debug examples following element restriction + adapt density_2d stat …

…& geom

NAMESPACE

@@ -201,6 +201,8 @@ export(StatCols)
 export(StatColsCenter)
 export(StatColsChull)
 export(StatColsCone)
+export(StatColsDensity2d)
+export(StatColsDensity2dFilled)
 export(StatColsEllipse)
 export(StatColsProjection)
 export(StatColsRule)
@@ -214,6 +216,8 @@ export(StatRows)
 export(StatRowsCenter)
 export(StatRowsChull)
 export(StatRowsCone)
+export(StatRowsDensity2d)
+export(StatRowsDensity2dFilled)
 export(StatRowsEllipse)
 export(StatRowsProjection)
 export(StatRowsRule)
@@ -240,6 +244,8 @@ export(draw_key_line)
 export(eigen_ord)
 export(geom_axis)
 export(geom_cols_axis)
+export(geom_cols_density_2d)
+export(geom_cols_density_2d_filled)
 export(geom_cols_interpolation)
 export(geom_cols_isoline)
 export(geom_cols_label)
@@ -261,6 +267,8 @@ export(geom_lineranges)
 export(geom_origin)
 export(geom_pointranges)
 export(geom_rows_axis)
+export(geom_rows_density_2d)
+export(geom_rows_density_2d_filled)
 export(geom_rows_interpolation)
 export(geom_rows_isoline)
 export(geom_rows_label)
@@ -328,6 +336,8 @@ export(stat_cols)
 export(stat_cols_center)
 export(stat_cols_chull)
 export(stat_cols_cone)
+export(stat_cols_density_2d)
+export(stat_cols_density_2d_filled)
 export(stat_cols_ellipse)
 export(stat_cols_projection)
 export(stat_cols_rule)
@@ -341,6 +351,8 @@ export(stat_rows)
 export(stat_rows_center)
 export(stat_rows_chull)
 export(stat_rows_cone)
+export(stat_rows_density_2d)
+export(stat_rows_density_2d_filled)
 export(stat_rows_ellipse)
 export(stat_rows_projection)
 export(stat_rows_rule)

NEWS.md

@@ -29,6 +29,17 @@ The 'projection' referential stat prepares segment endpoints between `x,y` posit
 
 A new 'rule' statistical transformation computes additional position aesthetics that the 'axis' geom uses to limit and offset axes. The stat is referential and expects a set of functions that compute limits `lower` and `upper` along the axes and `yintercept` and `xintercept` associated with offset axes. The 'axis' geom preprocesses these aesthetics to rule endpoints `xmin,ymin,xmax,ymax` and offset vectors `xend,yend` to force the plotting window to contain the limited axis segments or, if the axes remain lines, the offsets where they are centered.
 
+## standardized and restrictive elements parameter (breaking change)
+
+The `elements` parameter is now standardized across all statistical transformations (through the code generation process) and accepts more restrictive options:
+The value is argument-matched to `"active"`, `"score"`, or `"structure"`; these options may expand as additional supplementary elements are introduced.
+Moreover, the former default `"all"` is no longer accepted, which forecloses the trick of passing the element type to an aesthetic, e.g. `size = .element == "active"`, as had been used in several examples.
+
+## adapted density stat & geom
+
+Aided by element standardization, the classic `density_2d` statistical transformation and geometric construction are adapted to biplots.
+Currently, source code generation does not respect fixed parameters passed to `layer()` by the `stat_*()` and `geom_*()` shortcuts; as a consequence, `contour = TRUE` must be manually passed to `geom_*_density_2d()`.
+
 ## scaffold theme
 
 The 'biplot' theme has been renamed 'scaffold', with an alias for backward compatibility.

R/stat-projection.r

@@ -40,7 +40,6 @@
 #' @export
 stat_projection <- function(
     mapping = NULL, data = NULL, geom = "segment", position = "identity",
-    subset = NULL,
     referent = NULL,
     ...,
     show.legend = NA, inherit.aes = TRUE
@@ -71,7 +70,7 @@ StatProjection <- ggproto(
   "StatProjection", StatReferent,
 
   compute_group = function(data, scales,
-                           subset = NULL, referent = NULL, na.rm = FALSE) {
+                           referent = NULL, na.rm = FALSE) {
 
     # no referent means no projection
     if (is.null(referent) || ! is.data.frame(referent)) return(data.frame())

R/stat-referent.r

@@ -32,7 +32,6 @@
 stat_referent <- function(
     mapping = NULL, data = NULL,
     geom = "blank", position = "identity",
-    subset = NULL,
     referent = NULL,
     show.legend = NA,
     inherit.aes = TRUE,
@@ -96,7 +95,8 @@ StatReferent <- ggproto(
     params
   },
 
-  compute_group = function(data, scales, subset = NULL, referent = NULL) data
+  compute_group = function(data, scales,
+                           referent = NULL) data
 )
 
 # QUESTION: Why are the arguments apparently out of order?

R/zzz-biplot-geoms.r

@@ -25,6 +25,8 @@
 #' @inheritParams ggplot2::geom_point
 #' @inheritParams ggplot2::geom_path
 #' @inheritParams ggplot2::geom_polygon
+#' @inheritParams ggplot2::geom_density_2d
+#' @inheritParams ggplot2::geom_density_2d_filled
 #' @inheritParams ggplot2::geom_text
 #' @inheritParams ggplot2::geom_label
 #' @inheritParams ggrepel::geom_text_repel
@@ -229,6 +231,134 @@ geom_cols_polygon <- function(
   )
 }
 
+#' @rdname biplot-geoms
+#' @export
+geom_rows_density_2d <- function(
+  mapping = NULL,
+  data = NULL,
+  stat = "density_2d",
+  position = "identity",
+  ...,
+  contour_var = "density",
+  lineend = "butt",
+  linejoin = "round",
+  linemitre = 10,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+) {
+  layer(
+    mapping = mapping,
+    data = data,
+    stat = rows_stat(stat),
+    geom = GeomDensity2d,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      contour_var = contour_var,
+      lineend = lineend,
+      linejoin = linejoin,
+      linemitre = linemitre,
+      na.rm = na.rm,
+      ...
+    )
+  )
+}
+
+#' @rdname biplot-geoms
+#' @export
+geom_cols_density_2d <- function(
+  mapping = NULL,
+  data = NULL,
+  stat = "density_2d",
+  position = "identity",
+  ...,
+  contour_var = "density",
+  lineend = "butt",
+  linejoin = "round",
+  linemitre = 10,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+) {
+  layer(
+    mapping = mapping,
+    data = data,
+    stat = cols_stat(stat),
+    geom = GeomDensity2d,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      contour_var = contour_var,
+      lineend = lineend,
+      linejoin = linejoin,
+      linemitre = linemitre,
+      na.rm = na.rm,
+      ...
+    )
+  )
+}
+
+#' @rdname biplot-geoms
+#' @export
+geom_rows_density_2d_filled <- function(
+  mapping = NULL,
+  data = NULL,
+  stat = "density_2d_filled",
+  position = "identity",
+  ...,
+  contour_var = "density",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+) {
+  layer(
+    mapping = mapping,
+    data = data,
+    stat = rows_stat(stat),
+    geom = GeomDensity2dFilled,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      contour_var = contour_var,
+      na.rm = na.rm,
+      ...
+    )
+  )
+}
+
+#' @rdname biplot-geoms
+#' @export
+geom_cols_density_2d_filled <- function(
+  mapping = NULL,
+  data = NULL,
+  stat = "density_2d_filled",
+  position = "identity",
+  ...,
+  contour_var = "density",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+) {
+  layer(
+    mapping = mapping,
+    data = data,
+    stat = cols_stat(stat),
+    geom = GeomDensity2dFilled,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      contour_var = contour_var,
+      na.rm = na.rm,
+      ...
+    )
+  )
+}
+
 #' @rdname biplot-geoms
 #' @export
 geom_rows_text <- function(