add .discrete_x and .discrete_y in the ggplot2 data

R/align-gg.R

@@ -34,26 +34,20 @@
 #' layout (including left and right annotation) and `aes(x = .data$.x)`
 #' for vertical stack layout (including top and bottom annotation).
 #'
-#' `matrix` input will be automatically melted into a long foramted data frame.
-#'
-#' Atomic vector will be put in the `value` column of the data frame.
-#'
-#' In the case where the input data is already a data frame, 4 additional
-#' columns (`.x`/`.y`, `.names`, `.index`, and `.panel`) are added to the data
-#' frame.
-#'
 #' The data in the underlying `ggplot` object will contain following columns:
 #'
 #'  - `.panel`: the panel for the aligned axis. It means `x-axis` for vertical
 #'    stack layout (including top and bottom annotation), `y-axis` for
 #'    horizontal stack layout (including left and right annotation).
 #'
-#'  - `.x` or `.y`: the `x` or `y` coordinates
+#'  - `.x`/`y` and `.discrete_x`/`.discrete_y`: an integer index of `x`/`y`
+#'    coordinates and a factor of the data labels (only applicable when names
+#'    exists).
 #'
 #'  - `.names` ([`vec_names()`][vctrs::vec_names]) and `.index`
-#'    ([`vec_size()`][vctrs::vec_size()]/[`NROW()`]): A factor of the names
-#'    (only applicable when names exists) and an integer of index of the
-#'    original data.
+#'    ([`vec_size()`][vctrs::vec_size()]/[`NROW()`]): a character names (only
+#'    applicable when names exists) and an integer of index of the original
+#'    data.
 #'
 #'  - `.row_names` and `.row_index`: the row names and an integer of
 #'    row index of the original matrix (only applicable if `data` is a
@@ -65,7 +59,16 @@
 #'  - `value`: the actual value (only applicable if `data` is a `matrix` or
 #'    atomic vector).
 #'
-#' It is recommended to use `.x`/`.y`, or `.names` as the `x`/`y` mapping.
+#' `matrix` input will be automatically melted into a long foramted data frame.
+#'
+#' Atomic vector will be put in the `value` column of the data frame.
+#'
+#' In the case where the input data is already a data frame, following columns
+#' (`.panel`, `.index`, `.names`, `.x`/`.y`, `.discrete_x`/`.discrete_y`) are
+#' added to the data frame.
+#'
+#' It is recommended to use `.x`/`.y`, or `.discrete_x`/`.discrete_y` as the
+#' `x`/`y` mapping.
 #'
 #' If the data inherits from [`quad_layout()`]/[`ggheatmap()`], an additional
 #' column will be added.
@@ -80,8 +83,8 @@
 #'     ggalign() +
 #'     geom_point(aes(y = value))
 #'
-#' # if data is `NULL`, a three column data frame will be created
-#' # (`.panel`, `.index`, `.x`/`.y`)
+#' # if data is `NULL`, a data frame with following column will be created
+#' # (`.panel`, `.index`, `.names`, `.x`/`.y`, `.discrete_x`/`.discrete_y`)
 #' ggheatmap(matrix(rnorm(81), nrow = 9)) +
 #'     anno_top(size = 0.5) +
 #'     align_dendro(k = 3L) +
@@ -180,11 +183,19 @@ AlignGG <- ggproto("AlignGG", Align,
         axis <- to_coord_axis(direction)
         coord_name <- paste0(".", axis)
         ans <- data_frame0(
-            .panel = panel, .index = index,
+            .panel = panel,
+            .index = index,
             # `data_frame0` will omit `NULL`
             .names = .subset(self$labels, index)
         )
         ans[[coord_name]] <- seq_along(index)
+        if (!is.null(.subset2(ans, ".names"))) {
+            ans[[paste0(".discrete_", axis)]] <- reorder(
+                .subset2(ans, ".names"),
+                .subset2(ans, coord_name),
+                order = FALSE
+            )
+        }
 
         # if inherit from the parent layout
         if (is.waive(.subset2(self, "input_data")) && !is.null(extra_panel)) {
@@ -202,13 +213,6 @@ AlignGG <- ggproto("AlignGG", Align,
         } else if (!is.null(data)) {
             ans <- full_join(data, ans, by.x = ".index", by.y = ".index")
         }
-        if (!is.null(.subset2(ans, ".names"))) {
-            ans$.names <- reorder(
-                .subset2(ans, ".names"),
-                .subset2(ans, coord_name),
-                order = FALSE
-            )
-        }
         plot$data <- ggalign_attr_restore(ans, data)
         plot
     }

R/layout-heatmap-.R

@@ -40,17 +40,19 @@
 #' @param guides `r lifecycle::badge("deprecated")` Please use
 #' [`scheme_align()`] function instead.
 #' @section ggplot2 specification:
-#' The data input in `ggheatmap` will be converted into the long formated data
-#' frame when drawing. The default mapping will use `aes(.data$.x, .data$.y)`,
-#' you can use `mapping` argument to control it. The data in the underlying
-#' `ggplot` object contains following columns:
+#' The default mapping will use `aes(.data$.x, .data$.y)`, you can use `mapping`
+#' argument to control it. The data in the underlying `ggplot` object contains
+#' following columns:
 #'
 #'  - `.xpanel` and `.ypanel`: the column and row panel
 #'
-#'  - `.x` and `.y`: the `x` and `y` coordinates
+#'  - `.x` and `.y`: an integer index of `x` and `y` coordinates
 #'
-#'  - `.row_names` and `.column_names`: A factor of the row and column names of
-#'    the original matrix (only applicable when names exist).
+#'  - `.discrete_x` and `.discrete_y`: a factor of the data labels (only
+#'    applicable when `.row_names`` and `.column_names` exists).
+#'
+#'  - `.row_names` and `.column_names`: A character of the row and column names
+#'    of the original matrix (only applicable when names exist).
 #'
 #'  - `.row_index` and `.column_index`: the row and column index of the original
 #'    matrix.

R/layout-quad-.R

@@ -128,16 +128,18 @@ quad_free.uneval <- function(data, ...) {
 
 #########################################################################
 #' @section ggplot2 specification:
-#' For `quad_alignb`, `quad_alignh`, and `quad_alignv`, the data input will be
-#' converted into the long formated data frame when drawing. The data in the
+#' For `quad_alignb`, `quad_alignh`, and `quad_alignv`, the data in the
 #' underlying `ggplot` object contains following columns:
 #'
 #'  - `.xpanel` and `.ypanel`: the column and row panel
 #'
-#'  - `.x` and `.y`: the `x` and `y` coordinates
+#'  - `.x` and `.y`: an integer index of `x` and `y` coordinates
 #'
-#'  - `.row_names` and `.column_names`: A factor of the row and column names of
-#'    the original matrix (only applicable when names exist).
+#'  - `.discrete_x` and `.discrete_y`: a factor of the data labels (only
+#'    applicable when `.row_names`` and `.column_names` exists).
+#'
+#'  - `.row_names` and `.column_names`: A character of the row and column names
+#'    of the original matrix (only applicable when names exist).
 #'
 #'  - `.row_index` and `.column_index`: the row and column index of the original
 #'    matrix.

R/layout-quad-build.R

@@ -296,16 +296,16 @@ quad_build_data <- function(data, row_coords, column_coords) {
     ans <- fortify_data_frame.matrix(data)
     ans <- full_join(ans, coords, by.x = by.x, by.y = by.y)
     if (!is.null(.subset2(ans, ".row_names")) &&
-        !is.null(.subset2(ans, ".y"))) {
-        ans$.row_names <- reorder(
+        !is.null(row_coords)) {
+        ans$.discrete_y <- reorder(
             .subset2(ans, ".row_names"),
             .subset2(ans, ".y"),
             order = FALSE
         )
     }
     if (!is.null(.subset2(ans, ".column_names")) &&
-        !is.null(.subset2(ans, ".x"))) {
-        ans$.column_names <- reorder(
+        !is.null(column_coords)) {
+        ans$.discrete_x <- reorder(
             .subset2(ans, ".column_names"),
             .subset2(ans, ".x"),
             order = FALSE

R/plot-align-cross.R

@@ -22,6 +22,8 @@
 #'    horizontal stack layout (including left and right annotation).
 #'
 #'  - `.index`: an integer of the data index.
+#' 
+#'  - `.names`: a character of data labels.
 #'
 #'  - `.hand`: a factor indicates the index groups.
 #'

tests/testthat/test-layout_heatmap.R

@@ -141,29 +141,29 @@ testthat::test_that("`breaks` of `scale_*_()` works well", {
     expect_doppelganger(
         "discrete_no_breaks",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(breaks = NULL)
     )
     expect_doppelganger(
         "discrete_character_breaks",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(breaks = c("column3", "column5")) +
             anno_top() +
             align_dendro(k = 3L)
     )
     expect_doppelganger(
         "discrete_integer_breaks",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(breaks = c(3, 5)) +
             anno_top() +
             align_dendro(k = 3L)
     )
     expect_doppelganger(
         "discrete_integer_as_is_breaks",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(breaks = I(3:4)) +
             anno_top() +
             align_dendro(k = 3L)
@@ -212,37 +212,37 @@ testthat::test_that("`labels` of `scale_*_()` works well", {
     expect_doppelganger(
         "discrete_no_labels",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(labels = NULL) +
             anno_top() +
             align_dendro(k = 3L)
     )
     expect_doppelganger(
         "discrete_labels",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(labels = letters[seq_len(ncol(small_mat))]) +
             anno_top() +
             align_dendro(k = 3L)
     )
     expect_doppelganger(
         "discrete_labels_as_is",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(labels = I(letters[seq_len(ncol(small_mat))])) +
             anno_top() +
             align_dendro(k = 3L)
     )
     expect_doppelganger(
         "discrete_labels_match_breaks",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(breaks = c(5, 3), labels = c("a", "b"))
     )
     expect_doppelganger(
         "discrete_labels_as_is_match_breaks",
         ggheatmap(small_mat, filling = FALSE) +
-            geom_tile(aes(.column_names, .row_names, fill = value)) +
+            geom_tile(aes(.discrete_x, .discrete_y, fill = value)) +
             scale_x_discrete(breaks = c(5, 3), labels = I(c("a", "b")))
     )
 })