item \code{"orange"}, -#' \item \code{"deep-orange"} -#' \item \code{"brown"} -#' \item \code{"grey"} -#' \item \code{"blue-grey"}} -#' See \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system} -#' for details. +#' Material Design color palettes +#' +#' The Material Design 2 color palettes. +#' +#' @param palette Palette type. There are 19 available options: +#' - `"red"` +#' - `"pink"` +#' - `"purple"` +#' - `"deep-purple"` +#' - `"indigo"` +#' - `"blue"` +#' - `"light-blue"` +#' - `"cyan"` +#' - `"teal"` +#' - `"green"` +#' - `"light-green"` +#' - `"lime"` +#' - `"yellow"` +#' - `"amber"` +#' - `"orange"`, +#' - `"deep-orange"` +#' - `"brown"` +#' - `"grey"` +#' - `"blue-grey"` +#' +#' For details, see [Material Design color +#' system](https://m2.material.io/design/color/the-color-system.html). +#' #' @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. +#' See `alpha` in [grDevices::rgb()] for details. #' @param reverse Logical. Should the order of the colors be reversed? #' #' @export rgb_material @@ -36,11 +36,10 @@ #' @importFrom grDevices colorRamp rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @references -#' \url{https://m2.material.io/design/color/the-color-system.html} +#' #' #' @examples #' library("scales") @@ -69,9 +68,9 @@ rgb_material <- function( alpha_cols } -#' Material Design Color Palettes +#' Material Design color palettes #' -#' The Material Design color palettes. +#' The Material Design 2 color palettes. #' #' @inheritParams rgb_material #' @@ -79,8 +78,7 @@ rgb_material <- function( #' #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -98,19 +96,18 @@ pal_material <- function( manual_pal(unname(alpha_cols)) } -#' Material Design Color Palettes +#' Material Design color palettes #' -#' See \code{\link{pal_material}} for details. +#' See [pal_material()] for details. #' #' @inheritParams pal_material -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_material #' #' @importFrom ggplot2 scale_color_gradientn #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_material #' diff --git a/R/discrete-aaas.R b/R/discrete-aaas.R index 14e4979..98e0dc0 100644 --- a/R/discrete-aaas.R +++ b/R/discrete-aaas.R @@ -1,22 +1,21 @@ -#' AAAS Journal Color Palettes +#' AAAS journal color palettes #' #' Color palettes inspired by plots in journals published by #' American Association for the Advancement of Science (AAAS), -#' such as \emph{Science} and \emph{Science Translational Medicine}. +#' such as _Science_ and _Science Translational Medicine_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (10-color palette inspired by \emph{Science}). +#' Currently there is one available option: `"default"` +#' (10-color palette inspired by _Science_). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_aaas #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -38,19 +37,18 @@ pal_aaas <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' AAAS Journal Color Scales +#' AAAS journal color scales #' -#' See \code{\link{pal_aaas}} for details. +#' See [pal_aaas()] for details. #' #' @inheritParams pal_aaas -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_aaas #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_aaas #' diff --git a/R/discrete-bmj.R b/R/discrete-bmj.R index 38d53c3..0673378 100644 --- a/R/discrete-bmj.R +++ b/R/discrete-bmj.R @@ -1,19 +1,22 @@ -#' BMJ Color Palettes +#' BMJ color palettes #' #' Color palette from the BMJ living style guide. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (9-color palette). +#' Currently there is one available option: `"default"` +#' (9-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_bmj #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Hui Chen <\email{huichen@@zju.edu.cn}> +#' @author Hui Chen | \email{huichen@zju.edu.cn} +#' +#' @references +#' #' #' @examples #' library("scales") @@ -35,21 +38,24 @@ pal_bmj <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' BMJ Color Scales +#' BMJ color scales #' -#' See \code{\link{pal_bmj}} for details. +#' See [pal_bmj()] for details. #' #' @inheritParams pal_bmj -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_bmj #' #' @importFrom ggplot2 discrete_scale #' -#' @author Hui Chen <\email{huichen@@zju.edu.cn}> +#' @author Hui Chen | \email{huichen@zju.edu.cn} #' #' @rdname scale_bmj #' +#' @references +#' +#' #' @examples #' library("ggplot2") #' data("diamonds") diff --git a/R/discrete-cosmic.R b/R/discrete-cosmic.R index f2ca97e..d8c048e 100644 --- a/R/discrete-cosmic.R +++ b/R/discrete-cosmic.R @@ -1,25 +1,26 @@ -#' COSMIC Color Palettes +#' COSMIC color palettes #' #' Color palettes inspired by the colors used in projects from the -#' \href{https://cancer.sanger.ac.uk/cosmic}{Catalogue Of -#' Somatic Mutations in Cancers (COSMIC)} +#' [Catalogue Of +#' Somatic Mutations in Cancers (COSMIC)](https://cancer.sanger.ac.uk/cosmic). #' #' @param palette Palette type. Currently there are three available options: -#' \code{"signature_substitutions"} (6-color palette), -#' \code{"hallmarks_light"} (10-color palette), and \code{"hallmarks_dark"} -#' (10-color palette). The \code{"hallmarks_light"} option is from -#' \href{https://pubmed.ncbi.nlm.nih.gov/21376230/}{Hanahan and Weinberg (2011)}. +#' - `"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 \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' 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}> | -#' <\href{https://github.com/jhrcook}{GitHub/jhrcook}> +#' @author Joshua H. Cook | \email{joshuacook0023@gmail.com} | +#' [@jhrcook](https://github.com/jhrcook) #' #' @examples #' library("scales") @@ -47,19 +48,19 @@ pal_cosmic <- function( manual_pal(unname(alpha_cols)) } -#' COSMIC Color Scales +#' COSMIC color scales #' -#' See \code{\link{pal_cosmic}} for details. +#' See [pal_cosmic()] for details. #' #' @inheritParams pal_cosmic -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_cosmic #' #' @importFrom ggplot2 discrete_scale #' -#' @author Joshua H. Cook <\email{joshuacook0023@@gmail.com}> | -#' <\href{https://github.com/jhrcook}{GitHub/jhrcook}> +#' @author Joshua H. Cook | \email{joshuacook0023@gmail.com} | +#' [@jhrcook](https://github.com/jhrcook) #' #' @rdname scale_cosmic #' diff --git a/R/discrete-d3.R b/R/discrete-d3.R index 9478115..e5bee25 100644 --- a/R/discrete-d3.R +++ b/R/discrete-d3.R @@ -1,25 +1,24 @@ -#' D3.js Color Palettes +#' 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 palette Palette type. There are four available options: +#' - `"category10"` (10-color palette). +#' - `"category20"` (20-color palette). +#' - `"category20b"` (20-color palette). +#' - `"category20c"` (20-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_d3 #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' -#' @references \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md} +#' @references +#' #' #' @examples #' library("scales") @@ -43,21 +42,21 @@ pal_d3 <- function(palette = c("category10", "category20", "category20b", "categ manual_pal(unname(alpha_cols)) } -#' D3.js Color Scales +#' D3.js color scales #' -#' See \code{\link{pal_d3}} for details. +#' See [pal_d3()] for details. #' #' @inheritParams pal_d3 -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_d3 #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' -#' @references \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md} +#' @references +#' #' #' @rdname scale_d3 #' diff --git a/R/discrete-flatui.R b/R/discrete-flatui.R index f41d464..9c5c2d5 100644 --- a/R/discrete-flatui.R +++ b/R/discrete-flatui.R @@ -1,21 +1,20 @@ -#' Flat UI Color Palettes +#' Flat UI color palettes #' -#' Color palettes inspired by the colors used in \emph{Flat UI Colors}. +#' Color palettes inspired by the Flat UI colors. #' -#' @param palette Palette type. -#' Currently there are three available option: -#' \code{"default"} (10-color palette). -#' \code{"flattastic"} (12-color palette). -#' \code{"aussie"} (10-color palette). +#' @param palette Palette type. Currently there are three available options: +#' - `"default"` (10-color palette). +#' - `"flattastic"` (12-color palette). +#' - `"aussie"` (10-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_flatui #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Clara Jégousse <\email{cat3@@hi.is}> +#' @author Clara Jégousse | \email{cat3@hi.is} #' #' @examples #' library("scales") @@ -39,18 +38,18 @@ pal_flatui <- function(palette = c("default", "flattastic", "aussie"), alpha = 1 manual_pal(unname(alpha_cols)) } -#' Flat UI Color Scales +#' Flat UI color scales #' -#' See \code{\link{pal_flatui}} for details. +#' See [pal_flatui()] for details. #' #' @inheritParams pal_flatui -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_flatui #' #' @importFrom ggplot2 discrete_scale #' -#' @author Clara Jégousse <\email{cat3@@hi.is}> +#' @author Clara Jégousse | \email{cat3@hi.is} #' #' @rdname scale_flatui #' diff --git a/R/discrete-frontiers.R b/R/discrete-frontiers.R index ff328a5..7128840 100644 --- a/R/discrete-frontiers.R +++ b/R/discrete-frontiers.R @@ -1,19 +1,19 @@ -#' Frontiers Color Palettes +#' Frontiers journal color palettes #' -#' Color palettes inspired by the colors used in \emph{Frontiers}. +#' Color palettes inspired by the colors used in _Frontiers_ journals. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (10-color palette). +#' Currently there is one available option: `"default"` +#' (10-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_frontiers #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Clara Jégousse <\email{cat3@@hi.is}> +#' @author Clara Jégousse | \email{cat3@hi.is} #' #' @examples #' library("scales") @@ -35,18 +35,18 @@ pal_frontiers <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Frontiers Color Scales +#' Frontiers journal color scales #' -#' See \code{\link{pal_frontiers}} for details. +#' See [pal_frontiers()] for details. #' #' @inheritParams pal_frontiers -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_frontiers #' #' @importFrom ggplot2 discrete_scale #' -#' @author Clara Jégousse <\email{cat3@@hi.is}> +#' @author Clara Jégousse | \email{cat3@hi.is} #' #' @rdname scale_frontiers #' diff --git a/R/discrete-futurama.R b/R/discrete-futurama.R index ab85aa4..6f6b1c9 100644 --- a/R/discrete-futurama.R +++ b/R/discrete-futurama.R @@ -1,20 +1,19 @@ -#' The Futurama Color Palettes +#' Futurama color palettes #' -#' Color palettes inspired by the colors used in \emph{Futurama}. +#' Color palettes inspired by the colors used in _Futurama_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"planetexpress"} -#' (12-color palette). +#' Currently there is one available option: `"planetexpress"` +#' (12-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_futurama #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_futurama <- function(palette = c("planetexpress"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' The Futurama Color Scales +#' Futurama color scales #' -#' See \code{\link{pal_futurama}} for details. +#' See [pal_futurama()] for details. #' #' @inheritParams pal_futurama -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_futurama #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_futurama #' diff --git a/R/discrete-igv.R b/R/discrete-igv.R index ad70b2e..8923bb3 100644 --- a/R/discrete-igv.R +++ b/R/discrete-igv.R @@ -1,27 +1,26 @@ -#' Integrative Genomics Viewer (IGV) Color Palettes +#' Integrative Genomics Viewer (IGV) color palettes #' #' Color palettes based on the colors used by #' Integrative Genomics Viewer (IGV). #' #' @param palette Palette type. -#' There are two available options: -#' \code{"default"} (51-color palette); -#' \code{"alternating"} (2-color palette). +#' There are two available options: +#' - `"default"` (51-color palette). +#' - `"alternating"` (2-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_igv #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @references #' James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, #' Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. -#' Integrative Genomics Viewer. \emph{Nature Biotechnology} 29, 24--26 (2011). +#' Integrative Genomics Viewer. _Nature Biotechnology_ 29, 24--26 (2011). #' #' @examples #' library("scales") @@ -43,19 +42,18 @@ pal_igv <- function(palette = c("default", "alternating"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Integrative Genomics Viewer (IGV) Color Scales +#' Integrative Genomics Viewer (IGV) color scales #' -#' See \code{\link{pal_igv}} for details. +#' See [pal_igv()] for details. #' #' @inheritParams pal_igv -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_igv #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_igv #' diff --git a/R/discrete-jama.R b/R/discrete-jama.R index 0d32bec..b194515 100644 --- a/R/discrete-jama.R +++ b/R/discrete-jama.R @@ -1,21 +1,20 @@ -#' Journal of the American Medical Association Color Palettes +#' Journal of the American Medical Association color palettes #' #' Color palette inspired by plots in -#' \emph{The Journal of the American Medical Association}. +#' _The Journal of the American Medical Association_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (7-color palette). +#' Currently there is one available option: `"default"` +#' (7-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_jama #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -37,19 +36,18 @@ pal_jama <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Journal of the American Medical Association Color Scales +#' Journal of the American Medical Association color scales #' -#' See \code{\link{pal_jama}} for details. +#' See [pal_jama()] for details. #' #' @inheritParams pal_jama -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_jama #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_jama #' diff --git a/R/discrete-jco.R b/R/discrete-jco.R index 0246c06..e45474b 100644 --- a/R/discrete-jco.R +++ b/R/discrete-jco.R @@ -1,20 +1,19 @@ -#' Journal of Clinical Oncology Color Palettes +#' Journal of Clinical Oncology color palettes #' -#' Color palette inspired by plots in \emph{Journal of Clinical Oncology}. +#' Color palette inspired by plots in _Journal of Clinical Oncology_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (10-color palette). +#' Currently there is one available option: `"default"` +#' (10-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_jco #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_jco <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Journal of Clinical Oncology Color Scales +#' Journal of Clinical Oncology color scales #' -#' See \code{\link{pal_jco}} for details. +#' See [pal_jco()] for details. #' #' @inheritParams pal_jco -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_jco #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_jco #' diff --git a/R/discrete-lancet.R b/R/discrete-lancet.R index 48a909d..b0e62ad 100644 --- a/R/discrete-lancet.R +++ b/R/discrete-lancet.R @@ -1,21 +1,20 @@ -#' Lancet Journal Color Palettes +#' Lancet journal color palettes #' #' Color palettes inspired by plots in Lancet journals, -#' such as \emph{Lancet Oncology}. +#' such as _Lancet Oncology_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"lanonc"} -#' (9-color palette inspired by \emph{Lancet Oncology}). +#' Currently there is one available option: `"lanonc"` +#' (9-color palette inspired by _Lancet Oncology_). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_lancet #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -37,19 +36,18 @@ pal_lancet <- function(palette = c("lanonc"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Lancet Journal Color Scales +#' Lancet journal color scales #' -#' See \code{\link{pal_lancet}} for details. +#' See [pal_lancet()] for details. #' #' @inheritParams pal_lancet -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_lancet #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_lancet #' diff --git a/R/discrete-locuszoom.R b/R/discrete-locuszoom.R index 3178517..54485e8 100644 --- a/R/discrete-locuszoom.R +++ b/R/discrete-locuszoom.R @@ -1,24 +1,23 @@ -#' LocusZoom Color Palette +#' LocusZoom color palette #' #' Color palettes based on the colors used by LocusZoom. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (7-color palette). +#' Currently there is one available option: `"default"` +#' (7-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_locuszoom #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @references #' Pruim, Randall J., et al. (2010). LocusZoom: regional visualization of -#' genome-wide association scan results. \emph{Bioinformatics}, +#' genome-wide association scan results. _Bioinformatics_, #' 26(18), 2336--2337. #' #' @examples @@ -41,19 +40,18 @@ pal_locuszoom <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' LocusZoom Color Scales +#' LocusZoom color scales #' -#' See \code{\link{pal_locuszoom}} for details. +#' See [pal_locuszoom()] for details. #' #' @inheritParams pal_locuszoom -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_locuszoom #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_locuszoom #' diff --git a/R/discrete-nejm.R b/R/discrete-nejm.R index 79191e3..56ac48b 100644 --- a/R/discrete-nejm.R +++ b/R/discrete-nejm.R @@ -1,21 +1,20 @@ -#' NEJM Color Palettes +#' NEJM color palettes #' #' Color palette inspired by plots in -#' \emph{The New England Journal of Medicine}. +#' _The New England Journal of Medicine_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (8-color palette). +#' Currently there is one available option: `"default"` +#' (8-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_nejm #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -37,19 +36,18 @@ pal_nejm <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' NEJM Color Scales +#' NEJM color scales #' -#' See \code{\link{pal_nejm}} for details. +#' See [pal_nejm()] for details. #' #' @inheritParams pal_nejm -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_nejm #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_nejm #' diff --git a/R/discrete-npg.R b/R/discrete-npg.R index 0d28077..dd2ecd7 100644 --- a/R/discrete-npg.R +++ b/R/discrete-npg.R @@ -1,21 +1,20 @@ -#' NPG Journal Color Palettes +#' NPG journal color palettes #' #' Color palettes inspired by plots in journals published by -#' Nature Publishing Group, such as \emph{Nature Reviews Cancer}. +#' Nature Publishing Group, such as _Nature Reviews Cancer_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"nrc"} -#' (10-color palette inspired by \emph{Nature Reviews Cancer}). +#' Currently there is one available option: `"nrc"` +#' (10-color palette inspired by _Nature Reviews Cancer_). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_npg #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -37,19 +36,18 @@ pal_npg <- function(palette = c("nrc"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' NPG Journal Color Scales +#' NPG journal color scales #' -#' See \code{\link{pal_npg}} for details. +#' See [pal_npg()] for details. #' #' @inheritParams pal_npg -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_npg #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_npg #' diff --git a/R/discrete-rickandmorty.R b/R/discrete-rickandmorty.R index 157e8c6..bf44858 100644 --- a/R/discrete-rickandmorty.R +++ b/R/discrete-rickandmorty.R @@ -1,20 +1,19 @@ -#' Rick and Morty Color Palettes +#' Rick and Morty color palettes #' -#' Color palettes inspired by the colors used in \emph{Rick and Morty}. +#' Color palettes inspired by the colors used in _Rick and Morty_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"schwifty"} -#' (12-color palette). +#' Currently there is one available option: `"schwifty"` +#' (12-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_rickandmorty #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_rickandmorty <- function(palette = c("schwifty"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Rick and Morty Color Scales +#' Rick and Morty color scales #' -#' See \code{\link{pal_rickandmorty}} for details. +#' See [pal_rickandmorty()] for details. #' #' @inheritParams pal_rickandmorty -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_rickandmorty #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_rickandmorty #' diff --git a/R/discrete-simpsons.R b/R/discrete-simpsons.R index a92316d..516ed98 100644 --- a/R/discrete-simpsons.R +++ b/R/discrete-simpsons.R @@ -1,20 +1,19 @@ -#' The Simpsons Color Palettes +#' The Simpsons color palettes #' -#' Color palettes inspired by the colors used in \emph{The Simpsons}. +#' Color palettes inspired by the colors used in _The Simpsons_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"springfield"} -#' (16-color palette). +#' Currently there is one available option: `"springfield"` +#' (16-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_simpsons #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_simpsons <- function(palette = c("springfield"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' The Simpsons Color Scales +#' The Simpsons color scales #' -#' See \code{\link{pal_simpsons}} for details. +#' See [pal_simpsons()] for details. #' #' @inheritParams pal_simpsons -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_simpsons #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_simpsons #' diff --git a/R/discrete-startrek.R b/R/discrete-startrek.R index 2b53a86..fc6d183 100644 --- a/R/discrete-startrek.R +++ b/R/discrete-startrek.R @@ -1,20 +1,19 @@ -#' Star Trek Color Palettes +#' Star Trek color palettes #' -#' Color palettes inspired by the colors used in \emph{Star Trek}. +#' Color palettes inspired by the colors used in _Star Trek_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"uniform"} -#' (7-color palette). +#' Currently there is one available option: `"uniform"` +#' (7-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_startrek #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_startrek <- function(palette = c("uniform"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Star Trek Color Scales +#' Star Trek color scales #' -#' See \code{\link{pal_startrek}} for details. +#' See [pal_startrek()] for details. #' #' @inheritParams pal_startrek -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_startrek #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_startrek #' diff --git a/R/discrete-tron.R b/R/discrete-tron.R index cfb0cbd..746084e 100644 --- a/R/discrete-tron.R +++ b/R/discrete-tron.R @@ -1,20 +1,19 @@ -#' Tron Legacy Color Palettes +#' Tron Legacy color palettes #' -#' Color palettes inspired by the colors used in \emph{Tron Legacy}. +#' Color palettes inspired by the colors used in _Tron Legacy_. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"legacy"} -#' (7-color palette). +#' Currently there is one available option: `"legacy"` +#' (7-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_tron #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_tron <- function(palette = c("legacy"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' Tron Legacy Color Scales +#' Tron Legacy color scales #' -#' See \code{\link{pal_tron}} for details. +#' See [pal_tron()] for details. #' #' @inheritParams pal_tron -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_tron #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_tron #' diff --git a/R/discrete-uchicago.R b/R/discrete-uchicago.R index ac360e0..2e998c4 100644 --- a/R/discrete-uchicago.R +++ b/R/discrete-uchicago.R @@ -1,24 +1,24 @@ -#' The University of Chicago Color Palettes +#' The University of Chicago color palettes #' #' Color palettes based on the colors used by the University of Chicago. #' #' @param palette Palette type. -#' There are 3 available options: -#' \code{"default"} (9-color palette); -#' \code{"light"} (9-color light palette); -#' \code{"dark"} (9-color dark palette). +#' There are three available options: +#' - `"default"` (9-color palette); +#' - `"light"` (9-color light palette); +#' - `"dark"` (9-color dark palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_uchicago #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' -#' @references \url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf} +#' @references +#' #' #' @examples #' library("scales") @@ -41,21 +41,21 @@ pal_uchicago <- function(palette = c("default", "light", "dark"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' The University of Chicago Color Scales +#' The University of Chicago color scales #' -#' See \code{\link{pal_uchicago}} for details. +#' See [pal_uchicago()] for details. #' #' @inheritParams pal_uchicago -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_uchicago #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' -#' @references \url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf} +#' @references +#' #' #' @rdname scale_uchicago #' diff --git a/R/discrete-ucscgb.R b/R/discrete-ucscgb.R index 50352e9..9f4fae2 100644 --- a/R/discrete-ucscgb.R +++ b/R/discrete-ucscgb.R @@ -1,20 +1,19 @@ -#' UCSC Genome Browser Color Palette +#' UCSC Genome Browser color palette #' #' Color palette from UCSC Genome Browser chromosome colors. #' #' @param palette Palette type. -#' Currently there is one available option: \code{"default"} -#' (26-color palette). +#' Currently there is one available option: `"default"` +#' (26-color palette). #' @param alpha Transparency level, a real number in (0, 1]. -#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details. +#' See `alpha` in [grDevices::rgb()] for details. #' #' @export pal_ucscgb #' #' @importFrom grDevices col2rgb rgb #' @importFrom scales manual_pal #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @examples #' library("scales") @@ -36,19 +35,18 @@ pal_ucscgb <- function(palette = c("default"), alpha = 1) { manual_pal(unname(alpha_cols)) } -#' UCSC Genome Browser Color Scales +#' UCSC Genome Browser color scales #' -#' See \code{\link{pal_ucscgb}} for details. +#' See [pal_ucscgb()] for details. #' #' @inheritParams pal_ucscgb -#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}} +#' @param ... Additional parameters for [ggplot2::discrete_scale()]. #' #' @export scale_color_ucscgb #' #' @importFrom ggplot2 discrete_scale #' -#' @author Nan Xiao <\email{me@@nanx.me}> | -#' <\href{https://nanx.me}{https://nanx.me}> +#' @author Nan Xiao | \email{me@nanx.me} | #' #' @rdname scale_ucscgb #' diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 0000000..ad94f45 --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,44 @@ +AAAS +BMJ +Bioinformatics +CMD +Catalogue +Circos +ColorBrewer +Fi +Futurama +GSEA +GenePattern +Getz +Guttman +Hanahan +HeatMapImage +IGV +JAMA +JCO +LocusZoom +Mesirov +Morty +NEJM +NPG +ORCID +Pruim +RStudio +SSL +Schwifty +Thorvaldsdóttir +Translational +UCSC +UCSCGB +UChicago +UI +Winckler +al +et +ggplot +jhrcook +js +pandoc +pngquant +ragg +viridis diff --git a/man/pal_aaas.Rd b/man/pal_aaas.Rd index 1e73546..33bc3e3 100644 --- a/man/pal_aaas.Rd +++ b/man/pal_aaas.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-aaas.R \name{pal_aaas} \alias{pal_aaas} -\title{AAAS Journal Color Palettes} +\title{AAAS journal color palettes} \usage{ pal_aaas(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (10-color palette inspired by \emph{Science}).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by plots in journals published by @@ -25,6 +25,5 @@ show_col(pal_aaas("default")(10)) show_col(pal_aaas("default", alpha = 0.6)(10)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_bmj.Rd b/man/pal_bmj.Rd index 599dc8c..0e64622 100644 --- a/man/pal_bmj.Rd +++ b/man/pal_bmj.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-bmj.R \name{pal_bmj} \alias{pal_bmj} -\title{BMJ Color Palettes} +\title{BMJ color palettes} \usage{ pal_bmj(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (9-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palette from the BMJ living style guide. @@ -22,6 +22,9 @@ library("scales") show_col(pal_bmj("default")(9)) show_col(pal_bmj("default", alpha = 0.6)(9)) } +\references{ +\url{https://technology.bmj.com/living-style-guide/colour.html} +} \author{ -Hui Chen <\email{huichen@zju.edu.cn}> +Hui Chen | \email{huichen@zju.edu.cn} } diff --git a/man/pal_cosmic.Rd b/man/pal_cosmic.Rd index 57e7ad0..807bc75 100644 --- a/man/pal_cosmic.Rd +++ b/man/pal_cosmic.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-cosmic.R \name{pal_cosmic} \alias{pal_cosmic} -\title{COSMIC Color Palettes} +\title{COSMIC color palettes} \usage{ pal_cosmic( palette = c("hallmarks_light", "hallmarks_dark", "signature_substitutions"), @@ -11,18 +11,21 @@ pal_cosmic( } \arguments{ \item{palette}{Palette type. Currently there are three available options: -\code{"signature_substitutions"} (6-color palette), -\code{"hallmarks_light"} (10-color palette), and \code{"hallmarks_dark"} -(10-color palette). The \code{"hallmarks_light"} option is from +\itemize{ +\item \code{"signature_substitutions"} (6-color palette). +\item \code{"hallmarks_light"} (10-color palette). +\item \code{"hallmarks_dark"} (10-color palette). +} + +The \code{"hallmarks_light"} option is from \href{https://pubmed.ncbi.nlm.nih.gov/21376230/}{Hanahan and Weinberg (2011)}.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by the colors used in projects from the -\href{https://cancer.sanger.ac.uk/cosmic}{Catalogue Of -Somatic Mutations in Cancers (COSMIC)} +\href{https://cancer.sanger.ac.uk/cosmic}{Catalogue Of Somatic Mutations in Cancers (COSMIC)}. } \examples{ library("scales") @@ -34,6 +37,6 @@ show_col(pal_cosmic("signature_substitutions")(6)) show_col(pal_cosmic("signature_substitutions", alpha = 0.6)(6)) } \author{ -Joshua H. Cook <\email{joshuacook0023@gmail.com}> | -<\href{https://github.com/jhrcook}{GitHub/jhrcook}> +Joshua H. Cook | \email{joshuacook0023@gmail.com} | +\href{https://github.com/jhrcook}{@jhrcook} } diff --git a/man/pal_d3.Rd b/man/pal_d3.Rd index 7a308d2..c39ccb6 100644 --- a/man/pal_d3.Rd +++ b/man/pal_d3.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-d3.R \name{pal_d3} \alias{pal_d3} -\title{D3.js Color Palettes} +\title{D3.js color palettes} \usage{ pal_d3( palette = c("category10", "category20", "category20b", "category20c"), @@ -10,15 +10,16 @@ pal_d3( ) } \arguments{ -\item{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).} +\item{palette}{Palette type. There are four available options: +\itemize{ +\item \code{"category10"} (10-color palette). +\item \code{"category20"} (20-color palette). +\item \code{"category20b"} (20-color palette). +\item \code{"category20c"} (20-color palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes based on the colors used by D3.js. @@ -34,6 +35,5 @@ show_col(pal_d3("category20c")(20)) \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md} } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_flatui.Rd b/man/pal_flatui.Rd index 0fbae24..5e7a8d4 100644 --- a/man/pal_flatui.Rd +++ b/man/pal_flatui.Rd @@ -2,22 +2,23 @@ % Please edit documentation in R/discrete-flatui.R \name{pal_flatui} \alias{pal_flatui} -\title{Flat UI Color Palettes} +\title{Flat UI color palettes} \usage{ pal_flatui(palette = c("default", "flattastic", "aussie"), alpha = 1) } \arguments{ -\item{palette}{Palette type. -Currently there are three available option: -\code{"default"} (10-color palette). -\code{"flattastic"} (12-color palette). -\code{"aussie"} (10-color palette).} +\item{palette}{Palette type. Currently there are three available options: +\itemize{ +\item \code{"default"} (10-color palette). +\item \code{"flattastic"} (12-color palette). +\item \code{"aussie"} (10-color palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ -Color palettes inspired by the colors used in \emph{Flat UI Colors}. +Color palettes inspired by the Flat UI colors. } \examples{ library("scales") @@ -27,5 +28,5 @@ show_col(pal_flatui("aussie")(10)) show_col(pal_flatui("aussie", alpha = 0.6)(10)) } \author{ -Clara Jégousse <\email{cat3@hi.is}> +Clara Jégousse | \email{cat3@hi.is} } diff --git a/man/pal_frontiers.Rd b/man/pal_frontiers.Rd index 721cda1..c3e4e7e 100644 --- a/man/pal_frontiers.Rd +++ b/man/pal_frontiers.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-frontiers.R \name{pal_frontiers} \alias{pal_frontiers} -\title{Frontiers Color Palettes} +\title{Frontiers journal color palettes} \usage{ pal_frontiers(palette = c("default"), alpha = 1) } @@ -12,10 +12,10 @@ Currently there is one available option: \code{"default"} (10-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ -Color palettes inspired by the colors used in \emph{Frontiers}. +Color palettes inspired by the colors used in \emph{Frontiers} journals. } \examples{ library("scales") @@ -23,5 +23,5 @@ show_col(pal_frontiers("default")(7)) show_col(pal_frontiers("default", alpha = 0.6)(7)) } \author{ -Clara Jégousse <\email{cat3@hi.is}> +Clara Jégousse | \email{cat3@hi.is} } diff --git a/man/pal_futurama.Rd b/man/pal_futurama.Rd index 71f0604..b1227c3 100644 --- a/man/pal_futurama.Rd +++ b/man/pal_futurama.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-futurama.R \name{pal_futurama} \alias{pal_futurama} -\title{The Futurama Color Palettes} +\title{Futurama color palettes} \usage{ pal_futurama(palette = c("planetexpress"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"planetexpress"} (12-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by the colors used in \emph{Futurama}. @@ -23,6 +23,5 @@ show_col(pal_futurama("planetexpress")(12)) show_col(pal_futurama("planetexpress", alpha = 0.6)(12)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_gsea.Rd b/man/pal_gsea.Rd index 4227bc6..b465480 100644 --- a/man/pal_gsea.Rd +++ b/man/pal_gsea.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/continuous-gsea.R \name{pal_gsea} \alias{pal_gsea} -\title{The GSEA GenePattern Color Palettes} +\title{The GSEA GenePattern color palettes} \usage{ pal_gsea(palette = c("default"), n = 12, alpha = 1, reverse = FALSE) } @@ -14,7 +14,7 @@ Currently there is one available option: \code{"default"} \item{n}{Number of individual colors to be generated.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} \item{reverse}{Logical. Should the order of the colors be reversed?} } @@ -28,6 +28,5 @@ show_col(pal_gsea("default")(12)) show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_igv.Rd b/man/pal_igv.Rd index 376187e..d537e59 100644 --- a/man/pal_igv.Rd +++ b/man/pal_igv.Rd @@ -2,18 +2,20 @@ % Please edit documentation in R/discrete-igv.R \name{pal_igv} \alias{pal_igv} -\title{Integrative Genomics Viewer (IGV) Color Palettes} +\title{Integrative Genomics Viewer (IGV) color palettes} \usage{ pal_igv(palette = c("default", "alternating"), alpha = 1) } \arguments{ \item{palette}{Palette type. There are two available options: -\code{"default"} (51-color palette); -\code{"alternating"} (2-color palette).} +\itemize{ +\item \code{"default"} (51-color palette). +\item \code{"alternating"} (2-color palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes based on the colors used by @@ -30,6 +32,5 @@ Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. \emph{Nature Biotechnology} 29, 24--26 (2011). } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_jama.Rd b/man/pal_jama.Rd index ed04b9b..356d7e7 100644 --- a/man/pal_jama.Rd +++ b/man/pal_jama.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-jama.R \name{pal_jama} \alias{pal_jama} -\title{Journal of the American Medical Association Color Palettes} +\title{Journal of the American Medical Association color palettes} \usage{ pal_jama(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palette inspired by plots in @@ -24,6 +24,5 @@ show_col(pal_jama("default")(7)) show_col(pal_jama("default", alpha = 0.6)(7)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_jco.Rd b/man/pal_jco.Rd index b95e443..1a5dfd0 100644 --- a/man/pal_jco.Rd +++ b/man/pal_jco.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-jco.R \name{pal_jco} \alias{pal_jco} -\title{Journal of Clinical Oncology Color Palettes} +\title{Journal of Clinical Oncology color palettes} \usage{ pal_jco(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (10-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palette inspired by plots in \emph{Journal of Clinical Oncology}. @@ -23,6 +23,5 @@ show_col(pal_jco("default")(10)) show_col(pal_jco("default", alpha = 0.6)(10)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_lancet.Rd b/man/pal_lancet.Rd index 9258f4d..c3f06b9 100644 --- a/man/pal_lancet.Rd +++ b/man/pal_lancet.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-lancet.R \name{pal_lancet} \alias{pal_lancet} -\title{Lancet Journal Color Palettes} +\title{Lancet journal color palettes} \usage{ pal_lancet(palette = c("lanonc"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"lanonc"} (9-color palette inspired by \emph{Lancet Oncology}).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by plots in Lancet journals, @@ -24,6 +24,5 @@ show_col(pal_lancet("lanonc")(9)) show_col(pal_lancet("lanonc", alpha = 0.6)(9)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_locuszoom.Rd b/man/pal_locuszoom.Rd index b435c71..3b9a5ff 100644 --- a/man/pal_locuszoom.Rd +++ b/man/pal_locuszoom.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-locuszoom.R \name{pal_locuszoom} \alias{pal_locuszoom} -\title{LocusZoom Color Palette} +\title{LocusZoom color palette} \usage{ pal_locuszoom(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes based on the colors used by LocusZoom. @@ -28,6 +28,5 @@ genome-wide association scan results. \emph{Bioinformatics}, 26(18), 2336--2337. } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_material.Rd b/man/pal_material.Rd index 3f7dd77..86cbb1d 100644 --- a/man/pal_material.Rd +++ b/man/pal_material.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/continuous-material.R \name{pal_material} \alias{pal_material} -\title{Material Design Color Palettes} +\title{Material Design color palettes} \usage{ pal_material( palette = c("red", "pink", "purple", "deep-purple", "indigo", "blue", "light-blue", @@ -14,8 +14,7 @@ pal_material( ) } \arguments{ -\item{palette}{Palette type. -There are 19 available options: +\item{palette}{Palette type. There are 19 available options: \itemize{ \item \code{"red"} \item \code{"pink"} @@ -35,19 +34,20 @@ There are 19 available options: \item \code{"deep-orange"} \item \code{"brown"} \item \code{"grey"} -\item \code{"blue-grey"}} -See \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system} -for details.} +\item \code{"blue-grey"} +} + +For details, see \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system}.} \item{n}{Number of individual colors to be generated.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} \item{reverse}{Logical. Should the order of the colors be reversed?} } \description{ -The Material Design color palettes. +The Material Design 2 color palettes. } \examples{ library("scales") @@ -55,6 +55,5 @@ show_col(pal_material("indigo")(10)) show_col(pal_material("indigo", n = 30, alpha = 0.6, reverse = TRUE)(30)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_nejm.Rd b/man/pal_nejm.Rd index ddf9c03..d789ab6 100644 --- a/man/pal_nejm.Rd +++ b/man/pal_nejm.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-nejm.R \name{pal_nejm} \alias{pal_nejm} -\title{NEJM Color Palettes} +\title{NEJM color palettes} \usage{ pal_nejm(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (8-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palette inspired by plots in @@ -24,6 +24,5 @@ show_col(pal_nejm("default")(8)) show_col(pal_nejm("default", alpha = 0.6)(8)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_npg.Rd b/man/pal_npg.Rd index 0b62dcc..d162cfe 100644 --- a/man/pal_npg.Rd +++ b/man/pal_npg.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-npg.R \name{pal_npg} \alias{pal_npg} -\title{NPG Journal Color Palettes} +\title{NPG journal color palettes} \usage{ pal_npg(palette = c("nrc"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"nrc"} (10-color palette inspired by \emph{Nature Reviews Cancer}).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by plots in journals published by @@ -24,6 +24,5 @@ show_col(pal_npg("nrc")(10)) show_col(pal_npg("nrc", alpha = 0.6)(10)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_rickandmorty.Rd b/man/pal_rickandmorty.Rd index 7c9994f..a351e5f 100644 --- a/man/pal_rickandmorty.Rd +++ b/man/pal_rickandmorty.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-rickandmorty.R \name{pal_rickandmorty} \alias{pal_rickandmorty} -\title{Rick and Morty Color Palettes} +\title{Rick and Morty color palettes} \usage{ pal_rickandmorty(palette = c("schwifty"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"schwifty"} (12-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by the colors used in \emph{Rick and Morty}. @@ -23,6 +23,5 @@ show_col(pal_rickandmorty("schwifty")(12)) show_col(pal_rickandmorty("schwifty", alpha = 0.6)(12)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_simpsons.Rd b/man/pal_simpsons.Rd index 700ff2a..4bdd990 100644 --- a/man/pal_simpsons.Rd +++ b/man/pal_simpsons.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-simpsons.R \name{pal_simpsons} \alias{pal_simpsons} -\title{The Simpsons Color Palettes} +\title{The Simpsons color palettes} \usage{ pal_simpsons(palette = c("springfield"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"springfield"} (16-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by the colors used in \emph{The Simpsons}. @@ -23,6 +23,5 @@ show_col(pal_simpsons("springfield")(16)) show_col(pal_simpsons("springfield", alpha = 0.6)(16)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_startrek.Rd b/man/pal_startrek.Rd index 9d37a8f..66df8bc 100644 --- a/man/pal_startrek.Rd +++ b/man/pal_startrek.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-startrek.R \name{pal_startrek} \alias{pal_startrek} -\title{Star Trek Color Palettes} +\title{Star Trek color palettes} \usage{ pal_startrek(palette = c("uniform"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"uniform"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by the colors used in \emph{Star Trek}. @@ -23,6 +23,5 @@ show_col(pal_startrek("uniform")(7)) show_col(pal_startrek("uniform", alpha = 0.6)(7)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_tron.Rd b/man/pal_tron.Rd index 0d73704..a26a8ca 100644 --- a/man/pal_tron.Rd +++ b/man/pal_tron.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-tron.R \name{pal_tron} \alias{pal_tron} -\title{Tron Legacy Color Palettes} +\title{Tron Legacy color palettes} \usage{ pal_tron(palette = c("legacy"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"legacy"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes inspired by the colors used in \emph{Tron Legacy}. @@ -23,6 +23,5 @@ show_col(pal_tron("legacy")(7)) show_col(pal_tron("legacy", alpha = 0.6)(7)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_uchicago.Rd b/man/pal_uchicago.Rd index f6f3d5a..50f6aac 100644 --- a/man/pal_uchicago.Rd +++ b/man/pal_uchicago.Rd @@ -2,19 +2,21 @@ % Please edit documentation in R/discrete-uchicago.R \name{pal_uchicago} \alias{pal_uchicago} -\title{The University of Chicago Color Palettes} +\title{The University of Chicago color palettes} \usage{ pal_uchicago(palette = c("default", "light", "dark"), alpha = 1) } \arguments{ \item{palette}{Palette type. -There are 3 available options: -\code{"default"} (9-color palette); -\code{"light"} (9-color light palette); -\code{"dark"} (9-color dark palette).} +There are three available options: +\itemize{ +\item \code{"default"} (9-color palette); +\item \code{"light"} (9-color light palette); +\item \code{"dark"} (9-color dark palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palettes based on the colors used by the University of Chicago. @@ -29,6 +31,5 @@ show_col(pal_uchicago("dark")(9)) \url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf} } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/pal_ucscgb.Rd b/man/pal_ucscgb.Rd index fc8d684..0e7c220 100644 --- a/man/pal_ucscgb.Rd +++ b/man/pal_ucscgb.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/discrete-ucscgb.R \name{pal_ucscgb} \alias{pal_ucscgb} -\title{UCSC Genome Browser Color Palette} +\title{UCSC Genome Browser color palette} \usage{ pal_ucscgb(palette = c("default"), alpha = 1) } @@ -12,7 +12,7 @@ Currently there is one available option: \code{"default"} (26-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} } \description{ Color palette from UCSC Genome Browser chromosome colors. @@ -23,6 +23,5 @@ show_col(pal_ucscgb("default")(26)) show_col(pal_ucscgb("default", alpha = 0.6)(26)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/rgb_gsea.Rd b/man/rgb_gsea.Rd index 3a8fca7..13efc9f 100644 --- a/man/rgb_gsea.Rd +++ b/man/rgb_gsea.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/continuous-gsea.R \name{rgb_gsea} \alias{rgb_gsea} -\title{The GSEA GenePattern Color Palettes} +\title{The GSEA GenePattern color palettes} \usage{ rgb_gsea(palette = c("default"), n = 12, alpha = 1, reverse = FALSE) } @@ -14,7 +14,7 @@ Currently there is one available option: \code{"default"} \item{n}{Number of individual colors to be generated.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} \item{reverse}{Logical. Should the order of the colors be reversed?} } @@ -32,6 +32,5 @@ show_col(pal_gsea("default")(12)) show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30)) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/rgb_material.Rd b/man/rgb_material.Rd index ba43d62..43682d1 100644 --- a/man/rgb_material.Rd +++ b/man/rgb_material.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/continuous-material.R \name{rgb_material} \alias{rgb_material} -\title{Material Design Color Palettes} +\title{Material Design color palettes} \usage{ rgb_material( palette = c("red", "pink", "purple", "deep-purple", "indigo", "blue", "light-blue", @@ -14,8 +14,7 @@ rgb_material( ) } \arguments{ -\item{palette}{Palette type. -There are 19 available options: +\item{palette}{Palette type. There are 19 available options: \itemize{ \item \code{"red"} \item \code{"pink"} @@ -35,19 +34,20 @@ There are 19 available options: \item \code{"deep-orange"} \item \code{"brown"} \item \code{"grey"} -\item \code{"blue-grey"}} -See \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system} -for details.} +\item \code{"blue-grey"} +} + +For details, see \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system}.} \item{n}{Number of individual colors to be generated.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} \item{reverse}{Logical. Should the order of the colors be reversed?} } \description{ -The Material Design color palettes. +The Material Design 2 color palettes. } \examples{ library("scales") @@ -58,6 +58,5 @@ show_col(pal_material("indigo", n = 30, alpha = 0.6, reverse = TRUE)(30)) \url{https://m2.material.io/design/color/the-color-system.html} } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_aaas.Rd b/man/scale_aaas.Rd index 76d7ea7..78d1f91 100644 --- a/man/scale_aaas.Rd +++ b/man/scale_aaas.Rd @@ -4,7 +4,7 @@ \alias{scale_color_aaas} \alias{scale_colour_aaas} \alias{scale_fill_aaas} -\title{AAAS Journal Color Scales} +\title{AAAS journal color scales} \usage{ scale_color_aaas(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (10-color palette inspired by \emph{Science}).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_aaas}} for details. +See \code{\link[=pal_aaas]{pal_aaas()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_aaas() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_bmj.Rd b/man/scale_bmj.Rd index 489851e..3470045 100644 --- a/man/scale_bmj.Rd +++ b/man/scale_bmj.Rd @@ -4,7 +4,7 @@ \alias{scale_color_bmj} \alias{scale_colour_bmj} \alias{scale_fill_bmj} -\title{BMJ Color Scales} +\title{BMJ color scales} \usage{ scale_color_bmj(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (9-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_bmj}} for details. +See \code{\link[=pal_bmj]{pal_bmj()}} for details. } \examples{ library("ggplot2") @@ -46,6 +46,9 @@ ggplot( theme_bw() + scale_fill_bmj() } +\references{ +\url{https://technology.bmj.com/living-style-guide/colour.html} +} \author{ -Hui Chen <\email{huichen@zju.edu.cn}> +Hui Chen | \email{huichen@zju.edu.cn} } diff --git a/man/scale_cosmic.Rd b/man/scale_cosmic.Rd index 08a7b4e..aa8cacb 100644 --- a/man/scale_cosmic.Rd +++ b/man/scale_cosmic.Rd @@ -4,7 +4,7 @@ \alias{scale_color_cosmic} \alias{scale_colour_cosmic} \alias{scale_fill_cosmic} -\title{COSMIC Color Scales} +\title{COSMIC color scales} \usage{ scale_color_cosmic( palette = c("hallmarks_light", "hallmarks_dark", "signature_substitutions"), @@ -26,18 +26,22 @@ scale_fill_cosmic( } \arguments{ \item{palette}{Palette type. Currently there are three available options: -\code{"signature_substitutions"} (6-color palette), -\code{"hallmarks_light"} (10-color palette), and \code{"hallmarks_dark"} -(10-color palette). The \code{"hallmarks_light"} option is from +\itemize{ +\item \code{"signature_substitutions"} (6-color palette). +\item \code{"hallmarks_light"} (10-color palette). +\item \code{"hallmarks_dark"} (10-color palette). +} + +The \code{"hallmarks_light"} option is from \href{https://pubmed.ncbi.nlm.nih.gov/21376230/}{Hanahan and Weinberg (2011)}.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_cosmic}} for details. +See \code{\link[=pal_cosmic]{pal_cosmic()}} for details. } \examples{ library("ggplot2") @@ -61,6 +65,6 @@ ggplot( scale_fill_cosmic() } \author{ -Joshua H. Cook <\email{joshuacook0023@gmail.com}> | -<\href{https://github.com/jhrcook}{GitHub/jhrcook}> +Joshua H. Cook | \email{joshuacook0023@gmail.com} | +\href{https://github.com/jhrcook}{@jhrcook} } diff --git a/man/scale_d3.Rd b/man/scale_d3.Rd index 6fd19e8..7b4daac 100644 --- a/man/scale_d3.Rd +++ b/man/scale_d3.Rd @@ -4,7 +4,7 @@ \alias{scale_color_d3} \alias{scale_colour_d3} \alias{scale_fill_d3} -\title{D3.js Color Scales} +\title{D3.js color scales} \usage{ scale_color_d3( palette = c("category10", "category20", "category20b", "category20c"), @@ -25,20 +25,21 @@ scale_fill_d3( ) } \arguments{ -\item{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).} +\item{palette}{Palette type. There are four available options: +\itemize{ +\item \code{"category10"} (10-color palette). +\item \code{"category20"} (20-color palette). +\item \code{"category20b"} (20-color palette). +\item \code{"category20c"} (20-color palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_d3}} for details. +See \code{\link[=pal_d3]{pal_d3()}} for details. } \examples{ library("ggplot2") @@ -75,6 +76,5 @@ p2 + scale_fill_d3(palette = "category20c") \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md} } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_flatui.Rd b/man/scale_flatui.Rd index a3a823e..e7e5fcd 100644 --- a/man/scale_flatui.Rd +++ b/man/scale_flatui.Rd @@ -4,7 +4,7 @@ \alias{scale_color_flatui} \alias{scale_colour_flatui} \alias{scale_fill_flatui} -\title{Flat UI Color Scales} +\title{Flat UI color scales} \usage{ scale_color_flatui( palette = c("default", "flattastic", "aussie"), @@ -25,19 +25,20 @@ scale_fill_flatui( ) } \arguments{ -\item{palette}{Palette type. -Currently there are three available option: -\code{"default"} (10-color palette). -\code{"flattastic"} (12-color palette). -\code{"aussie"} (10-color palette).} +\item{palette}{Palette type. Currently there are three available options: +\itemize{ +\item \code{"default"} (10-color palette). +\item \code{"flattastic"} (12-color palette). +\item \code{"aussie"} (10-color palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_flatui}} for details. +See \code{\link[=pal_flatui]{pal_flatui()}} for details. } \examples{ library("ggplot2") @@ -71,5 +72,5 @@ p1 + scale_color_flatui(palette = "aussie") p2 + scale_fill_flatui(palette = "aussie") } \author{ -Clara Jégousse <\email{cat3@hi.is}> +Clara Jégousse | \email{cat3@hi.is} } diff --git a/man/scale_frontiers.Rd b/man/scale_frontiers.Rd index 1221889..6f864ca 100644 --- a/man/scale_frontiers.Rd +++ b/man/scale_frontiers.Rd @@ -4,7 +4,7 @@ \alias{scale_color_frontiers} \alias{scale_colour_frontiers} \alias{scale_fill_frontiers} -\title{Frontiers Color Scales} +\title{Frontiers journal color scales} \usage{ scale_color_frontiers(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (10-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_frontiers}} for details. +See \code{\link[=pal_frontiers]{pal_frontiers()}} for details. } \examples{ library("ggplot2") @@ -54,5 +54,5 @@ ggplot( scale_fill_frontiers() } \author{ -Clara Jégousse <\email{cat3@hi.is}> +Clara Jégousse | \email{cat3@hi.is} } diff --git a/man/scale_futurama.Rd b/man/scale_futurama.Rd index 31b7a39..82692cd 100644 --- a/man/scale_futurama.Rd +++ b/man/scale_futurama.Rd @@ -4,7 +4,7 @@ \alias{scale_color_futurama} \alias{scale_colour_futurama} \alias{scale_fill_futurama} -\title{The Futurama Color Scales} +\title{Futurama color scales} \usage{ scale_color_futurama(palette = c("planetexpress"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"planetexpress"} (12-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_futurama}} for details. +See \code{\link[=pal_futurama]{pal_futurama()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_futurama() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_gsea.Rd b/man/scale_gsea.Rd index 45e89a1..6a2617a 100644 --- a/man/scale_gsea.Rd +++ b/man/scale_gsea.Rd @@ -4,7 +4,7 @@ \alias{scale_color_gsea} \alias{scale_colour_gsea} \alias{scale_fill_gsea} -\title{The GSEA GenePattern Color Scales} +\title{The GSEA GenePattern color scales} \usage{ scale_color_gsea(palette = c("default"), alpha = 1, reverse = FALSE, ...) @@ -18,14 +18,14 @@ Currently there is one available option: \code{"default"} (continuous palette with 12 base colors).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} \item{reverse}{Logical. Should the order of the colors be reversed?} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_gsea}} for details. +See \code{\link[=pal_gsea]{pal_gsea()}} for details. } \examples{ library("ggplot2") @@ -44,6 +44,5 @@ ggplot( scale_fill_gsea() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_igv.Rd b/man/scale_igv.Rd index feb7eaf..ac8229a 100644 --- a/man/scale_igv.Rd +++ b/man/scale_igv.Rd @@ -4,7 +4,7 @@ \alias{scale_color_igv} \alias{scale_colour_igv} \alias{scale_fill_igv} -\title{Integrative Genomics Viewer (IGV) Color Scales} +\title{Integrative Genomics Viewer (IGV) color scales} \usage{ scale_color_igv(palette = c("default", "alternating"), alpha = 1, ...) @@ -15,16 +15,18 @@ scale_fill_igv(palette = c("default", "alternating"), alpha = 1, ...) \arguments{ \item{palette}{Palette type. There are two available options: -\code{"default"} (51-color palette); -\code{"alternating"} (2-color palette).} +\itemize{ +\item \code{"default"} (51-color palette). +\item \code{"alternating"} (2-color palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_igv}} for details. +See \code{\link[=pal_igv]{pal_igv()}} for details. } \examples{ library("ggplot2") @@ -56,6 +58,5 @@ p2 + scale_fill_manual( ) } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_jama.Rd b/man/scale_jama.Rd index 1831ff3..8490ff3 100644 --- a/man/scale_jama.Rd +++ b/man/scale_jama.Rd @@ -4,7 +4,7 @@ \alias{scale_color_jama} \alias{scale_colour_jama} \alias{scale_fill_jama} -\title{Journal of the American Medical Association Color Scales} +\title{Journal of the American Medical Association color scales} \usage{ scale_color_jama(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_jama}} for details. +See \code{\link[=pal_jama]{pal_jama()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_jama() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_jco.Rd b/man/scale_jco.Rd index fbb5a4e..95b2216 100644 --- a/man/scale_jco.Rd +++ b/man/scale_jco.Rd @@ -4,7 +4,7 @@ \alias{scale_color_jco} \alias{scale_colour_jco} \alias{scale_fill_jco} -\title{Journal of Clinical Oncology Color Scales} +\title{Journal of Clinical Oncology color scales} \usage{ scale_color_jco(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (10-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_jco}} for details. +See \code{\link[=pal_jco]{pal_jco()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_jco() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_lancet.Rd b/man/scale_lancet.Rd index f42d332..267e353 100644 --- a/man/scale_lancet.Rd +++ b/man/scale_lancet.Rd @@ -4,7 +4,7 @@ \alias{scale_color_lancet} \alias{scale_colour_lancet} \alias{scale_fill_lancet} -\title{Lancet Journal Color Scales} +\title{Lancet journal color scales} \usage{ scale_color_lancet(palette = c("lanonc"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"lanonc"} (9-color palette inspired by \emph{Lancet Oncology}).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_lancet}} for details. +See \code{\link[=pal_lancet]{pal_lancet()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_lancet() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_locuszoom.Rd b/man/scale_locuszoom.Rd index e01fa45..d478f0f 100644 --- a/man/scale_locuszoom.Rd +++ b/man/scale_locuszoom.Rd @@ -4,7 +4,7 @@ \alias{scale_color_locuszoom} \alias{scale_colour_locuszoom} \alias{scale_fill_locuszoom} -\title{LocusZoom Color Scales} +\title{LocusZoom color scales} \usage{ scale_color_locuszoom(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_locuszoom}} for details. +See \code{\link[=pal_locuszoom]{pal_locuszoom()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_locuszoom() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_material.Rd b/man/scale_material.Rd index 20b94e6..daf1755 100644 --- a/man/scale_material.Rd +++ b/man/scale_material.Rd @@ -4,7 +4,7 @@ \alias{scale_color_material} \alias{scale_colour_material} \alias{scale_fill_material} -\title{Material Design Color Palettes} +\title{Material Design color palettes} \usage{ scale_color_material( palette = c("red", "pink", "purple", "deep-purple", "indigo", "blue", "light-blue", @@ -34,8 +34,7 @@ scale_fill_material( ) } \arguments{ -\item{palette}{Palette type. -There are 19 available options: +\item{palette}{Palette type. There are 19 available options: \itemize{ \item \code{"red"} \item \code{"pink"} @@ -55,19 +54,20 @@ There are 19 available options: \item \code{"deep-orange"} \item \code{"brown"} \item \code{"grey"} -\item \code{"blue-grey"}} -See \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system} -for details.} +\item \code{"blue-grey"} +} + +For details, see \href{https://m2.material.io/design/color/the-color-system.html}{Material Design color system}.} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} \item{reverse}{Logical. Should the order of the colors be reversed?} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_material}} for details. +See \code{\link[=pal_material]{pal_material()}} for details. } \examples{ library("ggplot2") @@ -86,6 +86,5 @@ ggplot( scale_fill_material("blue-grey") } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_nejm.Rd b/man/scale_nejm.Rd index b2b08cb..483a6cd 100644 --- a/man/scale_nejm.Rd +++ b/man/scale_nejm.Rd @@ -4,7 +4,7 @@ \alias{scale_color_nejm} \alias{scale_colour_nejm} \alias{scale_fill_nejm} -\title{NEJM Color Scales} +\title{NEJM color scales} \usage{ scale_color_nejm(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (8-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_nejm}} for details. +See \code{\link[=pal_nejm]{pal_nejm()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_nejm() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_npg.Rd b/man/scale_npg.Rd index b08d137..1cee97e 100644 --- a/man/scale_npg.Rd +++ b/man/scale_npg.Rd @@ -4,7 +4,7 @@ \alias{scale_color_npg} \alias{scale_colour_npg} \alias{scale_fill_npg} -\title{NPG Journal Color Scales} +\title{NPG journal color scales} \usage{ scale_color_npg(palette = c("nrc"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"nrc"} (10-color palette inspired by \emph{Nature Reviews Cancer}).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_npg}} for details. +See \code{\link[=pal_npg]{pal_npg()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_npg() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_rickandmorty.Rd b/man/scale_rickandmorty.Rd index 2e8eb1d..b144ac1 100644 --- a/man/scale_rickandmorty.Rd +++ b/man/scale_rickandmorty.Rd @@ -4,7 +4,7 @@ \alias{scale_color_rickandmorty} \alias{scale_colour_rickandmorty} \alias{scale_fill_rickandmorty} -\title{Rick and Morty Color Scales} +\title{Rick and Morty color scales} \usage{ scale_color_rickandmorty(palette = c("schwifty"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"schwifty"} (12-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_rickandmorty}} for details. +See \code{\link[=pal_rickandmorty]{pal_rickandmorty()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_rickandmorty() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_simpsons.Rd b/man/scale_simpsons.Rd index eda73f3..0058bdf 100644 --- a/man/scale_simpsons.Rd +++ b/man/scale_simpsons.Rd @@ -4,7 +4,7 @@ \alias{scale_color_simpsons} \alias{scale_colour_simpsons} \alias{scale_fill_simpsons} -\title{The Simpsons Color Scales} +\title{The Simpsons color scales} \usage{ scale_color_simpsons(palette = c("springfield"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"springfield"} (16-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_simpsons}} for details. +See \code{\link[=pal_simpsons]{pal_simpsons()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_simpsons() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_startrek.Rd b/man/scale_startrek.Rd index 3ca8727..431ecd9 100644 --- a/man/scale_startrek.Rd +++ b/man/scale_startrek.Rd @@ -4,7 +4,7 @@ \alias{scale_color_startrek} \alias{scale_colour_startrek} \alias{scale_fill_startrek} -\title{Star Trek Color Scales} +\title{Star Trek color scales} \usage{ scale_color_startrek(palette = c("uniform"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"uniform"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_startrek}} for details. +See \code{\link[=pal_startrek]{pal_startrek()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_startrek() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_tron.Rd b/man/scale_tron.Rd index a1ccffb..5b99bc5 100644 --- a/man/scale_tron.Rd +++ b/man/scale_tron.Rd @@ -4,7 +4,7 @@ \alias{scale_color_tron} \alias{scale_colour_tron} \alias{scale_fill_tron} -\title{Tron Legacy Color Scales} +\title{Tron Legacy color scales} \usage{ scale_color_tron(palette = c("legacy"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"legacy"} (7-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_tron}} for details. +See \code{\link[=pal_tron]{pal_tron()}} for details. } \examples{ library("ggplot2") @@ -54,6 +54,5 @@ ggplot( scale_fill_tron() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_uchicago.Rd b/man/scale_uchicago.Rd index 38b2ac4..9317cd0 100644 --- a/man/scale_uchicago.Rd +++ b/man/scale_uchicago.Rd @@ -4,7 +4,7 @@ \alias{scale_color_uchicago} \alias{scale_colour_uchicago} \alias{scale_fill_uchicago} -\title{The University of Chicago Color Scales} +\title{The University of Chicago color scales} \usage{ scale_color_uchicago(palette = c("default", "light", "dark"), alpha = 1, ...) @@ -14,18 +14,20 @@ scale_fill_uchicago(palette = c("default", "light", "dark"), alpha = 1, ...) } \arguments{ \item{palette}{Palette type. -There are 3 available options: -\code{"default"} (9-color palette); -\code{"light"} (9-color light palette); -\code{"dark"} (9-color dark palette).} +There are three available options: +\itemize{ +\item \code{"default"} (9-color palette); +\item \code{"light"} (9-color light palette); +\item \code{"dark"} (9-color dark palette). +}} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_uchicago}} for details. +See \code{\link[=pal_uchicago]{pal_uchicago()}} for details. } \examples{ library("ggplot2") @@ -59,6 +61,5 @@ p2 + scale_fill_uchicago(palette = "dark") \url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf} } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/man/scale_ucscgb.Rd b/man/scale_ucscgb.Rd index 48967e1..2d83c26 100644 --- a/man/scale_ucscgb.Rd +++ b/man/scale_ucscgb.Rd @@ -4,7 +4,7 @@ \alias{scale_color_ucscgb} \alias{scale_colour_ucscgb} \alias{scale_fill_ucscgb} -\title{UCSC Genome Browser Color Scales} +\title{UCSC Genome Browser color scales} \usage{ scale_color_ucscgb(palette = c("default"), alpha = 1, ...) @@ -18,12 +18,12 @@ Currently there is one available option: \code{"default"} (26-color palette).} \item{alpha}{Transparency level, a real number in (0, 1]. -See \code{alpha} in \code{\link[grDevices]{rgb}} for details.} +See \code{alpha} in \code{\link[grDevices:rgb]{grDevices::rgb()}} for details.} -\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}} +\item{...}{Additional parameters for \code{\link[ggplot2:discrete_scale]{ggplot2::discrete_scale()}}.} } \description{ -See \code{\link{pal_ucscgb}} for details. +See \code{\link[=pal_ucscgb]{pal_ucscgb()}} for details. } \examples{ library("ggplot2") @@ -47,6 +47,5 @@ ggplot( scale_fill_ucscgb() } \author{ -Nan Xiao <\email{me@nanx.me}> | -<\href{https://nanx.me}{https://nanx.me}> +Nan Xiao | \email{me@nanx.me} | \url{https://nanx.me} } diff --git a/vignettes/ggsci.Rmd b/vignettes/ggsci.Rmd index 602abb0..e3dec61 100644 --- a/vignettes/ggsci.Rmd +++ b/vignettes/ggsci.Rmd @@ -489,7 +489,7 @@ grid.arrange( ``` From the figure above, we can see that even though an identical matrix -was visualized by all plots, some palettes are more preferrable +was visualized by all plots, some palettes are more preferable than the others because our eyes are more sensitive to the changes of their saturation levels.