Merge branch 'main' into contour_rotation

Author: teunbrand

.github/workflows/R-CMD-check.yaml

@@ -63,7 +63,7 @@ jobs:
           cache-version: 3
           extra-packages: >
             any::rcmdcheck,
-            Hmisc=?ignore-before-r=4.1.0,
+            Hmisc=?ignore-before-r=4.2.0,
             quantreg=?ignore-before-r=4.3.0
           needs: check
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggplot2
-Version: 3.5.1.9000
 Title: Create Elegant Data Visualisations Using the Grammar of Graphics
+Version: 3.5.1.9000
 Authors@R: c(
     person("Hadley", "Wickham", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0003-4757-117X")),
@@ -30,7 +30,7 @@ License: MIT + file LICENSE
 URL: https://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2
 BugReports: https://github.com/tidyverse/ggplot2/issues
 Depends:
-    R (>= 3.5)
+    R (>= 4.0)
 Imports: 
     cli,
     grDevices,
@@ -39,11 +39,9 @@ Imports:
     isoband,
     lifecycle (> 1.0.1),
     MASS,
-    mgcv,
     rlang (>= 1.1.0),
     scales (>= 1.3.0),
     stats,
-    tibble,
     vctrs (>= 0.6.0),
     withr (>= 2.5.0)
 Suggests:
@@ -55,6 +53,7 @@ Suggests:
     knitr,
     mapproj,
     maps,
+    mgcv,
     multcomp,
     munsell,
     nlme,
@@ -67,6 +66,7 @@ Suggests:
     sf (>= 0.7-3),
     svglite (>= 2.1.2),
     testthat (>= 3.1.5),
+    tibble,
     vdiffr (>= 1.0.6),
     xml2
 Enhances: 
@@ -75,6 +75,7 @@ VignetteBuilder:
     knitr
 Config/Needs/website: ggtext, tidyr, forcats, tidyverse/tidytemplate
 Config/testthat/edition: 3
+Config/usethis/last-upkeep: 2024-10-24
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
@@ -276,7 +277,6 @@ Collate:
     'utilities-break.R'
     'utilities-grid.R'
     'utilities-help.R'
-    'utilities-matrix.R'
     'utilities-patterns.R'
     'utilities-resolution.R'
     'utilities-tidy-eval.R'

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2020 ggplot2 authors
+Copyright (c) 2024 ggplot2 core developer team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -84,8 +84,6 @@ S3method(guide_train,default)
 S3method(guide_transform,default)
 S3method(heightDetails,titleGrob)
 S3method(heightDetails,zeroGrob)
-S3method(interleave,default)
-S3method(interleave,unit)
 S3method(limits,Date)
 S3method(limits,POSIXct)
 S3method(limits,POSIXlt)
@@ -126,8 +124,6 @@ S3method(scale_type,logical)
 S3method(scale_type,numeric)
 S3method(scale_type,ordered)
 S3method(scale_type,sfc)
-S3method(single_value,default)
-S3method(single_value,factor)
 S3method(summary,ggplot)
 S3method(vec_cast,character.mapped_discrete)
 S3method(vec_cast,double.mapped_discrete)
@@ -344,6 +340,7 @@ export(draw_key_vpath)
 export(dup_axis)
 export(el_def)
 export(element_blank)
+export(element_geom)
 export(element_grob)
 export(element_line)
 export(element_rect)
@@ -367,6 +364,7 @@ export(find_panel)
 export(flip_data)
 export(flipped_names)
 export(fortify)
+export(from_theme)
 export(geom_abline)
 export(geom_area)
 export(geom_bar)
@@ -422,7 +420,9 @@ export(geom_violin)
 export(geom_vline)
 export(get_alt_text)
 export(get_element_tree)
+export(get_geom_defaults)
 export(get_guide_data)
+export(get_labs)
 export(get_last_plot)
 export(get_layer_data)
 export(get_layer_grob)
@@ -460,10 +460,21 @@ export(guide_transform)
 export(guides)
 export(has_flipped_aes)
 export(is.Coord)
+export(is.coord)
 export(is.facet)
+export(is.geom)
 export(is.ggplot)
 export(is.ggproto)
+export(is.guide)
+export(is.guides)
+export(is.layer)
+export(is.mapping)
+export(is.margin)
+export(is.position)
+export(is.scale)
+export(is.stat)
 export(is.theme)
+export(is.theme_element)
 export(label_both)
 export(label_bquote)
 export(label_context)
@@ -513,6 +524,8 @@ export(remove_missing)
 export(render_axes)
 export(render_strips)
 export(replace_theme)
+export(reset_geom_defaults)
+export(reset_stat_defaults)
 export(reset_theme_settings)
 export(resolution)
 export(scale_alpha)
@@ -733,7 +746,6 @@ importFrom(grid,unit)
 importFrom(lifecycle,deprecated)
 importFrom(scales,alpha)
 importFrom(stats,setNames)
-importFrom(tibble,tibble)
 importFrom(utils,.DollarNames)
 importFrom(utils,head)
 importFrom(utils,tail)

NEWS.md

@@ -2,6 +2,49 @@
 
 * `geom_contour()` should be able to recognise a rotated grid of points 
   (@teunbrand, #4320)
+* `geom_boxplot()` gains additional arguments to style the colour, linetype and
+  linewidths of the box, whiskers, median line and staples (@teunbrand, #5126)
+* (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now
+  evaluated in the context of data (@teunbrand, #6135)
+* Fixed bug where binned scales wouldn't simultaneously accept transformations
+  and function-limits (@teunbrand, #6144).
+* Fixed bug where the `ggplot2::`-prefix did not work with `stage()` 
+  (@teunbrand, #6104).
+* New `get_labs()` function for retrieving completed plot labels 
+  (@teunbrand, #6008).
+* Built-in `theme_*()` functions now have `ink` and `paper` arguments to control
+  foreground and background colours respectively (@teunbrand)
+* The `summary()` method for ggplots is now more terse about facets 
+  (@teunbrand, #5989).
+* `guide_bins()`, `guide_colourbar()` and `guide_coloursteps()` gain an `angle`
+  argument to overrule theme settings, similar to `guide_axis(angle)` 
+  (@teunbrand, #4594).
+* `coord_*(expand)` can now take a logical vector to control expansion at any
+  side of the panel (top, right, bottom, left) (@teunbrand, #6020)
+* (Breaking) The defaults for all geoms can be set at one in the theme. 
+  (@teunbrand based on pioneering work by @dpseidel, #2239)
+    * A new `theme(geom)` argument is used to track these defaults.
+    * The `element_geom()` function can be used to populate that argument.
+    * The `from_theme()` function allows access to the theme default fields from
+      inside the `aes()` function.
+* Passing empty unmapped aesthetics to layers raises a warning instead of
+  throwing an error (@teunbrand, #6009).
+* Moved {mgcv} from Imports to Suggests (@teunbrand, #5986)
+* New `reset_geom_defaults()` and `reset_stat_defaults()` to restore all geom or
+  stat default aesthetics at once (@teunbrand, #5975).
+* `facet_wrap()` can have `space = "free_x"` with 1-row layouts and 
+  `space = "free_y"` with 1-column layouts (@teunbrand)
+* Secondary axes respect `n.breaks` setting in continuous scales (@teunbrand, #4483).
+* Layers can have names (@teunbrand, #4066).
+* (internal) improvements to `pal_qualitative()` (@teunbrand, #5013)
+* `coord_radial(clip = "on")` clips to the panel area when the graphics device
+  supports clipping paths (@teunbrand, #5952).
+* (internal) Panel clipping responsibility moved from Facet class to Coord 
+  class through new `Coord$draw_panel()` method.
+* `theme(strip.clip)` now defaults to `"on"` and is independent of Coord 
+  clipping (@teunbrand, 5952).
+* (internal) rearranged the code of `Facet$draw_panels()` method (@teunbrand).
+* Axis labels are now justified across facet panels (@teunbrand, #5820)
 * Fixed bug in `stat_function()` so x-axis title now produced automatically 
   when no data added. (@phispu, #5647).
 * geom_sf now accepts shape names (@sierrajohnson, #5808)
@@ -139,6 +182,17 @@
   (@teunbrand, #5938, #4327).
 * Fixed bug where empty discrete scales weren't recognised as such 
   (@teunbrand, #5945).
+* (internal) The summary function of `stat_summary()` and `stat_summary_bin()` 
+  is setup once in total instead of once per group (@teunbrand, #5971)
+* `facet_grid(space = "free")` can now be combined with `coord_fixed()` 
+  (@teunbrand, #4584).
+* `theme_classic()` now has black ticks and text instead of dark gray. In 
+  addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978).
+* {tibble} is now suggested instead of imported (@teunbrand, #5986)
+* The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, 
+  `labs()` and several guides (@teunbrand, #3196).
+* `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647).
+* Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449)
 
 # ggplot2 3.5.1
 
@@ -185,6 +239,7 @@ documentation updates.
 * `annotate()` now warns about `stat` or `position` arguments (@teunbrand, #5151)
 * `guide_coloursteps(even.steps = FALSE)` now works with discrete data that has 
   been formatted by `cut()` (@teunbrand, #3877).
+* `ggsave()` now offers to install svglite if needed (@eliocamp, #6166).
 
 # ggplot2 3.5.0
 

R/aes-evaluation.R

@@ -32,7 +32,7 @@
 #' Below follows an overview of the three stages of evaluation and how aesthetic
 #' evaluation can be controlled.
 #'
-#' ## Stage 1: direct input
+#' ## Stage 1: direct input at the start
 #' The default is to map at the beginning, using the layer data provided by
 #' the user. If you want to map directly from the layer data you should not do
 #' anything special. This is the only stage where the original layer data can
@@ -87,17 +87,19 @@
 #' ```
 #'
 #' ## Complex staging
-#' If you want to map the same aesthetic multiple times, e.g. map `x` to a
-#' data column for the stat, but remap it for the geom, you can use the
-#' `stage()` function to collect multiple mappings.
+#' Sometimes, you may want to map the same aesthetic multiple times, e.g. map
+#' `x` to a data column at the start for the layer stat, but remap it later to
+#' a variable from the stat transformation for the layer geom. The `stage()`
+#' function allows you to control multiple mappings for the same aesthetic
+#' across all three stages of evaluation.
 #'
 #' ```r
 #' # Use stage to modify the scaled fill
 #' ggplot(mpg, aes(class, hwy)) +
 #'   geom_boxplot(aes(fill = stage(class, after_scale = alpha(fill, 0.4))))
 #'
 #' # Using data for computing summary, but placing label elsewhere.
-#' # Also, we're making our own computed variable to use for the label.
+#' # Also, we're making our own computed variables to use for the label.
 #' ggplot(mpg, aes(class, displ)) +
 #'   geom_violin() +
 #'   stat_summary(
@@ -109,6 +111,18 @@
 #'     fun.data = ~ round(data.frame(mean = mean(.x), sd = sd(.x)), 2)
 #'   )
 #' ```
+#'
+#' Conceptually, `aes(x)` is equivalent to `aes(stage(start = x))`, and
+#' `aes(after_stat(count))` is equivalent to `aes(stage(after_stat = count))`,
+#' and so on. `stage()` is most useful when at least two of its arguments are
+#' specified.
+#'
+#' ## Theme access
+#' The `from_theme()` function can be used to acces the [`element_geom()`]
+#' fields of the `theme(geom)` argument. Using `aes(colour = from_theme(ink))`
+#' and `aes(colour = from_theme(accent))` allows swapping between foreground and
+#' accent colours.
+#'
 #' @rdname aes_eval
 #' @name aes_eval
 #'
@@ -192,6 +206,13 @@ stat <- function(x) {
 after_scale <- function(x) {
   x
 }
+
+#' @rdname aes_eval
+#' @export
+from_theme <- function(x) {
+  x
+}
+
 #' @rdname aes_eval
 #' @export
 stage <- function(start = NULL, after_stat = NULL, after_scale = NULL) {
@@ -205,12 +226,10 @@ stage_scaled <- function(start = NULL, after_stat = NULL, after_scale = NULL) {
 }
 
 # Regex to determine if an identifier refers to a calculated aesthetic
+# The pattern includes ye olde '...var...' syntax, which was
+# deprecated in 3.4.0 in favour of `after_stat()`
 match_calculated_aes <- "^\\.\\.([a-zA-Z._]+)\\.\\.$"
 
-is_dotted_var <- function(x) {
-  grepl(match_calculated_aes, x)
-}
-
 # Determine if aesthetic is calculated
 is_calculated_aes <- function(aesthetics, warn = FALSE) {
   vapply(aesthetics, is_calculated, warn = warn, logical(1), USE.NAMES = FALSE)
@@ -221,6 +240,9 @@ is_scaled_aes <- function(aesthetics) {
 is_staged_aes <- function(aesthetics) {
   vapply(aesthetics, is_staged, logical(1), USE.NAMES = FALSE)
 }
+is_themed_aes <- function(aesthetics) {
+  vapply(aesthetics, is_themed, logical(1), USE.NAMES = FALSE)
+}
 is_calculated <- function(x, warn = FALSE) {
   if (is_call(get_expr(x), "after_stat")) {
     return(TRUE)
@@ -229,7 +251,8 @@ is_calculated <- function(x, warn = FALSE) {
   if (is.null(x) || is.atomic(x)) {
     FALSE
   } else if (is.symbol(x)) {
-    res <- is_dotted_var(as.character(x))
+    # Test if x is a dotted variable
+    res <- grepl(match_calculated_aes, as.character(x))
     if (res && warn) {
       what <- I(paste0("The dot-dot notation (`", x, "`)"))
       var <- gsub(match_calculated_aes, "\\1", as.character(x))
@@ -263,6 +286,9 @@ is_scaled <- function(x) {
 is_staged <- function(x) {
   is_call(get_expr(x), "stage")
 }
+is_themed <- function(x) {
+  is_call(get_expr(x), "from_theme")
+}
 
 # Strip dots from expressions
 strip_dots <- function(expr, env, strip_pronoun = FALSE) {
@@ -313,7 +339,7 @@ strip_stage <- function(expr) {
   } else if (is_call(uq_expr, "stage")) {
     uq_expr <- call_match(uq_expr, stage)
     # Prefer stat mapping if present, otherwise original mapping (fallback to
-    # scale mapping) but there should always be two arguments to stage()
+    # scale mapping)
     uq_expr$after_stat %||% uq_expr$start %||% uq_expr$after_scale
   } else {
     expr
@@ -339,3 +365,39 @@ make_labels <- function(mapping) {
   }
   Map(default_label, names(mapping), mapping)
 }
+
+eval_aesthetics <- function(aesthetics, data, mask = NULL) {
+
+  env <- child_env(base_env())
+
+  # Here we mask functions, often to replace `stage()` with context appropriate
+  # functions `stage_calculated()`/`stage_scaled()`.
+  if (length(mask) > 0) {
+    aesthetics <- substitute_aes(aesthetics, mask_function, mask = mask)
+  }
+
+  evaled <- lapply(aesthetics, eval_tidy, data = data, env = env)
+  names(evaled) <- names(aesthetics)
+  compact(rename_aes(evaled))
+}
+
+# `mask` is a list of functions where `names(mask)` indicate names of functions
+# that need to be replaced, and `mask[[i]]` is the function to replace it
+# with.
+mask_function <- function(x, mask) {
+  if (!is.call(x)) {
+    return(x)
+  }
+  nms <- names(mask)
+  x[-1] <- lapply(x[-1], mask_function, mask = mask)
+  if (!is_call(x, nms)) {
+    return(x)
+  }
+  for (nm in nms) {
+    if (is_call(x, nm)) {
+      x[[1]] <- mask[[nm]]
+      return(x)
+    }
+  }
+}
+