re-design cross functions

DESCRIPTION

@@ -73,6 +73,8 @@ Collate:
     'alignpatch-patchwork.R'
     'alignpatch-title.R'
     'alignpatch-wrap.R'
+    'cross-.R'
+    'cross-gg.R'
     'dendrogram.R'
     'fortify-data_frame.R'
     'fortify-matrix.R'
@@ -109,7 +111,6 @@ Collate:
     'layout-stack-switch.R'
     'object-name.R'
     'plot-add.R'
-    'plot-align-cross.R'
     'plot-free-.R'
     'plot-free-gg.R'
     'raster-magick.R'

NAMESPACE

@@ -2,7 +2,7 @@
 
 S3method("$<-",AlignProto)
 S3method("+",alignpatches)
-S3method("[",alignLinkGtable)
+S3method("[",alignLineGtable)
 S3method("[",alignRangeGtable)
 S3method(.raster_magick,Layer)
 S3method(.raster_magick,QuadLayout)
@@ -26,7 +26,7 @@ S3method(alignpatch,Heatmap)
 S3method(alignpatch,HeatmapAnnotation)
 S3method(alignpatch,HeatmapList)
 S3method(alignpatch,LayoutProto)
-S3method(alignpatch,align_link_plot)
+S3method(alignpatch,align_line_plot)
 S3method(alignpatch,align_range_plot)
 S3method(alignpatch,alignpatches)
 S3method(alignpatch,default)
@@ -154,7 +154,7 @@ S3method(layout_and_add,QuadLayout)
 S3method(layout_and_add,StackLayout)
 S3method(layout_subtract,QuadLayout)
 S3method(layout_subtract,StackLayout)
-S3method(makeContent,alignLinkGtable)
+S3method(makeContent,alignLineGtable)
 S3method(makeContent,alignRangeGtable)
 S3method(makeContext,ggalign_raster_magick)
 S3method(make_wrap,alignpatches)
@@ -164,7 +164,9 @@ S3method(make_wrap,wrapped_plot)
 S3method(new_scheme_theme,scheme_theme)
 S3method(new_scheme_theme,theme)
 S3method(obj_print_footer,ggalign_area)
+S3method(object_name,AlignGg)
 S3method(object_name,AlignProto)
+S3method(object_name,CrossGg)
 S3method(object_name,QuadLayout)
 S3method(object_name,StackLayout)
 S3method(object_name,ggalign_align_plot)
@@ -252,7 +254,7 @@ S3method(stack_layout_add,QuadLayout)
 S3method(stack_layout_add,StackLayout)
 S3method(stack_layout_add,default)
 S3method(stack_layout_add,ggalign_align_plot)
-S3method(stack_layout_add,ggalign_cross_link)
+S3method(stack_layout_add,ggalign_cross)
 S3method(stack_layout_add,ggalign_free_plot)
 S3method(stack_layout_add,ggalign_with_quad)
 S3method(stack_layout_add,ggplot)
@@ -296,7 +298,7 @@ export(align_gg)
 export(align_group)
 export(align_hclust)
 export(align_kmeans)
-export(align_link)
+export(align_line)
 export(align_order)
 export(align_panel)
 export(align_plots)
@@ -311,8 +313,8 @@ export(area)
 export(cross_align)
 export(cross_alignh)
 export(cross_alignv)
+export(cross_gg)
 export(cross_layout)
-export(cross_link)
 export(dendrogram_data)
 export(draw_key_draw)
 export(element_polygon)
@@ -343,7 +345,6 @@ export(ggheatmap)
 export(ggoncoplot)
 export(ggpanel)
 export(ggside)
-export(ggstack)
 export(ggwrap)
 export(gpar)
 export(hclust2)

R/align-gg.R

@@ -111,7 +111,7 @@ align_gg <- function(data = waiver(), mapping = aes(), size = NULL,
     active <- deprecate_active(active, "align_gg",
         set_context = set_context, order = order, name = name
     )
-    align(AlignGG,
+    align(AlignGg,
         plot = ggplot(mapping = mapping),
         size = size, data = data,
         schemes = waiver(),
@@ -128,7 +128,7 @@ align_gg <- function(data = waiver(), mapping = aes(), size = NULL,
 ggalign <- align_gg
 
 #' @importFrom ggplot2 ggproto ggplot
-AlignGG <- ggproto("AlignGG", Align,
+AlignGg <- ggproto("AlignGg", Align,
     nobs = function(self) { # no input data
         axis <- to_coord_axis(.subset2(self, "direction"))
         cli_abort(c(

R/align-link.R

@@ -1,6 +1,6 @@
 #' Add a plot to annotate selected observations
 #'
-#' - `align_link`: Annotate a list of spread observations. Observations will be
+#' - `align_line`: Annotate a list of spread observations. Observations will be
 #'   connected to the panel by a line.
 #' - `align_range`: Annotate a list of ranges of observations. Observation
 #'   ranges will be connected to the panel by a polygon.
@@ -17,7 +17,7 @@
 #'
 #' - Link ranges can be customized using the `plot.ggalign_ranges` theme element
 #'   with [`element_polygon()`].
-#' - Link lines can be customized using the `plot.ggalign_links` theme element
+#' - Link lines can be customized using the `plot.ggalign_lines` theme element
 #'   with [`element_line()`].
 #'
 #' @section ggplot2 specification:
@@ -52,7 +52,7 @@
 #' (`.panel`, `.index`, `.names`) are added to the data frame.
 #'
 #' @export
-align_link <- function(data = waiver(), mapping = aes(),
+align_line <- function(data = waiver(), mapping = aes(),
                        links = waiver(), position = waiver(),
                        size = NULL, active = NULL) {
     assert_layout_position(position)
@@ -68,8 +68,8 @@ align_link <- function(data = waiver(), mapping = aes(),
         new_align_link(
             "AlignLink",
             arg = "links",
-            class = "align_link_plot",
-            element = "plot.ggalign_links"
+            class = "align_line_plot",
+            element = "plot.ggalign_lines"
         ),
         plot = ggplot(mapping = mapping),
         size = size, data = data,
@@ -81,15 +81,15 @@ align_link <- function(data = waiver(), mapping = aes(),
 
 #' @importFrom ggplot2 ggproto
 #' @export
-alignpatch.align_link_plot <- function(x) {
-    ggproto(NULL, PatchAlignLinkPlot, plot = x)
+alignpatch.align_line_plot <- function(x) {
+    ggproto(NULL, PatchAlignLinePlot, plot = x)
 }
 
 #' @export
-`[.alignLinkGtable` <- function(x, i, j) {
-    # subset will violate the `alignLinkGtable` `shape`
+`[.alignLineGtable` <- function(x, i, j) {
+    # subset will violate the `alignLineGtable` `shape`
     # we always use the next method
-    class(x) <- setdiff(class(x), "alignLinkGtable")
+    class(x) <- setdiff(class(x), "alignLineGtable")
     x$links_data <- NULL
     NextMethod()
 }
@@ -105,7 +105,7 @@ alignpatch.align_link_plot <- function(x) {
 #  - popgrobvp
 #' @importFrom grid makeContent unit convertHeight convertWidth viewport
 #' @export
-makeContent.alignLinkGtable <- function(x) {
+makeContent.alignLineGtable <- function(x) {
     # Grab viewport information
     width <- convertWidth(unit(1, "npc"), "mm", valueOnly = TRUE)
     height <- convertHeight(unit(1, "npc"), "mm", valueOnly = TRUE)
@@ -286,21 +286,21 @@ PatchAlignLinkProto <- ggproto(
     }
 )
 
-PatchAlignLinkPlot <- ggproto(
-    "PatchAlignLinkPlot", PatchAlignLinkProto,
+PatchAlignLinePlot <- ggproto(
+    "PatchAlignLinePlot", PatchAlignLinkProto,
     patch_gtable = function(self, plot = self$plot) {
         ans <- ggproto_parent(PatchAlignLinkProto, self)$patch_gtable(
             plot = plot
         )
         # re-define the draw method, we assign new class
-        ans <- add_class(ans, "alignLinkGtable")
+        ans <- add_class(ans, "alignLineGtable")
         ans$links_data <- .subset2(plot, "links_data")
         ans
     }
 )
 
 #' @importFrom ggplot2 ggproto ggplot margin element_rect
-AlignLinkProto <- ggproto("AlignLinkProto", AlignGG,
+AlignLinkProto <- ggproto("AlignLinkProto", AlignGg,
     class = NULL, element = NULL,
     finish_plot = function(self, plot, schemes, theme) {
         plot <- plot_add_schemes(plot, schemes)

R/align-range.R

@@ -1,5 +1,5 @@
 #' @export
-#' @rdname align_link
+#' @rdname align_line
 align_range <- function(data = waiver(), mapping = aes(),
                         ranges = waiver(), position = waiver(),
                         size = NULL, active = NULL) {

R/cross-.R

@@ -0,0 +1,16 @@
+# Since `ggalign_align_plot` object need act with the layout, we Use R6 object
+# here
+cross <- function(cross, ..., call = caller_call()) {
+    new_align_plot(
+        align = ggproto(NULL, cross),
+        ...,
+        class = "ggalign_cross",
+        call = call
+    )
+}
+
+#' @include plot-align-.R
+methods::setClass("ggalign_cross", contains = "ggalign_align_plot")
+
+#' @importFrom methods is
+is_cross_plot <- function(x) is(x, "ggalign_cross")

R/plot-align-cross.R → R/cross-gg.R

@@ -1,19 +1,20 @@
 #' Connect two layout crosswise
 #'
 #' @description
-#' `cross_link` resets the layout ordering index of a [`cross_align()`]. This
+#' `cross_gg` resets the layout ordering index of a [`cross_align()`]. This
 #' allows you to add other `align_*` objects to define a new layout ordering
-#' index. Any objects added after `cross_link` will use this updated layout
+#' index. Any objects added after `cross_gg` will use this updated layout
 #' ordering index. This feature is particularly useful for creating `tanglegram`
-#' visualizations.
+#' visualizations. `ggcross()` is an alias of `cross_gg()`.
+#'
 #' @inheritParams ggalign
 #' @section ggplot2 specification:
-#' `cross_link` initializes a ggplot `data` and `mapping`.
+#' `ggcross()` initializes a ggplot `data` and `mapping`.
 #'
-#' `cross_link()` always applies a default mapping for the axis of the data
-#' index in the layout. This mapping is `aes(y = .data$y)` for horizontal stack
-#' layout (including left and right annotation) and `aes(x = .data$x)` for
-#' vertical stack layout (including top and bottom annotation).
+#' `ggcross()` always applies a default mapping for the axis of the data index
+#' in the layout. This mapping is `aes(y = .data$y)` for horizontal stack layout
+#' (including left and right annotation) and `aes(x = .data$x)` for vertical
+#' stack layout (including top and bottom annotation).
 #'
 #' The data in the underlying `ggplot` object will contain following columns:
 #'
@@ -33,25 +34,23 @@
 #'
 #' @importFrom ggplot2 ggproto aes
 #' @export
-cross_link <- function(mapping = aes(), size = NULL,
-                       no_axes = NULL, active = NULL) {
+cross_gg <- function(mapping = aes(), size = NULL,
+                     no_axes = NULL, active = NULL) {
     active <- update_active(active, new_active(use = TRUE))
-    new_align_plot(
-        align = ggproto(NULL, CrossLink),
+    cross(
+        cross = CrossGg,
         plot = ggplot(mapping = mapping),
-        size = size, no_axes = no_axes, active = active,
-        class = "ggalign_cross_link"
+        size = size, no_axes = no_axes, active = active
     )
 }
 
-#' @include plot-align-.R
-methods::setClass("ggalign_cross_link", contains = "ggalign_align_plot")
-
-#' @importFrom methods is
-is_cross_link <- function(x) is(x, "ggalign_cross_link")
+#' @usage NULL
+#' @export
+#' @rdname cross_gg
+ggcross <- cross_gg
 
 #' @importFrom ggplot2 ggproto ggplot
-CrossLink <- ggproto("CrossLink", AlignProto,
+CrossGg <- ggproto("CrossGg", AlignProto,
     layout = function(self, layout_data, layout_coords, layout_name) {
         if (is.null(.subset2(layout_coords, "nobs"))) {
             cli_abort(sprintf(

R/ggplot-theme.R

@@ -173,7 +173,7 @@ theme_elements <- function() {
             linewidth = 0.5,
             linetype = 1
         ),
-        plot.ggalign_links = element_line(
+        plot.ggalign_lines = element_line(
             color = "black",
             linewidth = 0.5,
             linetype = 1,
@@ -191,7 +191,7 @@ theme_elements <- function() {
             plot.patch_title.position.bottom = el_def("character"),
             plot.patch_title.position.right = el_def("character"),
             plot.ggalign_ranges = el_def("element_polygon"),
-            plot.ggalign_links = el_def("element_line")
+            plot.ggalign_lines = el_def("element_line")
         )
     )
 }

R/layout-coords.R

@@ -132,7 +132,7 @@ update_layout_coords.CrossLayout <- function(layout, ..., coords, object_name,
             }
             index <- seq_len(index)
         } else { # update the tail plots
-            # one for the `cross_link()` plot itself
+            # one for the `ggcross()` plot itself
             index <- layout@cross_points[n_breaks] + 1L + 1L
             if (index > n_plots) {
                 return(layout)

R/layout-cross-.R

@@ -4,8 +4,8 @@
 #' `r lifecycle::badge('experimental')`
 #'
 #' The `cross_align` function aligns observations, and allow different layout
-#' ordering index in a single layout. Both `ggcross` and `cross_layout` are
-#' alias for `cross_align`.
+#' ordering index in a single layout. `cross_layout` is an alias for
+#' `cross_align`.
 #'
 #' Two aliases are provided for convenience:
 #' - `cross_alignv`: A special case of `cross_align` that sets `direction =
@@ -14,18 +14,13 @@
 #'   "horizontal"`.
 #'
 #' @inheritParams stack_align
-#' @seealso [`cross_link()`]
+#' @seealso [`ggcross()`]
 #' @export
 cross_align <- function(data = NULL, direction, ...,
                         theme = NULL, sizes = NA) {
     UseMethod("cross_align")
 }
 
-#' @usage NULL
-#' @export
-#' @rdname cross_align
-ggcross <- cross_align
-
 #' @usage NULL
 #' @export
 #' @rdname cross_align
@@ -67,10 +62,11 @@ stack_build_composer.CrossLayout <- function(stack, schemes, theme,
     layout_coords <- stack@layout
     if (!is.null(layout_coords) &&
         is.null(.subset2(layout_coords, "nobs")) &&
-        any(vapply(plot_list, is_cross_link, logical(1L), USE.NAMES = FALSE))) {
-        cli_abort(
-            "You must initialize the layout observations when used with a {.fn cross_link}"
-        )
+        any(vapply(plot_list, is_cross_plot, logical(1L), USE.NAMES = FALSE))) {
+        cli_abort(sprintf(
+            "You must initialize the layout observations to plot the %s",
+            object_name(stack)
+        ))
     }
     plot_list <- stack@plot_list
 
@@ -126,8 +122,8 @@ stack_build_composer.CrossLayout <- function(stack, schemes, theme,
 
         # we reorder the plots based on the `order` slot
         plot_order <- vapply(plots, function(plot) {
-            # always keep cross_link() in the start
-            if (is_cross_link(plot)) {
+            # always keep cross() in the start
+            if (is_cross_plot(plot)) {
                 1L
             } else if (is_ggalign_plot(plot)) {
                 .subset2(plot@active, "order")

R/layout-operator.R

@@ -42,7 +42,7 @@
 #'     # Modify the the color scales of all plots in the left annotation
 #'     scale_color_brewer(palette = "Dark2")
 #'
-#' # If the active layout is the `ggstack()`/`stack_layout()` itself, `-`
+#' # If the active layout is the `stack_layout()` itself, `-`
 #' # applies the elements to all plots in the layout except the nested
 #' # `ggheatmap()`/`quad_layout()`.
 #' stack_alignv(small_mat) +