Merge branch 'main' into violin_data_quantiles

Author: teunbrand

DESCRIPTION

@@ -274,6 +274,7 @@ Collate:
     'theme.R'
     'theme-defaults.R'
     'theme-current.R'
+    'theme-sub.R'
     'utilities-break.R'
     'utilities-grid.R'
     'utilities-help.R'

NAMESPACE

@@ -725,6 +725,17 @@ export(theme_linedraw)
 export(theme_minimal)
 export(theme_replace)
 export(theme_set)
+export(theme_sub_axis)
+export(theme_sub_axis_bottom)
+export(theme_sub_axis_left)
+export(theme_sub_axis_right)
+export(theme_sub_axis_top)
+export(theme_sub_axis_x)
+export(theme_sub_axis_y)
+export(theme_sub_legend)
+export(theme_sub_panel)
+export(theme_sub_plot)
+export(theme_sub_strip)
 export(theme_test)
 export(theme_transparent)
 export(theme_update)

NEWS.md

@@ -1,5 +1,14 @@
 # ggplot2 (development version)
 
+* New function family for setting parts of a theme. For example, you can now use 
+  `theme_sub_axis(line, text, ticks, ticks.length, line)` as a substitute for
+  `theme(axis.line, axis.text, axis.ticks, axis.ticks.length, axis.line)`. This
+  should allow slightly terser and more organised theme declarations 
+  (@teunbrand, #5301).
+* `scale_{x/y}_discrete(continuous.limits)` is a new argument to control the
+  display range of discrete scales (@teunbrand, #4174, #6259).
+* `geom_ribbon()` now appropriately warns about, and removes, missing values 
+  (@teunbrand, #6243).
 * `guide_*()` can now accept two inside legend theme elements:
   `legend.position.inside` and `legend.justification.inside`, allowing inside
   legends to be placed at different positions. Only inside legends with the same
@@ -250,6 +259,8 @@
 * `geom_abline()` clips to the panel range in the vertical direction too
   (@teunbrand, #6086).
 * Added `panel.widths` and `panel.heights` to `theme()` (#5338, @teunbrand).
+* Standardised the calculation of `width`, which are now implemented as
+  aesthetics (@teunbrand, #2800).
 
 # ggplot2 3.5.1
 

R/coord-radial.R

@@ -4,7 +4,7 @@
 #' @param end Position from 12 o'clock in radians where plot ends, to allow
 #'   for partial polar coordinates. The default, `NULL`, is set to
 #'   `start + 2 * pi`.
-#' @param expand If `TRUE`, the default, adds a small expansion factor the
+#' @param expand If `TRUE`, the default, adds a small expansion factor to
 #'   the limits to prevent overlap between data and axes. If `FALSE`, limits
 #'   are taken directly from the scale.
 #' @param r.axis.inside One of the following:

R/geom-bar.R

@@ -130,7 +130,7 @@ GeomBar <- ggproto("GeomBar", GeomRect,
   # limits, not just those for which x and y are outside the limits
   non_missing_aes = c("xmin", "xmax", "ymin", "ymax"),
 
-  default_aes = aes(!!!GeomRect$default_aes, width = NULL),
+  default_aes = aes(!!!GeomRect$default_aes, width = 0.9),
 
   setup_params = function(data, params) {
     params$flipped_aes <- has_flipped_aes(data, params)
@@ -139,14 +139,13 @@ GeomBar <- ggproto("GeomBar", GeomRect,
 
   extra_params = c("just", "na.rm", "orientation"),
 
-  setup_data = function(data, params) {
+  setup_data = function(self, data, params) {
     data$flipped_aes <- params$flipped_aes
     data <- flip_data(data, params$flipped_aes)
-    data$width <- data$width %||%
-      params$width %||% (min(vapply(
-        split(data$x, data$PANEL, drop = TRUE),
-        resolution, numeric(1), zero = FALSE
-      )) * 0.9)
+    data <- compute_data_size(
+      data, size = params$width,
+      default = self$default_aes$width, zero = FALSE
+    )
     data$just <- params$just %||% 0.5
     data <- transform(data,
       ymin = pmin(y, 0), ymax = pmax(y, 0),

R/geom-boxplot.R

@@ -236,21 +236,21 @@ geom_boxplot <- function(mapping = NULL, data = NULL,
 #' @export
 GeomBoxplot <- ggproto("GeomBoxplot", Geom,
 
-  # need to declare `width` here in case this geom is used with a stat that
-  # doesn't have a `width` parameter (e.g., `stat_identity`).
-  extra_params = c("na.rm", "width", "orientation", "outliers"),
+  extra_params = c("na.rm", "orientation", "outliers"),
 
   setup_params = function(data, params) {
     params$flipped_aes <- has_flipped_aes(data, params)
     params
   },
 
-  setup_data = function(data, params) {
+  setup_data = function(self, data, params) {
     data$flipped_aes <- params$flipped_aes
     data <- flip_data(data, params$flipped_aes)
-    data$width <- data$width %||%
-      params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9)
-
+    data <- compute_data_size(
+      data, params$width,
+      default = self$default_aes$width,
+      zero = FALSE, discrete = TRUE
+    )
     if (isFALSE(params$outliers)) {
       data$outliers <- NULL
     }
@@ -389,7 +389,8 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom,
     weight = 1, colour = from_theme(col_mix(ink, paper, 0.2)),
     fill = from_theme(paper), size = from_theme(pointsize),
     alpha = NA, shape = from_theme(pointshape), linetype = from_theme(bordertype),
-    linewidth = from_theme(borderwidth)
+    linewidth = from_theme(borderwidth),
+    width = 0.9
   ),
 
   required_aes = c("x|y", "lower|xlower", "upper|xupper", "middle|xmiddle", "ymin|xmin", "ymax|xmax"),

R/geom-dotplot.R

@@ -194,12 +194,16 @@ GeomDotplot <- ggproto("GeomDotplot", Geom,
     alpha = NA,
     stroke = from_theme(borderwidth * 2),
     linetype = from_theme(linetype),
-    weight = 1
+    weight = 1,
+    width = 0.9
   ),
 
-  setup_data = function(data, params) {
-    data$width <- data$width %||%
-      params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9)
+  setup_data = function(self, data, params) {
+    data <- compute_data_size(
+      data, params$width,
+      default = self$default_aes$width,
+      zero = FALSE, discrete = TRUE
+    )
 
     # Set up the stacking function and range
     if (is.null(params$stackdir) || params$stackdir == "up") {

R/geom-errorbar.R

@@ -62,7 +62,7 @@ GeomErrorbar <- ggproto("GeomErrorbar", Geom,
     colour = from_theme(ink),
     linewidth = from_theme(linewidth),
     linetype = from_theme(linetype),
-    width = 0.5,
+    width = 0.9,
     alpha = NA
   ),
 
@@ -76,17 +76,21 @@ GeomErrorbar <- ggproto("GeomErrorbar", Geom,
 
   extra_params = c("na.rm", "orientation"),
 
-  setup_data = function(data, params) {
+  setup_data = function(self, data, params) {
     data$flipped_aes <- params$flipped_aes
     data <- flip_data(data, params$flipped_aes)
-    data$width <- data$width %||%
-      params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9)
+    data <- compute_data_size(
+      data, params$width,
+      default = self$default_aes$width,
+      zero = FALSE, discrete = TRUE
+    )
     data <- transform(data,
       xmin = x - width / 2, xmax = x + width / 2, width = NULL
     )
     flip_data(data, params$flipped_aes)
   },
 
+  # Note: `width` is vestigial
   draw_panel = function(self, data, panel_params, coord, lineend = "butt",
                         width = NULL, flipped_aes = FALSE) {
     data <- check_linewidth(data, snake_class(self))

R/geom-ribbon.R

@@ -126,7 +126,31 @@ GeomRibbon <- ggproto("GeomRibbon", Geom,
 
   draw_key = draw_key_polygon,
 
-  handle_na = function(data, params) {
+  handle_na = function(self, data, params) {
+
+    vars <- vapply(
+      strsplit(self$required_aes, "|", fixed = TRUE),
+      `[[`, i = 1, character(1)
+    )
+    if (params$flipped_aes || any(data$flipped_aes) %||% FALSE) {
+      vars <- switch_orientation(vars)
+    }
+    vars <- c(vars, self$non_missing_aes)
+
+    missing <- detect_missing(data, vars, finite = FALSE)
+    if (!any(missing)) {
+      return(data)
+    }
+    # We're rearranging groups to account for missing values
+    data$group <- vec_identify_runs(data_frame0(missing, data$group))
+    data <- vec_slice(data, !missing)
+
+    if (!params$na.rm) {
+      cli::cli_warn(
+        "Removed {sum(missing)} row{?s} containing missing values or values \\
+          outside the scale range ({.fn {snake_class(self)}})."
+      )
+    }
     data
   },
 
@@ -135,7 +159,6 @@ GeomRibbon <- ggproto("GeomRibbon", Geom,
                         flipped_aes = FALSE, outline.type = "both") {
     data <- check_linewidth(data, snake_class(self))
     data <- flip_data(data, flipped_aes)
-    if (na.rm) data <- data[stats::complete.cases(data[c("x", "ymin", "ymax")]), ]
     data <- data[order(data$group), ]
 
     # Check that aesthetics are constant

R/geom-tile.R

@@ -109,13 +109,20 @@ geom_tile <- function(mapping = NULL, data = NULL,
 GeomTile <- ggproto("GeomTile", GeomRect,
   extra_params = c("na.rm"),
 
-  setup_data = function(data, params) {
-
-    data$width <- data$width %||% params$width %||%
-      stats::ave(data$x, data$PANEL, FUN = function(x) resolution(x, FALSE, TRUE))
-    data$height <- data$height %||% params$height %||%
-      stats::ave(data$y, data$PANEL, FUN = function(y) resolution(y, FALSE, TRUE))
+  setup_data = function(self, data, params) {
 
+    data <- compute_data_size(
+      data, params$width,
+      default = self$default_aes$width,
+      panels = "by", target = "width",
+      zero = FALSE, discrete = TRUE
+    )
+    data <- compute_data_size(
+      data, params$height,
+      default = self$default_aes$height,
+      panels = "by", target = "height",
+      zero = FALSE, discrete = TRUE
+    )
     transform(data,
       xmin = x - width / 2,  xmax = x + width / 2,  width = NULL,
       ymin = y - height / 2, ymax = y + height / 2, height = NULL
@@ -127,7 +134,7 @@ GeomTile <- ggproto("GeomTile", GeomRect,
     colour = NA,
     linewidth = from_theme(0.4 * borderwidth),
     linetype = from_theme(bordertype),
-    alpha = NA, width = NA, height = NA
+    alpha = NA, width = 1, height = 1
   ),
 
   required_aes = c("x", "y"),