Merge branch 'main' into boxplot_staples

NEWS.md

@@ -3,6 +3,26 @@
 * `geom_boxplot()` gains a new argument, `staplewidth` that can draw staples
   at the ends of whiskers (@teunbrand, #5126)
 
+* The `size` argument in `annotation_logticks()` has been deprecated in favour
+  of the `linewidth` argument (#5292).
+
+* `geom_boxplot()` gains an `outliers` argument to switch outliers on or off,
+  in a manner that does affects the scale range. For hiding outliers that does
+  not affect the scale range, you can continue to use `outlier.shape = NA` 
+  (@teunbrand, #4892).
+
+* Binned scales now treat `NA`s in limits the same way continuous scales do 
+  (#5355).
+
+* Binned scales work better with `trans = "reverse"` (#5355).
+
+* The `legend.text.align` and `legend.title.align` arguments in `theme()` are 
+  deprecated. The `hjust` setting of the `legend.text` and `legend.title` 
+  elements continues to fulfil the role of text alignment (@teunbrand, #5347).
+
+* Integers are once again valid input to theme arguments that expect numeric
+  input (@teunbrand, #5369)
+
 * Nicer error messages for xlim/ylim arguments in coord-* functions
   (@92amartins, #4601, #5297).
 
@@ -60,6 +80,8 @@
     * `guide_coloursteps()` and `guide_bins()` sort breaks (#5152).
     * `guide_axis()` gains a `cap` argument that can be used to trim the
       axis line to extreme breaks (#4907).
+    * Fixed regression in `guide_legend()` where the `linewidth` key size
+      wasn't adapted to the width of the lines (#5160).
 
 * `geom_label()` now uses the `angle` aesthetic (@teunbrand, #2785)
 * 'lines' units in `geom_label()`, often used in the `label.padding` argument, 

R/annotation-logticks.R

@@ -21,11 +21,12 @@
 #'   using `scale_y_log10()`. It should be `FALSE` when using
 #'   `coord_trans(y = "log10")`.
 #' @param colour Colour of the tick marks.
-#' @param size Thickness of tick marks, in mm.
+#' @param linewidth Thickness of tick marks, in mm.
 #' @param linetype Linetype of tick marks (`solid`, `dashed`, etc.)
 #' @param alpha The transparency of the tick marks.
 #' @param color An alias for `colour`.
 #' @param ... Other parameters passed on to the layer
+#' @param size `r lifecycle::badge("deprecated")`
 #'
 #' @export
 #' @seealso [scale_y_continuous()], [scale_y_log10()] for log scale
@@ -81,11 +82,17 @@
 #' )
 annotation_logticks <- function(base = 10, sides = "bl", outside = FALSE, scaled = TRUE,
     short = unit(0.1, "cm"), mid = unit(0.2, "cm"), long = unit(0.3, "cm"),
-    colour = "black", size = 0.5, linetype = 1, alpha = 1, color = NULL, ...)
+    colour = "black", linewidth = 0.5, linetype = 1, alpha = 1, color = NULL, ...,
+    size = deprecated())
 {
   if (!is.null(color))
     colour <- color
 
+  if (lifecycle::is_present(size)) {
+    deprecate_soft0("3.5.0", I("Using the `size` aesthetic in this geom"), I("`linewidth`"))
+    linewidth <- linewidth %||% size
+  }
+
   layer(
     data = dummy_data(),
     mapping = NULL,
@@ -103,7 +110,7 @@ annotation_logticks <- function(base = 10, sides = "bl", outside = FALSE, scaled
       mid = mid,
       long = long,
       colour = colour,
-      size = size,
+      linewidth = linewidth,
       linetype = linetype,
       alpha = alpha,
       ...
@@ -163,14 +170,14 @@ GeomLogticks <- ggproto("GeomLogticks", Geom,
         ticks$x_b <- with(data, segmentsGrob(
           x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"),
           y0 = unit(xticks$start, "cm"), y1 = unit(xticks$end, "cm"),
-          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = size * .pt)
+          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt)
         ))
       }
       if (grepl("t", sides) && nrow(xticks) > 0) {
         ticks$x_t <- with(data, segmentsGrob(
           x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"),
           y0 = unit(1, "npc") - unit(xticks$start, "cm"), y1 = unit(1, "npc") - unit(xticks$end, "cm"),
-          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = size * .pt)
+          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt)
         ))
       }
     }
@@ -201,22 +208,22 @@ GeomLogticks <- ggproto("GeomLogticks", Geom,
         ticks$y_l <- with(data, segmentsGrob(
           y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"),
           x0 = unit(yticks$start, "cm"), x1 = unit(yticks$end, "cm"),
-          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = size * .pt)
+          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt)
         ))
       }
       if (grepl("r", sides) && nrow(yticks) > 0) {
         ticks$y_r <- with(data, segmentsGrob(
           y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"),
           x0 = unit(1, "npc") - unit(yticks$start, "cm"), x1 = unit(1, "npc") - unit(yticks$end, "cm"),
-          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = size * .pt)
+          gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt)
         ))
       }
     }
 
     gTree(children = inject(gList(!!!ticks)))
   },
 
-  default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = 1)
+  default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = 1)
 )
 
 

R/coord-cartesian-.R

@@ -147,37 +147,9 @@ view_scales_from_scale <- function(scale, coord_limits = NULL, expand = TRUE) {
 }
 
 panel_guides_grob <- function(guides, position, theme) {
-  pair <- guide_for_position(guides, position) %||%
-    list(guide = guide_none(), params = NULL)
-  pair$guide$draw(theme, pair$params)
-}
-
-guide_for_position <- function(guides, position) {
-  params <- guides$params
-  has_position <- vapply(
-    params, function(p) identical(p$position, position), logical(1)
-  )
-  if (!any(has_position)) {
-    return(NULL)
-  }
-
-  # Subset guides and parameters
-  guides <- guides$get_guide(has_position)
-  params <- params[has_position]
-  # Pair up guides with parameters
-  pairs <- Map(list, guide = guides, params = params)
-
-  # Early exit, nothing to merge
-  if (length(pairs) == 1) {
-    return(pairs[[1]])
+  if (!inherits(guides, "Guides")) {
+    return(zeroGrob())
   }
-
-  # TODO: There must be a smarter way to merge these
-  order <- order(vapply(params, function(p) as.numeric(p$order), numeric(1)))
-  Reduce(
-    function(old, new) {
-      old$guide$merge(old$params, new$guide, new$params)
-    },
-    pairs[order]
-  )
+  pair <- guides$get_position(position)
+  pair$guide$draw(theme, pair$params)
 }

R/geom-boxplot.R

@@ -33,19 +33,19 @@
 #' @inheritParams geom_bar
 #' @param geom,stat Use to override the default connection between
 #'   `geom_boxplot()` and `stat_boxplot()`.
+#' @param outliers Whether to display (`TRUE`) or discard (`FALSE`) outliers
+#'   from the plot. Hiding or discarding outliers can be useful when, for
+#'   example, raw data points need to be displayed on top of the boxplot.
+#'   By discarding outliers, the axis limits will adapt to the box and whiskers
+#'   only, not the full data range. If outliers need to be hidden and the axes
+#'   needs to show the full data range, please use `outlier.shape = NA` instead.
 #' @param outlier.colour,outlier.color,outlier.fill,outlier.shape,outlier.size,outlier.stroke,outlier.alpha
 #'   Default aesthetics for outliers. Set to `NULL` to inherit from the
 #'   aesthetics used for the box.
 #'
 #'   In the unlikely event you specify both US and UK spellings of colour, the
 #'   US spelling will take precedence.
 #'
-#'   Sometimes it can be useful to hide the outliers, for example when overlaying
-#'   the raw data points on top of the boxplot. Hiding the outliers can be achieved
-#'   by setting `outlier.shape = NA`. Importantly, this does not remove the outliers,
-#'   it only hides them, so the range calculated for the y-axis will be the
-#'   same with outliers shown and outliers hidden.
-#'
 #' @param notch If `FALSE` (default) make a standard box plot. If
 #'   `TRUE`, make a notched box plot. Notches are used to compare groups;
 #'   if the notches of two boxes do not overlap, this suggests that the medians
@@ -111,6 +111,7 @@
 geom_boxplot <- function(mapping = NULL, data = NULL,
                          stat = "boxplot", position = "dodge2",
                          ...,
+                         outliers = TRUE,
                          outlier.colour = NULL,
                          outlier.color = NULL,
                          outlier.fill = NULL,
@@ -136,7 +137,9 @@ geom_boxplot <- function(mapping = NULL, data = NULL,
       position$preserve <- "single"
     }
   }
+
   check_number_decimal(staplewidth)
+  check_bool(outliers)
 
   layer(
     data = data,
@@ -147,6 +150,7 @@ geom_boxplot <- function(mapping = NULL, data = NULL,
     show.legend = show.legend,
     inherit.aes = inherit.aes,
     params = list2(
+      outliers = outliers,
       outlier.colour = outlier.color %||% outlier.colour,
       outlier.fill = outlier.fill,
       outlier.shape = outlier.shape,
@@ -172,7 +176,7 @@ 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"),
+  extra_params = c("na.rm", "width", "orientation", "outliers"),
 
   setup_params = function(data, params) {
     params$flipped_aes <- has_flipped_aes(data, params)
@@ -185,6 +189,10 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom,
     data$width <- data$width %||%
       params$width %||% (resolution(data$x, FALSE) * 0.9)
 
+    if (isFALSE(params$outliers)) {
+      data$outliers <- NULL
+    }
+
     if (!is.null(data$outliers)) {
       suppressWarnings({
         out_min <- vapply(data$outliers, min, numeric(1))

R/guide-.R

@@ -74,7 +74,79 @@ new_guide <- function(..., available_aes = "any", super) {
 #' To create a new type of Guide object, you typically will want to override
 #' one or more of the following:
 #'
-#'  TODO: Fill this in properly
+#' Properties:
+#'
+#' - `available_aes` A `character` vector with aesthetics that this guide
+#'   supports. The value `"any"` indicates all non-position aesthetics.
+#'
+#' - `params` A named `list` of parameters that the guide needs to function.
+#'   It has the following roles:
+#'
+#'   - `params` provides the defaults for a guide.
+#'   - `names(params)` determines what are valid arguments to `new_guide()`.
+#'   Some parameters are *required* to render the guide. These are: `title`,
+#'   `name`, `position`, `direction`, `order` and `hash`.
+#'   - During build stages, `params` holds information about the guide.
+#'
+#' - `elements` A named list of `character`s, giving the name of theme elements
+#'   that should be retrieved automatically, for example `"legend.text"`.
+#'
+#' - `hashables` An `expression` that can be evaluated in the context of
+#'   `params`. The hash of the evaluated expression determines the merge
+#'   compatibility of guides, and is stored in `params$hash`.
+#'
+#' Methods:
+#'
+#' - `extract_key()` Returns a `data.frame` with (mapped) breaks and labels
+#'   extracted from the scale, which will be stored in `params$key`.
+#'
+#' - `extract_decor()` Returns a `data.frame` containing other structured
+#'   information extracted from the scale, which will be stored in
+#'   `params$decor`. The `decor` has a guide-specific  meaning: it is the bar in
+#'   `guide_colourbar()`, but specifies the `axis.line` in `guide_axis()`.
+#'
+#' - `extract_params()` Updates the `params` with other, unstructured
+#'   information from the scale. An example of this is inheriting the guide's
+#'   title from the `scale$name` field.
+#'
+#' - `transform()` Updates the `params$key` based on the coordinates. This
+#'   applies to position guides, as it rescales the aesthetic to the \[0, 1\]
+#'   range.
+#'
+#' - `merge()` Combines information from multiple guides with the same
+#'   `params$hash`. This ensures that e.g. `guide_legend()` can display both
+#'   `shape` and `colour` in the same guide.
+#'
+#' - `get_layer_key()` Extract information from layers. This can be used to
+#'   check that the guide's aesthetic is actually in use, or to gather
+#'   information about how legend keys should be displayed.
+#'
+#' - `setup_params()` Set up parameters at the beginning of drawing stages.
+#'   It can be used to overrule user-supplied parameters or perform checks on
+#'   the `params` property.
+#'
+#' - `override_elements()` Take populated theme elements derived from the
+#'   `elements` property and allows overriding these theme settings.
+#'
+#' - `build_title()` Render the guide's title.
+#'
+#' - `build_labels()` Render the guide's labels.
+#'
+#' - `build_decor()` Render the `params$decor`, which is different for every
+#'   guide.
+#'
+#' - `build_ticks()` Render tick marks.
+#'
+#' - `measure_grobs()` Measure dimensions of the graphical objects produced
+#'   by the `build_*()` methods to be used in the layout or assembly.
+#'
+#' - `arrange_layout()` Set up a layout for how graphical objects produced by
+#'   the `build_*()` methods should be arranged.
+#'
+#' - `assemble_drawing()` Take the graphical objects produced by the `build_*()`
+#'   methods, the measurements from `measure_grobs()` and layout from
+#'   `arrange_layout()` to finalise the guide.
+#'
 #' @rdname ggplot2-ggproto
 #' @format NULL
 #' @usage NULL
@@ -117,14 +189,15 @@ Guide <- ggproto(
       return(NULL)
     }
     params$decor <- inject(self$extract_decor(scale, !!!params))
-    self$extract_params(scale, params, self$hashables, ...)
+    params <- self$extract_params(scale, params, ...)
+    # Make hash
+    # TODO: Maybe we only need the hash on demand during merging?
+    params$hash <- hash(lapply(unname(self$hashables), eval_tidy, data = params))
+    params
   },
 
   # Setup parameters that are only available after training
-  # TODO: Maybe we only need the hash on demand during merging?
-  extract_params = function(scale, params, hashables, ...) {
-    # Make hash
-    params$hash <- hash(lapply(unname(hashables), eval_tidy, data = params))
+  extract_params = function(scale, params, ...) {
     params
   },
 
@@ -137,13 +210,18 @@ Guide <- ggproto(
 
     mapped <- scale$map(breaks)
     labels <- scale$get_labels(breaks)
+    # {vctrs} doesn't play nice with expressions, convert to list.
+    # see also https://github.com/r-lib/vctrs/issues/559
+    if (is.expression(labels)) {
+      labels <- as.list(labels)
+    }
 
     key <- data_frame(mapped, .name_repair = ~ aesthetic)
     key$.value <- breaks
     key$.label <- labels
 
     if (is.numeric(breaks)) {
-      key[is.finite(breaks), , drop = FALSE]
+      vec_slice(key, is.finite(breaks))
     } else {
       key
     }
@@ -342,3 +420,14 @@ flip_names = c(
 # Shortcut for position argument matching
 .trbl <- c("top", "right", "bottom", "left")
 
+# Ensure that labels aren't a list of expressions, but proper expressions
+validate_labels <- function(labels) {
+  if (!is.list(labels)) {
+    return(labels)
+  }
+  if (any(vapply(labels, is.language, logical(1)))) {
+    do.call(expression, labels)
+  } else {
+    unlist(labels)
+  }
+}