R/AllGlobals.R

In acidgenomics/AcidPlots: Acid Genomics Plot Functions and Themes

.pkgName <- packageName()
.pkgVersion <- packageVersion(.pkgName)



#' Internal formals list, specific to package
#'
#' @note Updated 2023-08-17.
#' @noRd
.formalsList <- list(
    "continuousColor" = quote(
        getOption(
            x = "acid.continuous.color",
            default = ggplot2::scale_color_gradient(
                low = "gray75",
                high = "purple"
            )
        )
    ),
    "continuousColorPurpleOrange" = quote(
        getOption(
            x = "acid.continuous.color",
            default = ggplot2::scale_color_gradient2(
                low = "orange",
                mid = "gray75",
                high = "purple",
                midpoint = 0L
            )
        )
    ),
    "dark" = quote(
        getOption(
            x = "acid.dark",
            default = FALSE
        )
    ),
    "darkMarkerColors" = quote(
        ggplot2::scale_color_viridis_c(option = "plasma")
    ),
    "dims" = c(1L, 2L),
    "direction" = c("both", "up", "down"),
    "discreteColor" = quote(
        getOption(
            x = "acid.discrete.color",
            default = AcidPlots::acid_scale_color_synesthesia_d()
        )
    ),
    "expression" = c("mean", "sum"),
    "flip" = quote(
        getOption(
            x = "acid.flip",
            default = TRUE
        )
    ),
    "geom" = c(
        "histogram",
        "ecdf",
        "violin",
        "ridgeline",
        "boxplot"
    ),
    "headerLevel" = 2L,
    "heatmapColor" = quote(
        getOption(
            x = "acid.heatmap.color",
            default = AcidPlots::blueYellow
        )
    ),
    "heatmapCorrelationColor" = quote(
        getOption(
            x = "acid.heatmap.correlation.color",
            default = viridis::magma
        )
    ),
    "heatmapLegendColor" = quote(
        getOption(
            x = "acid.heatmap.legend.color",
            default = AcidPlots::synesthesia
        )
    ),
    "heatmapQuantileColor" = quote(
        getOption(
            x = "acid.heatmap.quantile.color",
            default = viridis::magma
        )
    ),
    "label" = quote(
        getOption(x = "acid.label", default = FALSE)
    ),
    "labelSize" = quote(
        getOption(x = "acid.label.size", default = 6L)
    ),
    "legend" = quote(
        getOption(x = "acid.legend", default = TRUE)
    ),
    "n" = 256L,
    "palette" = c(
        "lightPalette",
        "darkPalette",
        "draculaPalette",
        "macOSLightPalette",
        "macOSDarkPalette",
        "iOSLightPalette",
        "iOSDarkPalette"
    ),
    "pointAlpha" = quote(
        getOption(
            x = "acid.point.alpha",
            default = 0.9
        )
    ),
    "pointSize" = quote(
        getOption(
            x = "acid.point.size",
            default = 3L
        )
    ),
    "pointSize2" = quote(
        getOption(
            x = "acid.point.size",
            default = 1L
        )
    ),
    "pointsAsNumbers" = quote(
        getOption(
            x = "acid.points.as.numbers",
            default = FALSE
        )
    ),
    "reduction" = "UMAP" # or `1L`.
)



#' AcidPlots test data URL
#'
#' @keywords internal
#' @export
#'
#' @examples
#' AcidPlotsTestsUrl
AcidPlotsTestsUrl <- # nolint
    "https://r.acidgenomics.com/testdata/acidplots"



## Color palettes ==============================================================

## nolint start

#' Color palettes
#'
#' Color palette hexadecimal character vectors.
#'
#' @name palettes
#' @note Updated 2021-08-11.
#'
#' @return `character`.
#'
#' @seealso
#' - [iOS palette](https://developer.apple.com/design/human-interface-guidelines/ios/visual-design/color/)
#' - [macOS palette](https://developer.apple.com/design/human-interface-guidelines/macos/visual-design/color/)
#' - [Dracula palette](https://github.com/dracula/dracula-theme)
#'
#' @examples
#' lightPalette
NULL

## nolint end



#' Prepare exported palette global variable
#'
#' @note Updated 2021-08-11.
#' @noRd
.preparePalette <- function(name) {
    .palettes[[name]][sort(names(.palettes[[name]]))]
}



#' Improve the `rgb()` default to use 0:255, as expected
#'
#' @note Updated 2019-09-13.
#' @noRd
.rgb <- function(...) {
    rgb(..., maxColorValue = 255L)
}



#' Internal color palette hex values
#'
#' @note Updated 2021-08-11.
#' @noRd
#'
#' @details
#' Consider adding:
#' - gruvbox
#' - nord
#' - solarized
.palettes <- list(
    "dracula" = c(
        "background" = .rgb(40L, 42L, 54L),
        "foreground" = .rgb(248L, 248L, 242L),
        "border" = .rgb(54L, 57L, 72L),
        "blue" = .rgb(0L, 122L, 255L),
        "green" = .rgb(52L, 199L, 89L),
        "orange" = .rgb(255L, 149L, 0L),
        "pink" = .rgb(255L, 45L, 85L),
        "purple" = .rgb(175L, 82L, 222L),
        "red" = .rgb(255L, 59L, 48L),
        "teal" = .rgb(90L, 200L, 250L),
        "yellow" = .rgb(255L, 204L, 0L)
    ),
    "iOSDark" = c(
        "background" = .rgb(23L, 23L, 23L),
        "foreground" = .rgb(153L, 153L, 153L),
        "border" = .rgb(152L, 152L, 157L),
        "blue" = .rgb(10L, 132L, 255L),
        "gray" = .rgb(152L, 152L, 157L),
        "green" = .rgb(48L, 209L, 88L),
        "orange" = .rgb(255L, 159L, 10L),
        "pink" = .rgb(255L, 55L, 95L),
        "purple" = .rgb(191L, 90L, 242L),
        "red" = .rgb(255L, 69L, 58L),
        "teal" = .rgb(100L, 210L, 255L),
        "yellow" = .rgb(255L, 214L, 10L)
    ),
    "iOSLight" = c(
        "background" = .rgb(255L, 255L, 255L),
        "foreground" = .rgb(0L, 0L, 0L),
        "border" = .rgb(142L, 142L, 147L),
        "blue" = .rgb(0L, 122L, 255L),
        "gray" = .rgb(142L, 142L, 147L),
        "green" = .rgb(52L, 199L, 89L),
        "orange" = .rgb(255L, 149L, 0L),
        "pink" = .rgb(255L, 45L, 85L),
        "purple" = .rgb(175L, 82L, 222L),
        "red" = .rgb(255L, 59L, 48L),
        "teal" = .rgb(90L, 200L, 250L),
        "yellow" = .rgb(255L, 204L, 0L)
    )
)

.palettes[["macOSDark"]] <- .palettes[["iOSDark"]]
.palettes[["macOSDark"]][["green"]] <- .rgb(50L, 215L, 75L)

.palettes[["macOSLight"]] <- .palettes[["iOSLight"]]
.palettes[["macOSLight"]][["green"]] <- .rgb(40L, 205L, 65L)

.palettes[["dracula"]][["gray"]] <- .palettes[["macOSDark"]][["gray"]]

.palettes[["light"]] <- .palettes[["macOSLight"]]

.palettes[["dark"]] <- .palettes[["macOSDark"]]
.palettes[["dark"]][["background"]] <- .rgb(0L, 0L, 0L)
.palettes[["dark"]][["foreground"]] <- .rgb(255L, 255L, 255L)
.palettes[["dark"]][["gray"]] <- .rgb(26L, 26L, 26L) ## gray10



#' @rdname palettes
#' @export
draculaPalette <- .preparePalette("dracula")

#' @rdname palettes
#' @export
darkPalette <- .preparePalette("dark")

#' @rdname palettes
#' @export
lightPalette <- .preparePalette("light")

#' @rdname palettes
#' @export
iOSDarkPalette <- .preparePalette("iOSDark")

#' @rdname palettes
#' @export
iOSLightPalette <- .preparePalette("iOSLight")

#' @rdname palettes
#' @export
macOSDarkPalette <- .preparePalette("macOSDark")

#' @rdname palettes
#' @export
macOSLightPalette <- .preparePalette("macOSLight")