update sort, add new functions

jbengler · Jul 31, 2024 · 32bc195 · 32bc195
1 parent 9627378
commit 32bc195
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Showing 40 changed files with 471 additions and 788 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -63,14 +63,18 @@ export(add_test_asterisks)
 export(add_test_pvalue)
 export(add_title)
 export(add_violin)
+export(adjust_caption)
 export(adjust_colors)
-export(adjust_description)
 export(adjust_font)
-export(adjust_legend)
+export(adjust_legend_position)
+export(adjust_legend_title)
 export(adjust_padding)
 export(adjust_size)
+export(adjust_title)
 export(adjust_x_axis)
+export(adjust_x_axis_title)
 export(adjust_y_axis)
+export(adjust_y_axis_title)
 export(all_rows)
 export(as_tidyplot)
 export(colors_continuous_bluepinkyellow)
@@ -105,9 +109,11 @@ export(last_rows)
 export(max_rows)
 export(min_rows)
 export(new_color_scheme)
+export(remove_caption)
 export(remove_legend)
 export(remove_legend_title)
 export(remove_padding)
+export(remove_title)
 export(remove_x_axis)
 export(remove_x_axis_labels)
 export(remove_x_axis_line)
@@ -148,6 +154,7 @@ importFrom(lifecycle,deprecated)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(stats,density)
+importFrom(stats,median)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(utils,tail)
diff --git a/R/aaa.R b/R/aaa.R
@@ -1,5 +1,5 @@
 #' @importFrom grDevices col2rgb rgb dev.off pdf
-#' @importFrom stats density sd setNames
+#' @importFrom stats density sd setNames median
 #' @importFrom utils tail
 #' @importFrom rlang := .data
 NULL

diff --git a/R/add-general.R b/R/add-general.R
@@ -12,7 +12,7 @@
 #' @param preserve Should dodging preserve the `"total"` width of all elements at
 #'   a position, or the width of a `"single"` element?
 #' @param rasterize If `FALSE` (the default) the layer will be constructed of
-#'   vector shapes. If `TRUE` the layer will be rastered to a pixel image. This can
+#'   vector shapes. If `TRUE` the layer will be rasterized to a pixel image. This can
 #'   be useful when plotting many individual objects (1,000 or more) compromises
 #'   the performance of the generated PDF file.
 #' @param rasterize_dpi The resolution in dots per inch (dpi) used for rastering
@@ -45,6 +45,7 @@
 #' @param saturation A `number` between `0` and `1` for the color saturation of an object. A value of `0` is completely desaturated (white), `1` is the original color.
 #' @param group Variable in the dataset to be used for grouping.
 #' @param reverse Whether the order should be reversed or not. Defaults to `FALSE`, meaning not reversed.
+#' @param .reverse Whether the order should be reversed or not. Defaults to `FALSE`, meaning not reversed.
 #' @param scale_cut Scale cut function to be applied. See `scales::cut_short_scale()` and friends.
 #' @param fontsize Font size in points. Defaults to `7`.
 #' @param replace_na Whether to replace `count = NA` with `count = 0`.
@@ -61,7 +62,7 @@ NULL
 ## Error bar function factory
 ff_errorbar <- function(.fun.data) {
   function(plot, dodge_width = NULL, width = 0.4, linewidth = 0.25, preserve = "total", ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
     position <- ggplot2::position_dodge(width = dodge_width, preserve = preserve)
     plot + ggplot2::stat_summary(fun.data = .fun.data, geom = "errorbar",
@@ -130,7 +131,7 @@ add_ci95_errorbar <- ff_errorbar(.fun.data = mean_cl_boot)
 ## Ribbon function factory
 ff_ribbon <- function(.fun.data) {
   function(plot, dodge_width = NULL, alpha = 0.4, color = NA, ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     mapping <- ggplot2::aes()
     mapping$group <- plot$mapping$colour
     dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
@@ -195,7 +196,7 @@ add_ci95_ribbon <- ff_ribbon(.fun.data = ggplot2::mean_cl_boot)
 ## Bar function factory
 ff_bar <- function(.fun, .count = FALSE) {
   function(plot, dodge_width = NULL, width = 0.6, saturation = 1, preserve = "total", ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
     position <- ggplot2::position_dodge(width = dodge_width, preserve = preserve)
     if (saturation != 1) {
@@ -221,7 +222,7 @@ ff_bar <- function(.fun, .count = FALSE) {
 ## Dash function factory
 ff_dash <- function(.fun, .count = FALSE) {
   function(plot, dodge_width = NULL, width = 0.6, linewidth = 0.25, preserve = "total", ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
     position <- ggplot2::position_dodge(width = dodge_width, preserve = preserve)
     if (.count) {
@@ -237,7 +238,7 @@ ff_dash <- function(.fun, .count = FALSE) {
 ## Dot function factory
 ff_dot <- function(.fun, .count = FALSE) {
   function(plot, dodge_width = NULL, size = 2, preserve = "total", ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
     position <- ggplot2::position_dodge(width = dodge_width, preserve = preserve)
     if (.count) {
@@ -251,7 +252,7 @@ ff_dot <- function(.fun, .count = FALSE) {
 ff_value <- function(.fun, .count = FALSE) {
   function(plot, dodge_width = NULL, accuracy = 0.1, scale_cut = NULL, fontsize = 7,
            extra_padding = 0.15, vjust = NULL, hjust = NULL, preserve = "total", ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     ptype <- get_plottype(plot)
 
     if ((stringr::str_sub(ptype, 2, 2) == "c" || .count)) {
@@ -290,7 +291,7 @@ ff_value <- function(.fun, .count = FALSE) {
 ## Line function factory
 ff_line <- function(.fun, .count = FALSE, .geom) {
   function(plot, group, dodge_width = NULL, linewidth = 0.25, preserve = "total", ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     if(.geom == "area") linewidth = NA
     mapping <- NULL
     if (is_missing(plot, "group")) {

diff --git a/R/add-heatmap.R b/R/add-heatmap.R
@@ -4,7 +4,7 @@
 #' @inherit common_arguments
 #'
 #' @details
-#' * `add_heatmap()` supports rasterizing. See examples and [Advanced plotting](https://jbengler.github.io/tidyplots/articles/Advanced-plotting.html#rasterizing).
+#' * `add_heatmap()` supports rasterization. See examples and [Advanced plotting](https://jbengler.github.io/tidyplots/articles/Advanced-plotting.html#rasterization).
 #'
 #' @examples
 #' climate %>%
@@ -29,7 +29,7 @@
 #' @export
 add_heatmap <- function(plot, scale = c("none", "row", "column"), rotate_labels = 90,
                         rasterize = FALSE, rasterize_dpi = 300, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   mapping <- NULL
   scale <- match.arg(scale)
 

diff --git a/R/add-misc.R b/R/add-misc.R
@@ -35,7 +35,7 @@
 add_boxplot <- function(plot, dodge_width = NULL, saturation = 0.3, show_whiskers = TRUE, show_outliers = TRUE,
                         box_width = 0.6, whiskers_width = 0.8, outlier.size = 0.5, coef = 1.5,
                         outlier.shape = 19, linewidth = 0.25, preserve = "total", ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
   position <- ggplot2::position_dodge(width = dodge_width, preserve = preserve)
   if (saturation != 1) {
@@ -83,7 +83,7 @@ add_boxplot <- function(plot, dodge_width = NULL, saturation = 0.3, show_whisker
 #' @export
 add_violin <- function(plot, dodge_width = NULL, saturation = 0.3, draw_quantiles = NULL, trim = FALSE,
                        linewidth = 0.25, scale = "width", ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
   position <- ggplot2::position_dodge(width = dodge_width)
   plot <- plot %>% adjust_colors(saturation = saturation)
@@ -114,7 +114,7 @@ add_violin <- function(plot, dodge_width = NULL, saturation = 0.3, draw_quantile
 #'
 #' @export
 add_line <- function(plot, group, dodge_width = NULL, linewidth = 0.25, preserve = "total", ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   mapping <- NULL
   if (is_missing(plot, "group")) {
     mapping <- ggplot2::aes()
@@ -130,7 +130,7 @@ add_line <- function(plot, group, dodge_width = NULL, linewidth = 0.25, preserve
 #' @rdname add_line
 #' @export
 add_area <- function(plot, group, dodge_width = NULL, linewidth = 0.25, alpha = 0.4, preserve = "total", ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   ptype <- get_plottype(plot)
 
   # detect orientation
@@ -192,7 +192,7 @@ add_area <- function(plot, group, dodge_width = NULL, linewidth = 0.25, alpha =
 #' @export
 add_curve_fit <- function(plot, dodge_width = NULL, method = "loess", linewidth = 0.25, alpha = 0.4,
                           preserve = "total", ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   mapping <- ggplot2::aes()
   mapping$group <- plot$mapping$colour
   dodge_width <- dodge_width %||% plot$tidyplot$dodge_width
@@ -219,15 +219,15 @@ add_curve_fit <- function(plot, dodge_width = NULL, method = "loess", linewidth
 #'
 #' @export
 add_histogram <- function(plot, binwidth = NULL, bins = NULL, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   plot %>%
     remove_padding(force_continuous = TRUE) +
     ggplot2::geom_histogram(binwidth = binwidth, bins = bins, ...)
 }
 #' @rdname add_histogram
 #' @export
 add_density_histogram <- function(plot, binwidth = NULL, bins = NULL, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   plot %>%
     remove_padding(force_continuous = TRUE) +
     ggplot2::geom_histogram(ggplot2::aes(y = ggplot2::after_stat(density)),
@@ -236,7 +236,7 @@ add_density_histogram <- function(plot, binwidth = NULL, bins = NULL, ...) {
 #' @rdname add_histogram
 #' @export
 add_density_curve <- function(plot, bw = "nrd0", adjust = 1, kernel = "gaussian", n = 512, alpha = 0.4, color = "#D55E00",...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   plot %>%
     remove_padding(force_continuous = TRUE) +
     ggplot2::geom_density(bw = bw, adjust = adjust, kernel = kernel, n = n, color = color, fill = color, alpha = alpha, ...)
@@ -271,15 +271,15 @@ add_density_curve <- function(plot, bw = "nrd0", adjust = 1, kernel = "gaussian"
 #'
 #' @export
 add_title <- function(plot, title = ggplot2::waiver()) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   # parse title
   if (!is_waiver(title)) title <- tidyplot_parser(as.character(title))
   plot + ggplot2::labs(title = title)
 }
 #' @rdname add_title
 #' @export
 add_caption <- function(plot, caption = ggplot2::waiver()) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   # parse caption
   if (!is_waiver(caption)) caption <- tidyplot_parser(as.character(caption))
   plot + ggplot2::labs(caption = caption)
@@ -306,7 +306,7 @@ add_caption <- function(plot, caption = ggplot2::waiver()) {
 #'
 #' @export
 add_reference_lines <- function(plot, x = NULL, y = NULL, linetype = "dashed", linewidth = 0.25, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   out <- plot
   if(!is.null(x)) {
     out <- out + ggplot2::geom_vline(xintercept = x, linetype = linetype, linewidth = linewidth, ...)
@@ -377,7 +377,7 @@ add_reference_lines <- function(plot, x = NULL, y = NULL, linetype = "dashed", l
 add_data_labels <- function(plot, label, data = all_rows(), fontsize = 7,
                             background = FALSE, background_color = "#FFFFFF", background_alpha = 0.6,
                             label_position = c("below", "above", "left", "right", "center"), ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   size <- fontsize/ggplot2::.pt
   if (!background) background_alpha <- 0
   label.padding <- ggplot2::unit(0.1, "lines")
@@ -414,7 +414,7 @@ add_data_labels <- function(plot, label, data = all_rows(), fontsize = 7,
 add_data_labels_repel <- function(plot, label, data = all_rows(), fontsize = 7,
                                   segment.size = 0.2, box.padding = 0.2, max.overlaps = Inf,
                                   background = FALSE, background_color = "#FFFFFF", background_alpha = 0.6, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   size <- fontsize/ggplot2::.pt
   if (!background) background_alpha <- 0
   label.padding <- ggplot2::unit(0.1, "lines")

diff --git a/R/add-points.R b/R/add-points.R
@@ -14,7 +14,7 @@
 #' * `add_data_points_beeswarm()` is based on `ggbeeswarm::geom_beeswarm()`.
 #' Check there for additional arguments.
 #'
-#' * `add_data_points()` and friends support rasterizing. See examples and [Advanced plotting](https://jbengler.github.io/tidyplots/articles/Advanced-plotting.html#rasterizing).
+#' * `add_data_points()` and friends support rasterization. See examples and [Advanced plotting](https://jbengler.github.io/tidyplots/articles/Advanced-plotting.html#rasterization).
 #'
 #' * `add_data_points()` and friends support data subsetting. See examples and [Advanced plotting](https://jbengler.github.io/tidyplots/articles/Advanced-plotting.html#data-subsetting).
 #'
@@ -44,7 +44,7 @@
 #'   tidyplot(x = weight, y = size) %>%
 #'   add_data_points(alpha = 0.4)
 #'
-#' # Rasterizing
+#' # Rasterization
 #' animals %>%
 #'   tidyplot(x = weight, y = size) %>%
 #'   add_data_points(rasterize = TRUE, rasterize_dpi = 50)
@@ -61,7 +61,7 @@ add_data_points <- function(plot, data = all_rows(),
                             dodge_width = NULL,
                             preserve = "total",
                             rasterize = FALSE, rasterize_dpi = 300, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   f_points(plot = plot, data = data,
            shape = shape, size = size, white_border = white_border,
            dodge_width = dodge_width,
@@ -75,7 +75,7 @@ add_data_points_jitter <- function(plot, data = all_rows(),
                                    dodge_width = NULL,
                                    jitter_width = 0.2, jitter_height = 0, preserve = "total",
                                    rasterize = FALSE, rasterize_dpi = 300, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   f_points(plot = plot, data = data,
            shape = shape, size = size, white_border = white_border,
            dodge_width = dodge_width,
@@ -90,7 +90,7 @@ add_data_points_beeswarm <- function(plot, data = all_rows(),
                                      dodge_width = NULL,
                                      preserve = "total",
                                      rasterize = FALSE, rasterize_dpi = 300, ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   f_points(beeswarm = TRUE,
            plot = plot, data = data,
            shape = shape, size = size, white_border = white_border,

diff --git a/R/add-proportional.R b/R/add-proportional.R
@@ -1,7 +1,7 @@
 ## Pie function factory
 ff_pie <- function(.type = "pie") {
   function(plot, width = 1, reverse = FALSE, ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     plot <-
       plot %>%
       remove_padding() %>%
@@ -64,7 +64,7 @@ add_donut <- ff_pie(.type = "donut")
 ## Barstack function factory
 ff_barstack <- function(.position_fun) {
   function(plot, width = 0.8, reverse = FALSE, ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     ptype <- get_plottype(plot)
 
     if (is_missing(plot, "colour")) cli::cli_abort("Argument {.arg color} missing without default")
@@ -159,7 +159,7 @@ add_barstack_relative <- ff_barstack(.position_fun = ggplot2::position_fill)
 ## Areastack function factory
 ff_areastack <- function(.position_fun) {
   function(plot, linewidth = 0.25, alpha = 0.4, reverse = FALSE, replace_na = FALSE, ...) {
-    check_tidyplot(plot)
+    plot <- check_tidyplot(plot)
     ptype <- get_plottype(plot)
 
     # overwrite group aesthetic

diff --git a/R/add-stats.R b/R/add-stats.R
@@ -1,4 +1,4 @@
-#' Add statistics
+#' Add statistical test
 #' @param padding_top Extra padding above the data points to accommodate the statistical comparisons.
 #' @param hide_info Whether to hide details about the statistical testing as caption. Defaults to `FALSE`.
 #' @param ... Arguments passed on to `ggpubr::geom_pwc()`.
@@ -79,7 +79,7 @@ add_test_pvalue <- function(plot,
                       ),
                       hide_info = FALSE,
                       ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   # cli::cli_alert_success("add_test: {.pkg method} = {method}, {.pkg label} = {label}, {.pkg p.adjust.method} = {p.adjust.method}, {.pkg hide.ns} = {hide.ns}")
 
   plot <- plot  %>%
@@ -125,7 +125,7 @@ add_test_asterisks <- function(plot,
                              ),
                              hide_info = FALSE,
                              ...) {
-  check_tidyplot(plot)
+  plot <- check_tidyplot(plot)
   add_test_pvalue(plot,
             padding_top = padding_top,
             method = method,