Merge pull request #37 from nanxstats/roxygen2md

Convert Rd syntax to Markdown
nanxstats · May 21, 2024 · 0e0b28d · 0e0b28d
2 parents 7e30687 + c7bfe46
commit 0e0b28d
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diff --git 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
@@ -1,26 +1,25 @@
-#' 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
 #'
 #' @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} | <https://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} | <https://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} | <https://nanx.me>
 #'
 #' @rdname scale_gsea
 #'

diff --git a/R/continuous-material.R b/R/continuous-material.R
@@ -1,46 +1,45 @@
-#' 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
 #'
 #' @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} | <https://nanx.me>
 #'
 #' @references
-#' \url{https://m2.material.io/design/color/the-color-system.html}
+#' <https://m2.material.io/design/color/the-color-system.html>
 #'
 #' @examples
 #' library("scales")
@@ -69,18 +68,17 @@ 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
 #'
 #' @export pal_material
 #'
 #' @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} | <https://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} | <https://nanx.me>
 #'
 #' @rdname scale_material
 #'

diff --git 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} | <https://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} | <https://nanx.me>
 #'
 #' @rdname scale_aaas
 #'

diff --git 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
+#' <https://technology.bmj.com/living-style-guide/colour.html>
 #'
 #' @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
+#' <https://technology.bmj.com/living-style-guide/colour.html>
+#'
 #' @examples
 #' library("ggplot2")
 #' data("diamonds")

diff --git 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
 #'