resolve merge conflict

Merge branch 'main' into scale_palettes

# Conflicts:
#	tests/testthat/test-guides.R

.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", , "hadley@posit.co", 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,
@@ -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)

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

@@ -461,7 +461,6 @@ export(guides)
 export(has_flipped_aes)
 export(is.Coord)
 export(is.coord)
-export(is.element)
 export(is.facet)
 export(is.geom)
 export(is.ggplot)
@@ -475,6 +474,7 @@ 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)

NEWS.md

@@ -1,5 +1,11 @@
 # ggplot2 (development version)
 
+* (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
@@ -182,6 +188,7 @@
 * 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
 
@@ -228,6 +235,7 @@ 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(
@@ -110,6 +112,11 @@
 #'   )
 #' ```
 #'
+#' 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))`
@@ -332,7 +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
@@ -358,3 +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)
+    }
+  }
+}
+

R/aes.R

@@ -198,9 +198,12 @@ rename_aes <- function(x) {
   }
   x
 }
-substitute_aes <- function(x) {
+
+# `x` is assumed to be a strict list of quosures;
+# it should have no non-quosure constants in it, even though `aes()` allows it.
+substitute_aes <- function(x, fun = standardise_aes_symbols, ...) {
   x <- lapply(x, function(aesthetic) {
-    as_quosure(standardise_aes_symbols(quo_get_expr(aesthetic)), env = environment(aesthetic))
+    as_quosure(fun(quo_get_expr(aesthetic), ...), env = environment(aesthetic))
   })
   class(x) <- "uneval"
   x

R/backports.R

@@ -67,6 +67,6 @@ on_load({
     as.mask <- grid::as.mask
   }
   if ("linearGradient" %in% getNamespaceExports("grid")) {
-    linearGradient <- grid::linearGradient()
+    linearGradient <- grid::linearGradient
   }
 })

R/bin.R

@@ -54,9 +54,7 @@ bin_breaks <- function(breaks, closed = c("right", "left")) {
 
 bin_breaks_width <- function(x_range, width = NULL, center = NULL,
                              boundary = NULL, closed = c("right", "left")) {
-  if (length(x_range) != 2) {
-    cli::cli_abort("{.arg x_range} must have two elements.")
-  }
+  check_length(x_range, 2L)
 
   # binwidth seems to be the argument name supplied to width. (stat-bin and stat-bindot)
   check_number_decimal(width, min = 0, allow_infinite = FALSE, arg = "binwidth")
@@ -106,9 +104,7 @@ bin_breaks_width <- function(x_range, width = NULL, center = NULL,
 
 bin_breaks_bins <- function(x_range, bins = 30, center = NULL,
                             boundary = NULL, closed = c("right", "left")) {
-  if (length(x_range) != 2) {
-    cli::cli_abort("{.arg x_range} must have two elements.")
-  }
+  check_length(x_range, 2L)
 
   check_number_whole(bins, min = 1)
   if (zero_range(x_range)) {

R/coord-.R

@@ -281,14 +281,6 @@ check_coord_limits <- function(
   if (is.null(limits)) {
     return(invisible(NULL))
   }
-  if (!obj_is_vector(limits) || length(limits) != 2) {
-    what <- "{.obj_type_friendly {limits}}"
-    if (is.vector(limits)) {
-      what <- paste0(what, " of length {length(limits)}")
-    }
-    cli::cli_abort(
-      paste0("{.arg {arg}} must be a vector of length 2, not ", what, "."),
-      call = call
-    )
-  }
+  check_object(limits, is_vector, "a vector", arg = arg, call = call)
+  check_length(limits, 2L, arg = arg, call = call)
 }

R/facet-.R

@@ -237,8 +237,8 @@ Facet <- ggproto("Facet", NULL,
     # Set panel names
     table$layout$name <- paste(
       "panel",
-      rep(seq_len(dim[2]), dim[1]),
-      rep(seq_len(dim[1]), each = dim[2]),
+      rep(seq_len(dim[2]), each = dim[1]),
+      rep(seq_len(dim[1]), dim[2]),
       sep = "-"
     )
 

R/facet-wrap.R

@@ -447,16 +447,8 @@ FacetWrap <- ggproto("FacetWrap", Facet,
 
   draw_panels = function(self, panels, layout, x_scales, y_scales, ranges, coord, data, theme, params) {
     if (inherits(coord, "CoordFlip")) {
-      if (params$free$x) {
-        layout$SCALE_X <- seq_len(nrow(layout))
-      } else {
-        layout$SCALE_X <- 1L
-      }
-      if (params$free$y) {
-        layout$SCALE_Y <- seq_len(nrow(layout))
-      } else {
-        layout$SCALE_Y <- 1L
-      }
+      # Switch the scales back
+      layout[c("SCALE_X", "SCALE_Y")] <- layout[c("SCALE_Y", "SCALE_X")]
     }
 
     panel_order <- order(layout$ROW, layout$COL)

R/geom-.R

@@ -136,6 +136,13 @@ Geom <- ggproto("Geom",
     themed_defaults <- eval_from_theme(default_aes, theme)
     default_aes[names(themed_defaults)] <- themed_defaults
 
+    # Mark staged/scaled defaults as modifier (#6135)
+    delayed <- is_scaled_aes(default_aes) | is_staged_aes(default_aes)
+    if (any(delayed)) {
+      modifiers <- defaults(modifiers, default_aes[delayed])
+      default_aes <- default_aes[!delayed]
+    }
+
     missing_eval <- lapply(default_aes, eval_tidy)
     # Needed for geoms with defaults set to NULL (e.g. GeomSf)
     missing_eval <- compact(missing_eval)
@@ -157,12 +164,10 @@ Geom <- ggproto("Geom",
     # This order means that they will have access to all default aesthetics
     if (length(modifiers) != 0) {
       # Set up evaluation environment
-      env <- child_env(baseenv(), after_scale = after_scale)
-      # Mask stage with stage_scaled so it returns the correct expression
-      stage_mask <- child_env(emptyenv(), stage = stage_scaled)
-      mask <- new_data_mask(as_environment(data, stage_mask), stage_mask)
-      mask$.data <- as_data_pronoun(mask)
-      modified_aes <- lapply(substitute_aes(modifiers),  eval_tidy, mask, env)
+      modified_aes <- eval_aesthetics(
+        substitute_aes(modifiers), data,
+        mask = list(stage = stage_scaled)
+      )
 
       # Check that all output are valid data
       nondata_modified <- check_nondata_cols(modified_aes)
@@ -177,11 +182,9 @@ Geom <- ggproto("Geom",
         ))
       }
 
-      names(modified_aes) <- names(rename_aes(modifiers))
-
       modified_aes <- cleanup_mismatched_data(modified_aes, nrow(data), "after_scale")
 
-      modified_aes <- data_frame0(!!!compact(modified_aes))
+      modified_aes <- data_frame0(!!!modified_aes)
 
       data <- data_frame0(!!!defaults(modified_aes, data))
     }

R/geom-defaults.R

@@ -11,7 +11,17 @@
 #' @keywords internal
 #' @note
 #' Please note that geom defaults can be set *en masse* via the `theme(geom)`
-#' argument.
+#' argument. The guidelines for when to use which function are as follows:
+#'
+#' * If you want to change defaults for all geoms in all plots, use
+#'   `theme_update(geom = element_geom(...))`.
+#' * If you want to change defaults for all geoms in a single plot, use
+#'   `+ theme(geom = element_geom(...))`.
+#' * If you want to change defaults for one geom in all plots, use
+#'   `update_geom_defaults()`.
+#' * If you want to change settings for one geom in a single plot, use fixed
+#'   aesthetic parameters in a layer, like so: `geom_point(colour = "red")`.
+#'
 #' @export
 #' @examples
 #'

R/geom-histogram.R

@@ -17,6 +17,12 @@
 #' one change at a time. You may need to look at a few options to uncover
 #' the full story behind your data.
 #'
+#' By default, the _height_ of the bars represent the counts within each bin.
+#' However, there are situations where this behavior might produce misleading
+#' plots (e.g., when non-equal-width bins are used), in which case it might be
+#' preferable to have the _area_ of the bars represent the counts (by setting
+#' `aes(y = after_stat(count / width))`). See example below.
+#'
 #' In addition to `geom_histogram()`, you can create a histogram plot by using
 #' `scale_x_binned()` with [geom_bar()]. This method by default plots tick marks
 #' in between each bar.
@@ -63,6 +69,18 @@
 #' ggplot(diamonds, aes(price, after_stat(density), colour = cut)) +
 #'   geom_freqpoly(binwidth = 500)
 #'
+#'
+#' # When using the non-equal-width bins, we should set the area of the bars to
+#' # represent the counts (not the height).
+#' # Here we're using 10 equi-probable bins:
+#' price_bins <- quantile(diamonds$price, probs = seq(0, 1, length = 11))
+#'
+#' ggplot(diamonds, aes(price)) +
+#'   geom_histogram(breaks = price_bins, color = "black") # misleading (height = count)
+#'
+#' ggplot(diamonds, aes(price, after_stat(count / width))) +
+#'   geom_histogram(breaks = price_bins, color = "black") # area = count
+#'
 #' if (require("ggplot2movies")) {
 #' # Often we don't want the height of the bar to represent the
 #' # count of observations, but the sum of some other variable.

R/geom-map.R

@@ -22,7 +22,7 @@ NULL
 #' # how `geom_map()` works. It requires two data frames:
 #' # One contains the coordinates of each polygon (`positions`), and is
 #' # provided via the `map` argument. The other contains the
-#' # other the values associated with each polygon (`values`).  An id
+#' # values associated with each polygon (`values`).  An id
 #' # variable links the two together.
 #'
 #' ids <- factor(c("1.1", "2.1", "1.2", "2.2", "1.3", "2.3"))

R/geom-sf.R

@@ -238,7 +238,8 @@ GeomSf <- ggproto("GeomSf", Geom,
     linewidth[is_point] <- stroke[is_point]
 
     gp <- gpar(
-      col = colour, fill = fill, fontsize = font_size, lwd = linewidth,
+      col = colour, fill = fill, fontsize = font_size,
+      lwd = linewidth, lty = data$linetype,
       lineend = lineend, linejoin = linejoin, linemitre = linemitre
     )
 

R/guide-.R

@@ -381,7 +381,7 @@ Guide <- ggproto(
   # Renders tickmarks
   build_ticks = function(key, elements, params, position = params$position,
                          length = elements$ticks_length) {
-    if (!is.element(elements)) {
+    if (!is.theme_element(elements)) {
       elements <- elements$ticks
     }
     if (!inherits(elements, "element_line")) {