From bb77f9d0a610622cabcc3165f7fa796b19893bbb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Fri, 21 Nov 2025 12:31:45 +0000
Subject: [PATCH 01/24] feat: support categorical variables in association and
 bivariate

---
 NEWS.md                     |  1 +
 R/custom_mosaic.R           | 87 +++++++++++++++++++++++++++++++++++++
 R/tm_g_bivariate.R          |  5 ++-
 man/create_mosaic_layers.Rd | 24 ++++++++++
 4 files changed, 116 insertions(+), 1 deletion(-)
 create mode 100644 R/custom_mosaic.R
 create mode 100644 man/create_mosaic_layers.Rd

diff --git a/NEWS.md b/NEWS.md
index 71f2ecf30..c95d96a59 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,7 @@
 ### Enhancements
 
 - Modules now return a `teal_report` object that contains the data, code and reporter. All the reporter buttons were removed from the modules' UI.
+- Support case when both variables are categorical in association and bivariate plots.
 
 # teal.modules.general 0.5.1
 
diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
new file mode 100644
index 000000000..503f17fa2
--- /dev/null
+++ b/R/custom_mosaic.R
@@ -0,0 +1,87 @@
+#' Minimal mosaic plot
+#'
+#' Provides a minimal mosaic plot implementation using ggplot2.
+#' @param data_name Name of the data frame to use.
+#' @param x_var Name of the variable to use on the x-axis.
+#' @param y_var Name of the variable to use for fill colors.
+#' @param reduce_plot_call Function that takes multiple ggplot2 layers and combines them into a single plot call.
+#' @return An expression that creates a mosaic plot when evaluated.
+#' @keywords internal
+create_mosaic_layers <- function(data_name, x_var, y_var, reduce_plot_call) {
+  data_call <- substitute(
+    mosaic_data <- data_name |>
+      # Count combinations of X and Y
+      dplyr::count(x_var, y_var) |>
+      # Compute total for each X group
+      dplyr::group_by(x_var) |>
+      dplyr::mutate(
+        x_total = sum(n),
+        prop = n / x_total
+      ) |>
+      dplyr::ungroup() |>
+      # Compute total sample size to turn counts into widths
+      dplyr::mutate(N_total = sum(x_total)) |>
+      # Convert counts to x widths
+      dplyr::group_by(x_var) |>
+      dplyr::mutate(
+        x_width = x_total / unique(N_total)
+      ) |>
+      # Compute x-min/x-max for each group
+      dplyr::group_by(x_var) |>
+      dplyr::mutate(
+        x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
+      ) |>
+      dplyr::ungroup() |>
+      dplyr::mutate(
+        xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
+        xmax = xmin + x_width
+      ) |>
+      # Compute y-min/y-max for stacked proportions
+      dplyr::group_by(x_var) |>
+      dplyr::arrange(x_var, y_var) |>
+      dplyr::mutate(
+        ymin = c(0, head(cumsum(prop), -1)),
+        ymax = cumsum(prop)
+      ) |>
+      dplyr::ungroup(),
+    env = list(x_var = as.name(x_var), y_var = as.name(y_var), data_name = as.name(data_name))
+  )
+
+  layer_rect <- substitute(
+    ggplot2::geom_rect(
+      ggplot2::aes(
+        xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax, fill = y_var
+      ),
+      data = mosaic_data,
+      color = "white"
+    ),
+    env = list(y_var = as.name(y_var))
+  )
+
+  layer_scale_x <- substitute(
+    ggplot2::scale_x_continuous(
+      breaks = mosaic_data |>
+        dplyr::distinct(x_var, xmin, xmax) |>
+        dplyr::rowwise() |>
+        dplyr::mutate(mid = (xmin + xmax) / 2) |>
+        dplyr::pull(mid),
+      labels = mosaic_data |>
+        dplyr::distinct(x_var) |>
+        dplyr::pull(x_var),
+      expand = c(0, 0)
+    ),
+    env = list(x_var = as.name(x_var))
+  )
+
+  bquote(
+    local({
+      .(data_call)
+
+      list(
+        .(layer_rect),
+        .(layer_scale_x),
+        ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
+      )
+    })
+  )
+}
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 4bb60d406..c59516a18 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -927,7 +927,10 @@ bivariate_ggplot_call <- function(x_class,
     )
     # Factor and character plots
   } else if (x_class == "factor" && y_class == "factor") {
-    stop("Categorical variables 'x' and 'y' are currently not supported.")
+    plot_call <- reduce_plot_call(
+      plot_call,
+      create_mosaic_layers(data_name, x_var = x, y_var = y, reduce_plot_call = reduce_plot_call)
+    )
   } else {
     stop("x y type combination not allowed")
   }
diff --git a/man/create_mosaic_layers.Rd b/man/create_mosaic_layers.Rd
new file mode 100644
index 000000000..17ed7503c
--- /dev/null
+++ b/man/create_mosaic_layers.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_mosaic.R
+\name{create_mosaic_layers}
+\alias{create_mosaic_layers}
+\title{Minimal mosaic plot}
+\usage{
+create_mosaic_layers(data_name, x_var, y_var, reduce_plot_call)
+}
+\arguments{
+\item{data_name}{Name of the data frame to use.}
+
+\item{x_var}{Name of the variable to use on the x-axis.}
+
+\item{y_var}{Name of the variable to use for fill colors.}
+
+\item{reduce_plot_call}{Function that takes multiple ggplot2 layers and combines them into a single plot call.}
+}
+\value{
+An expression that creates a mosaic plot when evaluated.
+}
+\description{
+Provides a minimal mosaic plot implementation using ggplot2.
+}
+\keyword{internal}

From f3c2020fea1468eb8c75a9950b7663b6bb2e5367 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Fri, 21 Nov 2025 12:45:26 +0000
Subject: [PATCH 02/24] chore: prefix internal function with dot

---
 R/custom_mosaic.R                                           | 2 +-
 R/tm_g_bivariate.R                                          | 2 +-
 ...{create_mosaic_layers.Rd => dot-create_mosaic_layers.Rd} | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename man/{create_mosaic_layers.Rd => dot-create_mosaic_layers.Rd} (82%)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 503f17fa2..2487d0afd 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -7,7 +7,7 @@
 #' @param reduce_plot_call Function that takes multiple ggplot2 layers and combines them into a single plot call.
 #' @return An expression that creates a mosaic plot when evaluated.
 #' @keywords internal
-create_mosaic_layers <- function(data_name, x_var, y_var, reduce_plot_call) {
+.create_mosaic_layers <- function(data_name, x_var, y_var, reduce_plot_call) {
   data_call <- substitute(
     mosaic_data <- data_name |>
       # Count combinations of X and Y
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index c59516a18..32b586048 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -929,7 +929,7 @@ bivariate_ggplot_call <- function(x_class,
   } else if (x_class == "factor" && y_class == "factor") {
     plot_call <- reduce_plot_call(
       plot_call,
-      create_mosaic_layers(data_name, x_var = x, y_var = y, reduce_plot_call = reduce_plot_call)
+      .create_mosaic_layers(data_name, x_var = x, y_var = y, reduce_plot_call = reduce_plot_call)
     )
   } else {
     stop("x y type combination not allowed")
diff --git a/man/create_mosaic_layers.Rd b/man/dot-create_mosaic_layers.Rd
similarity index 82%
rename from man/create_mosaic_layers.Rd
rename to man/dot-create_mosaic_layers.Rd
index 17ed7503c..5512ae9a3 100644
--- a/man/create_mosaic_layers.Rd
+++ b/man/dot-create_mosaic_layers.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/custom_mosaic.R
-\name{create_mosaic_layers}
-\alias{create_mosaic_layers}
+\name{.create_mosaic_layers}
+\alias{.create_mosaic_layers}
 \title{Minimal mosaic plot}
 \usage{
-create_mosaic_layers(data_name, x_var, y_var, reduce_plot_call)
+.create_mosaic_layers(data_name, x_var, y_var, reduce_plot_call)
 }
 \arguments{
 \item{data_name}{Name of the data frame to use.}

From 6fe6664c49bdf6293d3cbbb8f4ca7e1787c0ca85 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:24:29 +0000
Subject: [PATCH 03/24] pr: feedback from @llrs-roche

---
 R/custom_mosaic.R | 41 +++++++++++++++++------------------------
 1 file changed, 17 insertions(+), 24 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 2487d0afd..02088f511 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -9,41 +9,35 @@
 #' @keywords internal
 .create_mosaic_layers <- function(data_name, x_var, y_var, reduce_plot_call) {
   data_call <- substitute(
-    mosaic_data <- data_name |>
+    mosaic_data <- data_name %>%
       # Count combinations of X and Y
-      dplyr::count(x_var, y_var) |>
+      dplyr::count(x_var, y_var) %>%
       # Compute total for each X group
-      dplyr::group_by(x_var) |>
       dplyr::mutate(
+        .by = x_var,
         x_total = sum(n),
         prop = n / x_total
-      ) |>
-      dplyr::ungroup() |>
+      ) %>%
       # Compute total sample size to turn counts into widths
-      dplyr::mutate(N_total = sum(x_total)) |>
+      dplyr::mutate(N_total = sum(x_total)) %>%
       # Convert counts to x widths
-      dplyr::group_by(x_var) |>
-      dplyr::mutate(
-        x_width = x_total / unique(N_total)
-      ) |>
-      # Compute x-min/x-max for each group
-      dplyr::group_by(x_var) |>
       dplyr::mutate(
+        .by = x_var,
+        x_width = x_total / unique(N_total),
         x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
-      ) |>
-      dplyr::ungroup() |>
+      ) %>%
+      # Compute x-min/x-max for each group
       dplyr::mutate(
         xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
         xmax = xmin + x_width
-      ) |>
+      ) %>%
       # Compute y-min/y-max for stacked proportions
-      dplyr::group_by(x_var) |>
       dplyr::arrange(x_var, y_var) |>
       dplyr::mutate(
+        .by = x_var,
         ymin = c(0, head(cumsum(prop), -1)),
         ymax = cumsum(prop)
-      ) |>
-      dplyr::ungroup(),
+      ),
     env = list(x_var = as.name(x_var), y_var = as.name(y_var), data_name = as.name(data_name))
   )
 
@@ -60,13 +54,12 @@
 
   layer_scale_x <- substitute(
     ggplot2::scale_x_continuous(
-      breaks = mosaic_data |>
-        dplyr::distinct(x_var, xmin, xmax) |>
-        dplyr::rowwise() |>
-        dplyr::mutate(mid = (xmin + xmax) / 2) |>
+      breaks = mosaic_data %>%
+        dplyr::distinct(x_var, xmin, xmax) %>%
+        dplyr::mutate(mid = (xmin + xmax) / 2) %>%
         dplyr::pull(mid),
-      labels = mosaic_data |>
-        dplyr::distinct(x_var) |>
+      labels = mosaic_data %>%
+        dplyr::distinct(x_var) %>%
         dplyr::pull(x_var),
       expand = c(0, 0)
     ),

From fc0a48214d0ce5849c59d185ef356701dc79aada Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:34:51 +0000
Subject: [PATCH 04/24] pr: make mosaic call simpler

---
 R/custom_mosaic.R  | 15 +++++----------
 R/tm_g_bivariate.R |  8 +++++---
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 02088f511..d7b60a959 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -32,7 +32,7 @@
         xmax = xmin + x_width
       ) %>%
       # Compute y-min/y-max for stacked proportions
-      dplyr::arrange(x_var, y_var) |>
+      dplyr::arrange(x_var, y_var) %>%
       dplyr::mutate(
         .by = x_var,
         ymin = c(0, head(cumsum(prop), -1)),
@@ -46,7 +46,6 @@
       ggplot2::aes(
         xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax, fill = y_var
       ),
-      data = mosaic_data,
       color = "white"
     ),
     env = list(y_var = as.name(y_var))
@@ -67,14 +66,10 @@
   )
 
   bquote(
-    local({
-      .(data_call)
-
-      list(
-        .(layer_rect),
-        .(layer_scale_x),
+    .(data_call) %>%
+      ggplot2::ggplot() +
+        .(layer_rect) +
+        .(layer_scale_x) +
         ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
-      )
-    })
   )
 }
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 32b586048..4e9968c90 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -927,9 +927,11 @@ bivariate_ggplot_call <- function(x_class,
     )
     # Factor and character plots
   } else if (x_class == "factor" && y_class == "factor") {
-    plot_call <- reduce_plot_call(
-      plot_call,
-      .create_mosaic_layers(data_name, x_var = x, y_var = y, reduce_plot_call = reduce_plot_call)
+    plot_call <- .create_mosaic_layers(
+      data_name,
+      x_var = x,
+      y_var = y,
+      reduce_plot_call = reduce_plot_call
     )
   } else {
     stop("x y type combination not allowed")

From 54914e67f72dab060d2d6e35f7776afbae9f3f24 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:36:55 +0000
Subject: [PATCH 05/24] [skip style] [skip vbump] Restyle files

---
 R/custom_mosaic.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index d7b60a959..901ff7c66 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -68,8 +68,8 @@
   bquote(
     .(data_call) %>%
       ggplot2::ggplot() +
-        .(layer_rect) +
-        .(layer_scale_x) +
-        ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
+      .(layer_rect) +
+      .(layer_scale_x) +
+      ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
   )
 }

From e068c35afb94cf5d39281495afa9d52c95627500 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 24 Nov 2025 12:18:43 +0000
Subject: [PATCH 06/24] tests: re-adds tests that were removed

---
 tests/testthat/test_bivariate_ggplot_call.R | 47 ++++++++-------------
 1 file changed, 18 insertions(+), 29 deletions(-)

diff --git a/tests/testthat/test_bivariate_ggplot_call.R b/tests/testthat/test_bivariate_ggplot_call.R
index c85d4fd1b..d65d122f5 100644
--- a/tests/testthat/test_bivariate_ggplot_call.R
+++ b/tests/testthat/test_bivariate_ggplot_call.R
@@ -18,35 +18,24 @@ testthat::test_that("bivariate_ggplot_call with numerics", {
   )
 })
 
-testthat::test_that("bivariate_ggplot_call with factor, char, logical", {
-  error_message <- "Categorical variables 'x' and 'y' are currently not supported."
-  testthat::expect_error(
-    bivariate_ggplot_call("factor", "factor") %>% deparse(width.cutoff = 300),
-    error_message
-  )
-  testthat::expect_error(
-    bivariate_ggplot_call("logical", "factor") %>% deparse(width.cutoff = 300),
-    error_message
-  )
-  testthat::expect_error(
-    bivariate_ggplot_call("character", "factor") %>% deparse(width.cutoff = 300),
-    error_message
-  )
-  testthat::expect_error(
-    bivariate_ggplot_call("logical", "character") %>% deparse(width.cutoff = 300),
-    error_message
-  )
-  testthat::expect_error(
-    bivariate_ggplot_call("character", "logical") %>% deparse(width.cutoff = 300),
-    error_message
-  )
-  testthat::expect_error(
-    bivariate_ggplot_call("logical", "logical") %>% deparse(width.cutoff = 300),
-    error_message
-  )
-  testthat::expect_error(
-    bivariate_ggplot_call("character", "character") %>% deparse(width.cutoff = 300),
-    error_message
+testthat::describe("bivariate_ggplot_call with arguments:", {
+  possible_classes <- c("factor", "logical", "character")
+  comb <- expand.grid(a = possible_classes, b = possible_classes, stringsAsFactors = FALSE)
+  apply(
+    comb,
+    1,
+    function(x) {
+      it(sprintf("%s and %s", x[[1]], x[[2]]), {
+        testthat::expect_match(
+          deparse(
+            bivariate_ggplot_call(x[[1]], x[[2]], data_name = "ANL", x = "x", y = "y"),
+            width.cutoff = 300
+          ),
+          "mosaic_data <- ",
+          all = FALSE
+        )
+      })
+    }
   )
 })
 

From 9102fba1754666af250d77f96ae259eab259cab7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 25 Nov 2025 08:52:05 +0000
Subject: [PATCH 07/24] feat: adds datacall outside and supports multiple plots
 in association

---
 R/custom_mosaic.R    | 35 +++++++++++++++++++++++------------
 R/tm_g_association.R | 11 +++++++++--
 R/tm_g_bivariate.R   | 17 ++++++++++++-----
 3 files changed, 44 insertions(+), 19 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 901ff7c66..a015afe72 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -7,9 +7,11 @@
 #' @param reduce_plot_call Function that takes multiple ggplot2 layers and combines them into a single plot call.
 #' @return An expression that creates a mosaic plot when evaluated.
 #' @keywords internal
-.create_mosaic_layers <- function(data_name, x_var, y_var, reduce_plot_call) {
+.build_mosaic_plot <- function(data_name, x_var, y_var, reduce_plot_call) {
+  mosaic_data_name <- sprintf("%s_mosaic_%s_%s", data_name, as.character(x_var), as.character(y_var))
+  browser()
   data_call <- substitute(
-    mosaic_data <- data_name %>%
+    mosaic_data_name <- data_name %>%
       # Count combinations of X and Y
       dplyr::count(x_var, y_var) %>%
       # Compute total for each X group
@@ -38,7 +40,12 @@
         ymin = c(0, head(cumsum(prop), -1)),
         ymax = cumsum(prop)
       ),
-    env = list(x_var = as.name(x_var), y_var = as.name(y_var), data_name = as.name(data_name))
+    env = list(
+      x_var = as.name(x_var),
+      y_var = as.name(y_var),
+      data_name = as.name(data_name),
+      mosaic_data_name = as.name(mosaic_data_name)
+    )
   )
 
   layer_rect <- substitute(
@@ -53,23 +60,27 @@
 
   layer_scale_x <- substitute(
     ggplot2::scale_x_continuous(
-      breaks = mosaic_data %>%
+      breaks = mosaic_data_name %>%
         dplyr::distinct(x_var, xmin, xmax) %>%
         dplyr::mutate(mid = (xmin + xmax) / 2) %>%
         dplyr::pull(mid),
-      labels = mosaic_data %>%
+      labels = mosaic_data_name %>%
         dplyr::distinct(x_var) %>%
         dplyr::pull(x_var),
       expand = c(0, 0)
     ),
-    env = list(x_var = as.name(x_var))
+    env = list(x_var = as.name(x_var), mosaic_data_name = as.name(mosaic_data_name))
   )
 
-  bquote(
-    .(data_call) %>%
-      ggplot2::ggplot() +
-      .(layer_rect) +
-      .(layer_scale_x) +
-      ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
+  list(
+    data_call = data_call,
+    plot_call = bquote(
+      ggplot2::ggplot(.(as.name(mosaic_data_name))) +
+        .(layer_rect) +
+        .(layer_scale_x) +
+        ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
+    )
   )
 }
+
+
diff --git a/R/tm_g_association.R b/R/tm_g_association.R
index 8516efc9b..f2e65aa08 100644
--- a/R/tm_g_association.R
+++ b/R/tm_g_association.R
@@ -495,6 +495,10 @@ srv_tm_g_association <- function(id,
         }
       obj <- merged$anl_q_r()
       teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "### Plot")
+
+      data_calls <- Map(function(x) .subset2(x, "data_call"), var_calls)
+      plot_calls <- Map(function(x) .subset2(x, "plot_call"), var_calls)
+
       teal.code::eval_code(
         obj,
         substitute(
@@ -502,16 +506,19 @@ srv_tm_g_association <- function(id,
           env = list(new_title = new_title)
         )
       ) %>%
+        teal.code::eval_code(
+          bquote({..(data_calls)}, splice = TRUE)
+        ) %>%
         teal.code::eval_code(
           substitute(
             expr = {
               plots <- plot_calls
-              plot <- gridExtra::arrangeGrob(plots[[1]], plots[[2]], ncol = 1)
+              plot <- gridExtra::arrangeGrob(grobs = plots, ncol = 1)
             },
             env = list(
               plot_calls = do.call(
                 "call",
-                c(list("list", ref_call), var_calls),
+                c(list("list", ref_call$plot_call), plot_calls),
                 quote = TRUE
               )
             )
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 4e9968c90..807eae44e 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -632,7 +632,7 @@ srv_g_bivariate <- function(id,
 
       teal::validate_has_data(ANL[, c(x_name, y_name), drop = FALSE], 3, complete = TRUE, allow_inf = FALSE)
 
-      cl <- bivariate_plot_call(
+      bivariate_cl <- bivariate_plot_call(
         data_name = "ANL",
         x = x_name,
         y = y_name,
@@ -649,6 +649,8 @@ srv_g_bivariate <- function(id,
         ggplot2_args = ggplot2_args
       )
 
+      cl <- bivariate_cl$plot_call
+
       facetting <- (isTRUE(input$facetting) && (!is.null(row_facet_name) || !is.null(col_facet_name)))
 
       if (facetting) {
@@ -688,7 +690,9 @@ srv_g_bivariate <- function(id,
 
       obj <- merged$anl_q_r()
       teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "### Plot")
-      teal.code::eval_code(obj, substitute(expr = plot <- cl, env = list(cl = cl)))
+      browser()
+      teal.code::eval_code(obj, bivariate_cl$data_call %||% "") |>
+        teal.code::eval_code(substitute(expr = plot <- cl, env = list(cl = cl)))
     })
 
     decorated_output_q_facets <- srv_decorate_teal_data(
@@ -768,7 +772,7 @@ bivariate_plot_call <- function(data_name,
     y <- if (is.call(y)) y else as.name(y)
   }
 
-  cl <- bivariate_ggplot_call(
+  bivariate_ggplot_call(
     x_class = x_class,
     y_class = y_class,
     freq = freq,
@@ -832,6 +836,7 @@ bivariate_ggplot_call <- function(x_class,
     Reduce(function(x, y) call("+", x, y), args)
   }
 
+  data_call <- NULL
   plot_call <- substitute(ggplot2::ggplot(data_name), env = list(data_name = as.name(data_name)))
 
   # Single data plots
@@ -927,12 +932,14 @@ bivariate_ggplot_call <- function(x_class,
     )
     # Factor and character plots
   } else if (x_class == "factor" && y_class == "factor") {
-    plot_call <- .create_mosaic_layers(
+    mosaic_call <- .build_mosaic_plot(
       data_name,
       x_var = x,
       y_var = y,
       reduce_plot_call = reduce_plot_call
     )
+    plot_call <- mosaic_call$plot_call
+    data_call <- mosaic_call$data_call
   } else {
     stop("x y type combination not allowed")
   }
@@ -972,7 +979,7 @@ bivariate_ggplot_call <- function(x_class,
     plot_call <- reduce_plot_call(plot_call, quote(coord_flip()))
   }
 
-  plot_call
+  list(plot_call = plot_call, data_call = data_call)
 }
 
 # Create facet call

From 432eb3822e228a4f2e8100911409cdf109b6a803 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 25 Nov 2025 10:24:10 +0000
Subject: [PATCH 08/24] feat: using custom geom

---
 NAMESPACE                        |   4 +
 R/custom_mosaic.R                | 295 +++++++++++++++++++++++--------
 R/tm_g_association.R             |   9 +-
 R/tm_g_bivariate.R               |  30 ++--
 R/utils.R                        |   1 +
 man/dot-calculate_coordinates.Rd |  26 +++
 man/dot-create_mosaic_layers.Rd  |  24 ---
 man/geom_mosaic.Rd               |  46 +++++
 man/scale_type.mosaic.Rd         |  17 ++
 man/scale_x_mosaic.Rd            |  66 +++++++
 10 files changed, 392 insertions(+), 126 deletions(-)
 create mode 100644 man/dot-calculate_coordinates.Rd
 delete mode 100644 man/dot-create_mosaic_layers.Rd
 create mode 100644 man/geom_mosaic.Rd
 create mode 100644 man/scale_type.mosaic.Rd
 create mode 100644 man/scale_x_mosaic.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 302a2f68e..0392296ef 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,8 +8,11 @@ S3method(create_sparklines,default)
 S3method(create_sparklines,factor)
 S3method(create_sparklines,logical)
 S3method(create_sparklines,numeric)
+S3method(scale_type,mosaic)
 export(add_facet_labels)
+export(geom_mosaic)
 export(get_scatterplotmatrix_stats)
+export(scale_x_mosaic)
 export(tm_a_pca)
 export(tm_a_regression)
 export(tm_data_table)
@@ -30,4 +33,5 @@ import(shiny)
 import(teal)
 import(teal.transform)
 importFrom(dplyr,"%>%")
+importFrom(ggplot2,scale_type)
 importFrom(lifecycle,deprecated)
diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index a015afe72..f78e37264 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -1,86 +1,227 @@
-#' Minimal mosaic plot
+#' Mosaic Rectangles Layer for ggplot2
 #'
-#' Provides a minimal mosaic plot implementation using ggplot2.
-#' @param data_name Name of the data frame to use.
-#' @param x_var Name of the variable to use on the x-axis.
-#' @param y_var Name of the variable to use for fill colors.
-#' @param reduce_plot_call Function that takes multiple ggplot2 layers and combines them into a single plot call.
-#' @return An expression that creates a mosaic plot when evaluated.
-#' @keywords internal
-.build_mosaic_plot <- function(data_name, x_var, y_var, reduce_plot_call) {
-  mosaic_data_name <- sprintf("%s_mosaic_%s_%s", data_name, as.character(x_var), as.character(y_var))
-  browser()
-  data_call <- substitute(
-    mosaic_data_name <- data_name %>%
-      # Count combinations of X and Y
-      dplyr::count(x_var, y_var) %>%
-      # Compute total for each X group
-      dplyr::mutate(
-        .by = x_var,
-        x_total = sum(n),
-        prop = n / x_total
-      ) %>%
-      # Compute total sample size to turn counts into widths
-      dplyr::mutate(N_total = sum(x_total)) %>%
-      # Convert counts to x widths
-      dplyr::mutate(
-        .by = x_var,
-        x_width = x_total / unique(N_total),
-        x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
-      ) %>%
-      # Compute x-min/x-max for each group
-      dplyr::mutate(
-        xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
-        xmax = xmin + x_width
-      ) %>%
-      # Compute y-min/y-max for stacked proportions
-      dplyr::arrange(x_var, y_var) %>%
-      dplyr::mutate(
-        .by = x_var,
-        ymin = c(0, head(cumsum(prop), -1)),
-        ymax = cumsum(prop)
-      ),
-    env = list(
-      x_var = as.name(x_var),
-      y_var = as.name(y_var),
-      data_name = as.name(data_name),
-      mosaic_data_name = as.name(mosaic_data_name)
-    )
-  )
+#' Adds a mosaic-style rectangles layer to a ggplot, visualizing the joint distribution of categorical variables.
+#' Each rectangle's size reflects the proportion of observations for combinations of `x` and `fill`.
+#'
+#' @param mapping Set of aesthetic mappings created by `aes()`. Must specify `x` and `fill`.
+#' @param data The data to be displayed in this layer.
+#' @param stat The statistical transformation to use on the data. Defaults to `"rects"`.
+#' @param position Position adjustment. Defaults to `"identity"`.
+#' @param ... Other arguments passed to `layer()`.
+#' @param na.rm Logical. Should missing values be removed?
+#' @param show.legend Logical. Should this layer be included in the legends?
+#' @param inherit.aes Logical. If `FALSE`, overrides default aesthetics.
+#'
+#' @return A ggplot2 layer that adds mosaic rectangles to the plot.
+#'
+#' @examples
+#' df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
+#' library(ggplot2)
+#' ggplot(df, aes(x = RACE, fill = SEX)) + geom_rects()
+#' @export
+geom_mosaic <- function(mapping = NULL, data = NULL,
+                       stat = "mosaic", position = "identity",
+                       ...,
+                       na.rm = FALSE,
+                       show.legend = TRUE,
+                       inherit.aes = TRUE) {
+  aes_x <- list(rlang::quo_get_expr(mapping$x))
+  var_x <- sprintf("x__%s", as.character(aes_x))
+  aes_fill <- rlang::quo_text(mapping$fill)
+  var_fill <- sprintf("x__fill__%s", aes_fill)
 
-  layer_rect <- substitute(
-    ggplot2::geom_rect(
-      ggplot2::aes(
-        xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax, fill = y_var
-      ),
-      color = "white"
-    ),
-    env = list(y_var = as.name(y_var))
-  )
+  mapping[[var_x]] <- mapping$x
+  mapping$x <- structure(1L, class = "mosaic")
+  # mapping[[var_fill]] <- mapping$fill
 
-  layer_scale_x <- substitute(
-    ggplot2::scale_x_continuous(
-      breaks = mosaic_data_name %>%
-        dplyr::distinct(x_var, xmin, xmax) %>%
-        dplyr::mutate(mid = (xmin + xmax) / 2) %>%
-        dplyr::pull(mid),
-      labels = mosaic_data_name %>%
-        dplyr::distinct(x_var) %>%
-        dplyr::pull(x_var),
-      expand = c(0, 0)
-    ),
-    env = list(x_var = as.name(x_var), mosaic_data_name = as.name(mosaic_data_name))
+  layer <- ggplot2::layer(
+    geom = GeomMosaic,
+    stat = "mosaic",
+    data = data,
+    mapping = mapping,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    check.aes = FALSE,
+    params = list(na.rm = na.rm, ...)
   )
+  #list(layer, .scale_x_mosaic())
+  layer
+}
+
+GeomMosaic <- ggplot2::ggproto(
+  "GeomMosaic", ggplot2::GeomRect,
+  default_aes = ggplot2::aes(
+    colour = NA, linewidth = 0.5, linetype = 1, alpha = 1, fill = "grey30"
+  ),
+  draw_panel = function(data, panel_params, coord) {
+    if (all(is.na(data$colour))) data$colour <- scales::alpha(data$fill, data$alpha)
+    ggplot2::GeomRect$draw_panel(data, panel_params, coord)
+  },
+  required_aes = c("xmin", "xmax", "ymin", "ymax")
+)
+
+#' Calculate Rectangle Coordinates for Mosaic Plot
+#'
+#' Computes the coordinates for rectangles in a mosaic plot based on combinations of `x` and `fill` variables.
+#' For each unique `x` and `fill`, calculates the proportional widths and heights, stacking rectangles within each `x` group.
+#'
+#' @param data A data frame containing at least `x` and `fill` columns.
+#'
+#' @return A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`, representing the position and size of each rectangle.
+#'
+#' @details
+#' - Counts occurrences of each `x`/`fill` combination.
+#' - Calculates proportions within each `x` group.
+#' - Determines horizontal (`xmin`, `xmax`) and vertical (`ymin`, `ymax`) boundaries for each rectangle.
+#' - Adds small padding to each boundary for visual separation.
+.calculate_coordinates <- function(data) {
+  # Example: compute rectangles from x and y
+  result <- data |>
+    # Count combinations of X and Y
+    dplyr::count(x, fill) |>
+    # Compute total for each X group
+    dplyr::mutate(
+      .by = x,
+      x_total = sum(n),
+      prop = n / x_total
+    ) |>
+    # Change order from biggest group to smaller
+    dplyr::arrange(dplyr::desc(x_total), x, fill) |>
+    # Compute total sample size to turn counts into widths
+    dplyr::mutate(
+      N_total = dplyr::n(),
+      x_width = x_total / N_total
+    ) |>
+    # Convert counts to x widths
+    dplyr::mutate(
+      .by = x,
+      x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
+    ) |>
+    # Compute x-min/x-max for each group
+    dplyr::mutate(
+      xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
+      xmax = xmin + x_width
+    ) |>
+    # Compute y-min/y-max for stacked proportions
+    dplyr::mutate(
+      .by = x,
+      ymin = c(0, head(cumsum(prop), -1)),
+      ymax = cumsum(prop)
+    ) |>
+    dplyr::mutate(
+      xmin = xmin / max(xmax),
+      xmax = xmax / max(xmax),
+      xmin = xmin + 0.005,
+      xmax = xmax - 0.005,
+      ymin = ymin + 0.005,
+      ymax = ymax - 0.005
+    ) |>
+    dplyr::select(x, fill, xmin, xmax, ymin, ymax)
+  result
+}
 
-  list(
-    data_call = data_call,
-    plot_call = bquote(
-      ggplot2::ggplot(.(as.name(mosaic_data_name))) +
-        .(layer_rect) +
-        .(layer_scale_x) +
-        ggplot2::scale_y_continuous(expand = c(0, 0), labels = scales::percent_format(scale = 100))
-    )
+StatMosaic <- ggplot2::ggproto(
+  "StatMosaic", ggplot2::Stat,
+
+  required_aes = c("x", "fill"),
+
+  compute_group = function(data, scales) {
+    data
+  },
+  compute_panel = function(data, scales) {
+    data$x <- data[, grepl("x__", colnames(data))]
+    result <- .calculate_coordinates(data)
+
+    scale_x <- ggplot2::ScaleContinuous
+    scale_x[["breaks"]] <- result |>
+      dplyr::distinct(x, xmin, xmax) |>
+      dplyr::mutate(mid = (xmin + xmax) / 2) |>
+      dplyr::pull(mid)
+
+    scale_x[["labels"]] <- result |>
+      dplyr::distinct(x) |>
+      dplyr::pull(x)
+
+    result$x <- list(scale = scale_x)
+    result$group <- 1
+    result$PANEL <- unique(data$PANEL)
+    result
+  }
+)
+
+#' Helper function for determining scales
+#'
+#' Used internally to determine class of variable x
+#' @param x variable
+#' @return character string "productlist"
+#' @importFrom ggplot2 scale_type
+#' @export
+scale_type.mosaic <- function(x) {
+  #  cat("checking for type productlist\n")
+  #browser()
+  "mosaic"
+}
+
+
+#' Determining scales for mosaics
+#'
+#' @param name set to pseudo waiver function `product_names` by default.
+#' @param ... other arguments passed to `continuous_scale()`.
+#' @inheritParams ggplot2::continuous_scale
+#' @export
+scale_x_mosaic <- function(breaks = function() function(x) unique(x),
+                           minor_breaks = NULL,
+                           labels = function() function(x) unique(x),
+                           na.value = NA_real_,
+                           position = "bottom",
+                           ...) {
+  ggplot2::continuous_scale(
+    aesthetics = c(
+      "x", "xmin", "xmax", "xend", "xintercept", "xmin_final", "xmax_final",
+      "xlower", "xmiddle", "xupper"
+    ), palette = identity, breaks = breaks, minor_breaks = minor_breaks,
+    labels = labels, na.value = na.value, position = position,
+    super = ScaleContinuousProduct,, guide = ggplot2::waiver(), ...
   )
 }
 
+#' @rdname dot-scale_x_mosaic
+ScaleContinuousProduct <- ggplot2::ggproto(
+  "ScaleContinuousProduct", ggplot2::ScaleContinuousPosition,
+  train =function(self, x) {
+    if (is.list(x)) {
+      x <- x[[1]]
+      if ("Scale" %in% class(x)) {
+        # re-assign the scale values now that we have the information - but only if necessary
+        if (is.function(self$breaks)) self$breaks <- x$breaks
+        if (is.function(self$labels)) self$labels <- x$labels
+        return(NULL)
+      }
+    }
+    if (self$is.discrete(x)) {
+      self$range$train(x=c(0,1))
+      return(NULL)
+    }
+    self$range$train(x)
+  },
+  map = function(self, x, limits = self$get_limits()) {
+    if (self$is.discrete(x)) return(x)
+    if (is.list(x)) return(0) # need a number
+    scaled <- as.numeric(self$oob(x, limits))
+    ifelse(!is.na(scaled), scaled, self$na.value)
+  },
+  dimension = function(self, expand = c(0, 0)) {
+    c(-0.05,1.05)
+  },
+  make_title = function(..., self) {
+    title <- ggplot2::ggproto_parent(ggplot2::ScaleContinuousPosition, self)$make_title(...)
+    if (isTRUE(title %in% self$aesthetics)) {
+      title <- self$product_name
+    }
+    else title
+  },
+  is.discrete = function(self, x) is.factor(x) || is.character(x) || is.logical(x)
+)
+
 
diff --git a/R/tm_g_association.R b/R/tm_g_association.R
index f2e65aa08..3fbc19d2c 100644
--- a/R/tm_g_association.R
+++ b/R/tm_g_association.R
@@ -495,10 +495,6 @@ srv_tm_g_association <- function(id,
         }
       obj <- merged$anl_q_r()
       teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "### Plot")
-
-      data_calls <- Map(function(x) .subset2(x, "data_call"), var_calls)
-      plot_calls <- Map(function(x) .subset2(x, "plot_call"), var_calls)
-
       teal.code::eval_code(
         obj,
         substitute(
@@ -506,9 +502,6 @@ srv_tm_g_association <- function(id,
           env = list(new_title = new_title)
         )
       ) %>%
-        teal.code::eval_code(
-          bquote({..(data_calls)}, splice = TRUE)
-        ) %>%
         teal.code::eval_code(
           substitute(
             expr = {
@@ -518,7 +511,7 @@ srv_tm_g_association <- function(id,
             env = list(
               plot_calls = do.call(
                 "call",
-                c(list("list", ref_call$plot_call), plot_calls),
+                c(list("list", ref_call), var_calls),
                 quote = TRUE
               )
             )
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 807eae44e..96a4725aa 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -632,7 +632,7 @@ srv_g_bivariate <- function(id,
 
       teal::validate_has_data(ANL[, c(x_name, y_name), drop = FALSE], 3, complete = TRUE, allow_inf = FALSE)
 
-      bivariate_cl <- bivariate_plot_call(
+      cl <- bivariate_plot_call(
         data_name = "ANL",
         x = x_name,
         y = y_name,
@@ -649,8 +649,6 @@ srv_g_bivariate <- function(id,
         ggplot2_args = ggplot2_args
       )
 
-      cl <- bivariate_cl$plot_call
-
       facetting <- (isTRUE(input$facetting) && (!is.null(row_facet_name) || !is.null(col_facet_name)))
 
       if (facetting) {
@@ -690,9 +688,7 @@ srv_g_bivariate <- function(id,
 
       obj <- merged$anl_q_r()
       teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "### Plot")
-      browser()
-      teal.code::eval_code(obj, bivariate_cl$data_call %||% "") |>
-        teal.code::eval_code(substitute(expr = plot <- cl, env = list(cl = cl)))
+      teal.code::eval_code(obj, substitute(expr = plot <- cl, env = list(cl = cl)))
     })
 
     decorated_output_q_facets <- srv_decorate_teal_data(
@@ -728,7 +724,9 @@ srv_g_bivariate <- function(id,
       })
     )
 
-    plot_r <- reactive(req(decorated_output_q_facets())[["plot"]])
+    plot_r <- reactive({
+      req(decorated_output_q_facets())[["plot"]]
+    })
 
     pws <- teal.widgets::plot_with_settings_srv(
       id = "myplot",
@@ -738,7 +736,7 @@ srv_g_bivariate <- function(id,
     )
 
     set_chunk_dims(pws, decorated_output_q_facets)
-  })
+    })
 }
 
 # Get Substituted ggplot call
@@ -836,7 +834,6 @@ bivariate_ggplot_call <- function(x_class,
     Reduce(function(x, y) call("+", x, y), args)
   }
 
-  data_call <- NULL
   plot_call <- substitute(ggplot2::ggplot(data_name), env = list(data_name = as.name(data_name)))
 
   # Single data plots
@@ -932,14 +929,13 @@ bivariate_ggplot_call <- function(x_class,
     )
     # Factor and character plots
   } else if (x_class == "factor" && y_class == "factor") {
-    mosaic_call <- .build_mosaic_plot(
-      data_name,
-      x_var = x,
-      y_var = y,
-      reduce_plot_call = reduce_plot_call
+    plot_call <- reduce_plot_call(
+      plot_call,
+      substitute(
+        teal.modules.general::geom_mosaic(ggplot2::aes(x = xval, fill = yval)),
+        env = list(xval = x, yval = y)
+      )
     )
-    plot_call <- mosaic_call$plot_call
-    data_call <- mosaic_call$data_call
   } else {
     stop("x y type combination not allowed")
   }
@@ -979,7 +975,7 @@ bivariate_ggplot_call <- function(x_class,
     plot_call <- reduce_plot_call(plot_call, quote(coord_flip()))
   }
 
-  list(plot_call = plot_call, data_call = data_call)
+  plot_call
 }
 
 # Create facet call
diff --git a/R/utils.R b/R/utils.R
index 5f462ba0d..d625746a5 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -287,6 +287,7 @@ srv_decorate_teal_data <- function(id, data, decorators, expr) {
 
     reactive({
       req(decorated_output())
+      browser()
       if (no_expr) {
         decorated_output()
       } else {
diff --git a/man/dot-calculate_coordinates.Rd b/man/dot-calculate_coordinates.Rd
new file mode 100644
index 000000000..f17830c9c
--- /dev/null
+++ b/man/dot-calculate_coordinates.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_mosaic.R
+\name{.calculate_coordinates}
+\alias{.calculate_coordinates}
+\title{Calculate Rectangle Coordinates for Mosaic Plot}
+\usage{
+.calculate_coordinates(data)
+}
+\arguments{
+\item{data}{A data frame containing at least \code{x} and \code{fill} columns.}
+}
+\value{
+A data frame with columns: \code{x}, \code{fill}, \code{xmin}, \code{xmax}, \code{ymin}, \code{ymax}, representing the position and size of each rectangle.
+}
+\description{
+Computes the coordinates for rectangles in a mosaic plot based on combinations of \code{x} and \code{fill} variables.
+For each unique \code{x} and \code{fill}, calculates the proportional widths and heights, stacking rectangles within each \code{x} group.
+}
+\details{
+\itemize{
+\item Counts occurrences of each \code{x}/\code{fill} combination.
+\item Calculates proportions within each \code{x} group.
+\item Determines horizontal (\code{xmin}, \code{xmax}) and vertical (\code{ymin}, \code{ymax}) boundaries for each rectangle.
+\item Adds small padding to each boundary for visual separation.
+}
+}
diff --git a/man/dot-create_mosaic_layers.Rd b/man/dot-create_mosaic_layers.Rd
deleted file mode 100644
index 5512ae9a3..000000000
--- a/man/dot-create_mosaic_layers.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/custom_mosaic.R
-\name{.create_mosaic_layers}
-\alias{.create_mosaic_layers}
-\title{Minimal mosaic plot}
-\usage{
-.create_mosaic_layers(data_name, x_var, y_var, reduce_plot_call)
-}
-\arguments{
-\item{data_name}{Name of the data frame to use.}
-
-\item{x_var}{Name of the variable to use on the x-axis.}
-
-\item{y_var}{Name of the variable to use for fill colors.}
-
-\item{reduce_plot_call}{Function that takes multiple ggplot2 layers and combines them into a single plot call.}
-}
-\value{
-An expression that creates a mosaic plot when evaluated.
-}
-\description{
-Provides a minimal mosaic plot implementation using ggplot2.
-}
-\keyword{internal}
diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
new file mode 100644
index 000000000..679c6b4b3
--- /dev/null
+++ b/man/geom_mosaic.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_mosaic.R
+\name{geom_mosaic}
+\alias{geom_mosaic}
+\title{Mosaic Rectangles Layer for ggplot2}
+\usage{
+geom_mosaic(
+  mapping = NULL,
+  data = NULL,
+  stat = "mosaic",
+  position = "identity",
+  ...,
+  na.rm = FALSE,
+  show.legend = TRUE,
+  inherit.aes = TRUE
+)
+}
+\arguments{
+\item{mapping}{Set of aesthetic mappings created by \code{aes()}. Must specify \code{x} and \code{fill}.}
+
+\item{data}{The data to be displayed in this layer.}
+
+\item{stat}{The statistical transformation to use on the data. Defaults to \code{"rects"}.}
+
+\item{position}{Position adjustment. Defaults to \code{"identity"}.}
+
+\item{...}{Other arguments passed to \code{layer()}.}
+
+\item{na.rm}{Logical. Should missing values be removed?}
+
+\item{show.legend}{Logical. Should this layer be included in the legends?}
+
+\item{inherit.aes}{Logical. If \code{FALSE}, overrides default aesthetics.}
+}
+\value{
+A ggplot2 layer that adds mosaic rectangles to the plot.
+}
+\description{
+Adds a mosaic-style rectangles layer to a ggplot, visualizing the joint distribution of categorical variables.
+Each rectangle's size reflects the proportion of observations for combinations of \code{x} and \code{fill}.
+}
+\examples{
+df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
+library(ggplot2)
+ggplot(df, aes(x = RACE, fill = SEX)) + geom_rects()
+}
diff --git a/man/scale_type.mosaic.Rd b/man/scale_type.mosaic.Rd
new file mode 100644
index 000000000..9b98318e3
--- /dev/null
+++ b/man/scale_type.mosaic.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_mosaic.R
+\name{scale_type.mosaic}
+\alias{scale_type.mosaic}
+\title{Helper function for determining scales}
+\usage{
+\method{scale_type}{mosaic}(x)
+}
+\arguments{
+\item{x}{variable}
+}
+\value{
+character string "productlist"
+}
+\description{
+Used internally to determine class of variable x
+}
diff --git a/man/scale_x_mosaic.Rd b/man/scale_x_mosaic.Rd
new file mode 100644
index 000000000..27c62a872
--- /dev/null
+++ b/man/scale_x_mosaic.Rd
@@ -0,0 +1,66 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_mosaic.R
+\name{scale_x_mosaic}
+\alias{scale_x_mosaic}
+\title{Determining scales for mosaics}
+\usage{
+scale_x_mosaic(
+  breaks = function() function(x) unique(x),
+  minor_breaks = NULL,
+  labels = function() function(x) unique(x),
+  na.value = NA_real_,
+  position = "bottom",
+  ...
+)
+}
+\arguments{
+\item{breaks}{One of:
+\itemize{
+\item \code{NULL} for no breaks
+\item \code{waiver()} for the default breaks computed by the
+\link[scales:new_transform]{transformation object}
+\item A numeric vector of positions
+\item A function that takes the limits as input and returns breaks
+as output (e.g., a function returned by \code{\link[scales:breaks_extended]{scales::extended_breaks()}}).
+Note that for position scales, limits are provided after scale expansion.
+Also accepts rlang \link[rlang:as_function]{lambda} function notation.
+}}
+
+\item{minor_breaks}{One of:
+\itemize{
+\item \code{NULL} for no minor breaks
+\item \code{waiver()} for the default breaks (none for discrete, one minor break
+between each major break for continuous)
+\item A numeric vector of positions
+\item A function that given the limits returns a vector of minor breaks. Also
+accepts rlang \link[rlang:as_function]{lambda} function notation. When
+the function has two arguments, it will be given the limits and major
+break positions.
+}}
+
+\item{labels}{One of the options below. Please note that when \code{labels} is a
+vector, it is highly recommended to also set the \code{breaks} argument as a
+vector to protect against unintended mismatches.
+\itemize{
+\item \code{NULL} for no labels
+\item \code{waiver()} for the default labels computed by the
+transformation object
+\item A character vector giving labels (must be same length as \code{breaks})
+\item An expression vector (must be the same length as breaks). See ?plotmath for details.
+\item A function that takes the breaks as input and returns labels
+as output. Also accepts rlang \link[rlang:as_function]{lambda} function
+notation.
+}}
+
+\item{na.value}{Missing values will be replaced with this value.}
+
+\item{position}{For position scales, The position of the axis.
+\code{left} or \code{right} for y axes, \code{top} or \code{bottom} for x axes.}
+
+\item{...}{other arguments passed to \code{continuous_scale()}.}
+
+\item{name}{set to pseudo waiver function \code{product_names} by default.}
+}
+\description{
+Determining scales for mosaics
+}

From 56149078c2a69976f09c170a5966fdee5b715c2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 26 Nov 2025 11:45:25 +0000
Subject: [PATCH 09/24] feat: update mosaic to working version

---
 R/custom_mosaic.R | 208 +++++++++++++++++++++++-----------------------
 R/utils.R         |   1 -
 2 files changed, 105 insertions(+), 104 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index f78e37264..97be4a314 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -31,8 +31,7 @@ geom_mosaic <- function(mapping = NULL, data = NULL,
   var_fill <- sprintf("x__fill__%s", aes_fill)
 
   mapping[[var_x]] <- mapping$x
-  mapping$x <- structure(1L, class = "mosaic")
-  # mapping[[var_fill]] <- mapping$fill
+  mapping$x <- structure(1L)
 
   layer <- ggplot2::layer(
     geom = GeomMosaic,
@@ -45,10 +44,10 @@ geom_mosaic <- function(mapping = NULL, data = NULL,
     check.aes = FALSE,
     params = list(na.rm = na.rm, ...)
   )
-  #list(layer, .scale_x_mosaic())
-  layer
+  list(layer, .scale_x_mosaic())
 }
 
+#' @keywords internal
 GeomMosaic <- ggplot2::ggproto(
   "GeomMosaic", ggplot2::GeomRect,
   default_aes = ggplot2::aes(
@@ -61,66 +60,16 @@ GeomMosaic <- ggplot2::ggproto(
   required_aes = c("xmin", "xmax", "ymin", "ymax")
 )
 
-#' Calculate Rectangle Coordinates for Mosaic Plot
-#'
-#' Computes the coordinates for rectangles in a mosaic plot based on combinations of `x` and `fill` variables.
-#' For each unique `x` and `fill`, calculates the proportional widths and heights, stacking rectangles within each `x` group.
+#' Mosaic Statistic for ggplot2
 #'
-#' @param data A data frame containing at least `x` and `fill` columns.
-#'
-#' @return A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`, representing the position and size of each rectangle.
+#' Implements a custom statistic for mosaic plots in ggplot2,
+#' calculating coordinates and axis breaks/labels for categorical
+#' variables.
 #'
-#' @details
-#' - Counts occurrences of each `x`/`fill` combination.
-#' - Calculates proportions within each `x` group.
-#' - Determines horizontal (`xmin`, `xmax`) and vertical (`ymin`, `ymax`) boundaries for each rectangle.
-#' - Adds small padding to each boundary for visual separation.
-.calculate_coordinates <- function(data) {
-  # Example: compute rectangles from x and y
-  result <- data |>
-    # Count combinations of X and Y
-    dplyr::count(x, fill) |>
-    # Compute total for each X group
-    dplyr::mutate(
-      .by = x,
-      x_total = sum(n),
-      prop = n / x_total
-    ) |>
-    # Change order from biggest group to smaller
-    dplyr::arrange(dplyr::desc(x_total), x, fill) |>
-    # Compute total sample size to turn counts into widths
-    dplyr::mutate(
-      N_total = dplyr::n(),
-      x_width = x_total / N_total
-    ) |>
-    # Convert counts to x widths
-    dplyr::mutate(
-      .by = x,
-      x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
-    ) |>
-    # Compute x-min/x-max for each group
-    dplyr::mutate(
-      xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
-      xmax = xmin + x_width
-    ) |>
-    # Compute y-min/y-max for stacked proportions
-    dplyr::mutate(
-      .by = x,
-      ymin = c(0, head(cumsum(prop), -1)),
-      ymax = cumsum(prop)
-    ) |>
-    dplyr::mutate(
-      xmin = xmin / max(xmax),
-      xmax = xmax / max(xmax),
-      xmin = xmin + 0.005,
-      xmax = xmax - 0.005,
-      ymin = ymin + 0.005,
-      ymax = ymax - 0.005
-    ) |>
-    dplyr::select(x, fill, xmin, xmax, ymin, ymax)
-  result
-}
-
+#' This statistic processes input data to compute the positions
+#' and sizes of mosaic rectangles, as well as the appropriate
+#' axis breaks and labels for the plot.
+#' @keywords internal
 StatMosaic <- ggplot2::ggproto(
   "StatMosaic", ggplot2::Stat,
 
@@ -130,49 +79,33 @@ StatMosaic <- ggplot2::ggproto(
     data
   },
   compute_panel = function(data, scales) {
+    # old_x <- data$x
     data$x <- data[, grepl("x__", colnames(data))]
     result <- .calculate_coordinates(data)
 
-    scale_x <- ggplot2::ScaleContinuous
-    scale_x[["breaks"]] <- result |>
+    breaks <- result |>
       dplyr::distinct(x, xmin, xmax) |>
       dplyr::mutate(mid = (xmin + xmax) / 2) |>
       dplyr::pull(mid)
 
-    scale_x[["labels"]] <- result |>
-      dplyr::distinct(x) |>
-      dplyr::pull(x)
+    labels <- dplyr::pull(dplyr::distinct(result, x))
+    result$x <- list(list2env(list(breaks = breaks[breaks != 0], labels = labels[breaks != 0])))
 
-    result$x <- list(scale = scale_x)
     result$group <- 1
     result$PANEL <- unique(data$PANEL)
     result
   }
 )
 
-#' Helper function for determining scales
-#'
-#' Used internally to determine class of variable x
-#' @param x variable
-#' @return character string "productlist"
-#' @importFrom ggplot2 scale_type
-#' @export
-scale_type.mosaic <- function(x) {
-  #  cat("checking for type productlist\n")
-  #browser()
-  "mosaic"
-}
-
-
 #' Determining scales for mosaics
 #'
 #' @param name set to pseudo waiver function `product_names` by default.
 #' @param ... other arguments passed to `continuous_scale()`.
 #' @inheritParams ggplot2::continuous_scale
-#' @export
-scale_x_mosaic <- function(breaks = function() function(x) unique(x),
+#' @keywords internal
+.scale_x_mosaic <- function(breaks = function(x) unique(x),
                            minor_breaks = NULL,
-                           labels = function() function(x) unique(x),
+                           labels = function(x) unique(x),
                            na.value = NA_real_,
                            position = "bottom",
                            ...) {
@@ -180,33 +113,43 @@ scale_x_mosaic <- function(breaks = function() function(x) unique(x),
     aesthetics = c(
       "x", "xmin", "xmax", "xend", "xintercept", "xmin_final", "xmax_final",
       "xlower", "xmiddle", "xupper"
-    ), palette = identity, breaks = breaks, minor_breaks = minor_breaks,
-    labels = labels, na.value = na.value, position = position,
-    super = ScaleContinuousProduct,, guide = ggplot2::waiver(), ...
+    ),
+    palette = identity,
+    breaks = breaks,
+    minor_breaks = minor_breaks,
+    labels = labels,
+    na.value = na.value,
+    position = position,
+    super = ScaleContinuousMosaic,,
+    guide = ggplot2::waiver(),
+    ...
   )
 }
 
 #' @rdname dot-scale_x_mosaic
-ScaleContinuousProduct <- ggplot2::ggproto(
-  "ScaleContinuousProduct", ggplot2::ScaleContinuousPosition,
+#' @importFrom ggplot2 ggproto ScaleContinuousPosition
+#' @keywords internal
+ScaleContinuousMosaic <- ggproto(
+  "ScaleContinuousMosaic", ScaleContinuousPosition,
   train =function(self, x) {
+    if (length(x) == 0) {
+        return()
+    }
     if (is.list(x)) {
-      x <- x[[1]]
-      if ("Scale" %in% class(x)) {
-        # re-assign the scale values now that we have the information - but only if necessary
-        if (is.function(self$breaks)) self$breaks <- x$breaks
-        if (is.function(self$labels)) self$labels <- x$labels
-        return(NULL)
-      }
+      scale_x <- x[[1]]
+      # re-assign the scale values now that we have the information - but only if necessary
+      if (is.function(self$breaks)) self$breaks <- scale_x$breaks
+      if (is.function(self$labels)) self$labels <- as.vector(scale_x$labels)
+      return(NULL)
     }
-    if (self$is.discrete(x)) {
+    if (is.discrete(x)) {
       self$range$train(x=c(0,1))
       return(NULL)
     }
-    self$range$train(x)
+    self$range$train(x, call = self$call)
   },
   map = function(self, x, limits = self$get_limits()) {
-    if (self$is.discrete(x)) return(x)
+    if (is.discrete(x)) return(x)
     if (is.list(x)) return(0) # need a number
     scaled <- as.numeric(self$oob(x, limits))
     ifelse(!is.na(scaled), scaled, self$na.value)
@@ -220,8 +163,67 @@ ScaleContinuousProduct <- ggplot2::ggproto(
       title <- self$product_name
     }
     else title
-  },
-  is.discrete = function(self, x) is.factor(x) || is.character(x) || is.logical(x)
+  }
 )
+is.discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
 
-
+#' Calculate Rectangle Coordinates for Mosaic Plot
+#'
+#' Computes the coordinates for rectangles in a mosaic plot based on combinations of `x` and `fill` variables.
+#' For each unique `x` and `fill`, calculates the proportional widths and heights, stacking rectangles within each `x` group.
+#'
+#' @param data A data frame containing at least `x` and `fill` columns.
+#'
+#' @return A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`, representing the position and size of each rectangle.
+#'
+#' @details
+#' - Counts occurrences of each `x`/`fill` combination.
+#' - Calculates proportions within each `x` group.
+#' - Determines horizontal (`xmin`, `xmax`) and vertical (`ymin`, `ymax`) boundaries for each rectangle.
+#' - Adds small padding to each boundary for visual separation.
+#' @keywords internal
+.calculate_coordinates <- function(data) {
+  # Example: compute rectangles from x and y
+  result <- data |>
+    # Count combinations of X and Y
+    dplyr::count(x, fill, .drop = FALSE) |>
+    # Compute total for each X group
+    dplyr::mutate(
+      .by = x,
+      x_total = sum(n),
+      prop = n / x_total,
+      prop = dplyr::if_else(is.nan(prop), 0, prop)
+    ) |>
+    dplyr::arrange(dplyr::desc(x_total), x, fill) |>
+    # Compute total sample size to turn counts into widths
+    dplyr::mutate(
+      N_total = dplyr::n(),
+      x_width = x_total / N_total
+    ) |>
+    # Convert counts to x widths
+    dplyr::mutate(
+      .by = x,
+      x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
+    ) |>
+    # Compute x-min/x-max for each group
+    dplyr::mutate(
+      xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
+      xmax = xmin + x_width
+    ) |>
+    # Compute y-min/y-max for stacked proportions
+    dplyr::mutate(
+      .by = x,
+      ymin = c(0, head(cumsum(prop), -1)),
+      ymax = cumsum(prop)
+    ) |>
+    dplyr::mutate(
+      xmin = xmin / max(xmax),
+      xmax = xmax / max(xmax),
+      xmin = dplyr::if_else(n == 0, 0, xmin + 0.005),
+      xmax = dplyr::if_else(n == 0, 0, xmax - 0.005),
+      ymin = dplyr::if_else(n == 0, 0, ymin + 0.005),
+      ymax = dplyr::if_else(n == 0, 0, ymax - 0.005)
+    ) |>
+    dplyr::select(x, fill, xmin, xmax, ymin, ymax, .n = n)
+  result
+}
\ No newline at end of file
diff --git a/R/utils.R b/R/utils.R
index d625746a5..5f462ba0d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -287,7 +287,6 @@ srv_decorate_teal_data <- function(id, data, decorators, expr) {
 
     reactive({
       req(decorated_output())
-      browser()
       if (no_expr) {
         decorated_output()
       } else {

From ff1519f5a258641328c7700d2b5484f6ef005741 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 26 Nov 2025 11:51:30 +0000
Subject: [PATCH 10/24] docs: update docs and remove import

---
 NAMESPACE                                     |  3 ---
 R/custom_mosaic.R                             |  5 ++--
 man/StatMosaic.Rd                             | 23 +++++++++++++++++++
 man/dot-calculate_coordinates.Rd              |  1 +
 ...cale_x_mosaic.Rd => dot-scale_x_mosaic.Rd} | 18 +++++++++++----
 man/scale_type.mosaic.Rd                      | 17 --------------
 6 files changed, 39 insertions(+), 28 deletions(-)
 create mode 100644 man/StatMosaic.Rd
 rename man/{scale_x_mosaic.Rd => dot-scale_x_mosaic.Rd} (85%)
 delete mode 100644 man/scale_type.mosaic.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 0392296ef..e86cf0f54 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,11 +8,9 @@ S3method(create_sparklines,default)
 S3method(create_sparklines,factor)
 S3method(create_sparklines,logical)
 S3method(create_sparklines,numeric)
-S3method(scale_type,mosaic)
 export(add_facet_labels)
 export(geom_mosaic)
 export(get_scatterplotmatrix_stats)
-export(scale_x_mosaic)
 export(tm_a_pca)
 export(tm_a_regression)
 export(tm_data_table)
@@ -33,5 +31,4 @@ import(shiny)
 import(teal)
 import(teal.transform)
 importFrom(dplyr,"%>%")
-importFrom(ggplot2,scale_type)
 importFrom(lifecycle,deprecated)
diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 97be4a314..80691ce9d 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -127,10 +127,9 @@ StatMosaic <- ggplot2::ggproto(
 }
 
 #' @rdname dot-scale_x_mosaic
-#' @importFrom ggplot2 ggproto ScaleContinuousPosition
 #' @keywords internal
-ScaleContinuousMosaic <- ggproto(
-  "ScaleContinuousMosaic", ScaleContinuousPosition,
+ScaleContinuousMosaic <- ggplot2::ggproto(
+  "ScaleContinuousMosaic", ggplot2::ScaleContinuousPosition,
   train =function(self, x) {
     if (length(x) == 0) {
         return()
diff --git a/man/StatMosaic.Rd b/man/StatMosaic.Rd
new file mode 100644
index 000000000..fd8d091de
--- /dev/null
+++ b/man/StatMosaic.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_mosaic.R
+\docType{data}
+\name{StatMosaic}
+\alias{StatMosaic}
+\title{Mosaic Statistic for ggplot2}
+\format{
+An object of class \code{StatMosaic} (inherits from \code{Stat}, \code{ggproto}, \code{gg}) of length 4.
+}
+\usage{
+StatMosaic
+}
+\description{
+Implements a custom statistic for mosaic plots in ggplot2,
+calculating coordinates and axis breaks/labels for categorical
+variables.
+}
+\details{
+This statistic processes input data to compute the positions
+and sizes of mosaic rectangles, as well as the appropriate
+axis breaks and labels for the plot.
+}
+\keyword{internal}
diff --git a/man/dot-calculate_coordinates.Rd b/man/dot-calculate_coordinates.Rd
index f17830c9c..0118bc49f 100644
--- a/man/dot-calculate_coordinates.Rd
+++ b/man/dot-calculate_coordinates.Rd
@@ -24,3 +24,4 @@ For each unique \code{x} and \code{fill}, calculates the proportional widths and
 \item Adds small padding to each boundary for visual separation.
 }
 }
+\keyword{internal}
diff --git a/man/scale_x_mosaic.Rd b/man/dot-scale_x_mosaic.Rd
similarity index 85%
rename from man/scale_x_mosaic.Rd
rename to man/dot-scale_x_mosaic.Rd
index 27c62a872..4006a6281 100644
--- a/man/scale_x_mosaic.Rd
+++ b/man/dot-scale_x_mosaic.Rd
@@ -1,17 +1,24 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/custom_mosaic.R
-\name{scale_x_mosaic}
-\alias{scale_x_mosaic}
+\docType{data}
+\name{.scale_x_mosaic}
+\alias{.scale_x_mosaic}
+\alias{ScaleContinuousMosaic}
 \title{Determining scales for mosaics}
+\format{
+An object of class \code{ScaleContinuousMosaic} (inherits from \code{ScaleContinuousPosition}, \code{ScaleContinuous}, \code{Scale}, \code{ggproto}, \code{gg}) of length 5.
+}
 \usage{
-scale_x_mosaic(
-  breaks = function() function(x) unique(x),
+.scale_x_mosaic(
+  breaks = function(x) unique(x),
   minor_breaks = NULL,
-  labels = function() function(x) unique(x),
+  labels = function(x) unique(x),
   na.value = NA_real_,
   position = "bottom",
   ...
 )
+
+ScaleContinuousMosaic
 }
 \arguments{
 \item{breaks}{One of:
@@ -64,3 +71,4 @@ notation.
 \description{
 Determining scales for mosaics
 }
+\keyword{internal}
diff --git a/man/scale_type.mosaic.Rd b/man/scale_type.mosaic.Rd
deleted file mode 100644
index 9b98318e3..000000000
--- a/man/scale_type.mosaic.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/custom_mosaic.R
-\name{scale_type.mosaic}
-\alias{scale_type.mosaic}
-\title{Helper function for determining scales}
-\usage{
-\method{scale_type}{mosaic}(x)
-}
-\arguments{
-\item{x}{variable}
-}
-\value{
-character string "productlist"
-}
-\description{
-Used internally to determine class of variable x
-}

From 2fd5f4c72d244108355f86ec79d8370ba4f746ab Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 26 Nov 2025 11:53:41 +0000
Subject: [PATCH 11/24] [skip style] [skip vbump] Restyle files

---
 R/custom_mosaic.R  | 48 +++++++++++++++++++++++++---------------------
 R/tm_g_bivariate.R |  2 +-
 2 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 80691ce9d..8a2bb22ba 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -17,14 +17,15 @@
 #' @examples
 #' df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 #' library(ggplot2)
-#' ggplot(df, aes(x = RACE, fill = SEX)) + geom_rects()
+#' ggplot(df, aes(x = RACE, fill = SEX)) +
+#'   geom_rects()
 #' @export
 geom_mosaic <- function(mapping = NULL, data = NULL,
-                       stat = "mosaic", position = "identity",
-                       ...,
-                       na.rm = FALSE,
-                       show.legend = TRUE,
-                       inherit.aes = TRUE) {
+                        stat = "mosaic", position = "identity",
+                        ...,
+                        na.rm = FALSE,
+                        show.legend = TRUE,
+                        inherit.aes = TRUE) {
   aes_x <- list(rlang::quo_get_expr(mapping$x))
   var_x <- sprintf("x__%s", as.character(aes_x))
   aes_fill <- rlang::quo_text(mapping$fill)
@@ -72,9 +73,7 @@ GeomMosaic <- ggplot2::ggproto(
 #' @keywords internal
 StatMosaic <- ggplot2::ggproto(
   "StatMosaic", ggplot2::Stat,
-
   required_aes = c("x", "fill"),
-
   compute_group = function(data, scales) {
     data
   },
@@ -104,11 +103,11 @@ StatMosaic <- ggplot2::ggproto(
 #' @inheritParams ggplot2::continuous_scale
 #' @keywords internal
 .scale_x_mosaic <- function(breaks = function(x) unique(x),
-                           minor_breaks = NULL,
-                           labels = function(x) unique(x),
-                           na.value = NA_real_,
-                           position = "bottom",
-                           ...) {
+                            minor_breaks = NULL,
+                            labels = function(x) unique(x),
+                            na.value = NA_real_,
+                            position = "bottom",
+                            ...) {
   ggplot2::continuous_scale(
     aesthetics = c(
       "x", "xmin", "xmax", "xend", "xintercept", "xmin_final", "xmax_final",
@@ -120,7 +119,7 @@ StatMosaic <- ggplot2::ggproto(
     labels = labels,
     na.value = na.value,
     position = position,
-    super = ScaleContinuousMosaic,,
+    super = ScaleContinuousMosaic, ,
     guide = ggplot2::waiver(),
     ...
   )
@@ -130,9 +129,9 @@ StatMosaic <- ggplot2::ggproto(
 #' @keywords internal
 ScaleContinuousMosaic <- ggplot2::ggproto(
   "ScaleContinuousMosaic", ggplot2::ScaleContinuousPosition,
-  train =function(self, x) {
+  train = function(self, x) {
     if (length(x) == 0) {
-        return()
+      return()
     }
     if (is.list(x)) {
       scale_x <- x[[1]]
@@ -142,26 +141,31 @@ ScaleContinuousMosaic <- ggplot2::ggproto(
       return(NULL)
     }
     if (is.discrete(x)) {
-      self$range$train(x=c(0,1))
+      self$range$train(x = c(0, 1))
       return(NULL)
     }
     self$range$train(x, call = self$call)
   },
   map = function(self, x, limits = self$get_limits()) {
-    if (is.discrete(x)) return(x)
-    if (is.list(x)) return(0) # need a number
+    if (is.discrete(x)) {
+      return(x)
+    }
+    if (is.list(x)) {
+      return(0)
+    } # need a number
     scaled <- as.numeric(self$oob(x, limits))
     ifelse(!is.na(scaled), scaled, self$na.value)
   },
   dimension = function(self, expand = c(0, 0)) {
-    c(-0.05,1.05)
+    c(-0.05, 1.05)
   },
   make_title = function(..., self) {
     title <- ggplot2::ggproto_parent(ggplot2::ScaleContinuousPosition, self)$make_title(...)
     if (isTRUE(title %in% self$aesthetics)) {
       title <- self$product_name
+    } else {
+      title
     }
-    else title
   }
 )
 is.discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
@@ -225,4 +229,4 @@ is.discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
     ) |>
     dplyr::select(x, fill, xmin, xmax, ymin, ymax, .n = n)
   result
-}
\ No newline at end of file
+}
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 96a4725aa..20de5387c 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -736,7 +736,7 @@ srv_g_bivariate <- function(id,
     )
 
     set_chunk_dims(pws, decorated_output_q_facets)
-    })
+  })
 }
 
 # Get Substituted ggplot call

From 9300a7a6a30a12c2ba0b6929e4737634d4f031f1 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 26 Nov 2025 12:00:35 +0000
Subject: [PATCH 12/24] [skip roxygen] [skip vbump] Roxygen Man Pages Auto
 Update

---
 man/geom_mosaic.Rd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
index 679c6b4b3..f122dcc8d 100644
--- a/man/geom_mosaic.Rd
+++ b/man/geom_mosaic.Rd
@@ -42,5 +42,6 @@ Each rectangle's size reflects the proportion of observations for combinations o
 \examples{
 df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 library(ggplot2)
-ggplot(df, aes(x = RACE, fill = SEX)) + geom_rects()
+ggplot(df, aes(x = RACE, fill = SEX)) +
+  geom_rects()
 }

From 3dae9e16360f6b75593a57c80e81d419f9c6f178 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 26 Nov 2025 11:58:13 +0000
Subject: [PATCH 13/24] docs: clean up

---
 R/custom_mosaic.R                | 27 ++++-----------------------
 man/StatMosaic.Rd                | 23 -----------------------
 man/dot-calculate_coordinates.Rd | 27 ---------------------------
 man/dot-scale_x_mosaic.Rd        |  7 -------
 man/geom_mosaic.Rd               | 14 ++++++++++++++
 5 files changed, 18 insertions(+), 80 deletions(-)
 delete mode 100644 man/StatMosaic.Rd
 delete mode 100644 man/dot-calculate_coordinates.Rd

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 8a2bb22ba..78ff21774 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -61,24 +61,12 @@ GeomMosaic <- ggplot2::ggproto(
   required_aes = c("xmin", "xmax", "ymin", "ymax")
 )
 
-#' Mosaic Statistic for ggplot2
-#'
-#' Implements a custom statistic for mosaic plots in ggplot2,
-#' calculating coordinates and axis breaks/labels for categorical
-#' variables.
-#'
-#' This statistic processes input data to compute the positions
-#' and sizes of mosaic rectangles, as well as the appropriate
-#' axis breaks and labels for the plot.
 #' @keywords internal
 StatMosaic <- ggplot2::ggproto(
   "StatMosaic", ggplot2::Stat,
   required_aes = c("x", "fill"),
-  compute_group = function(data, scales) {
-    data
-  },
+  compute_group = function(data, scales) data,
   compute_panel = function(data, scales) {
-    # old_x <- data$x
     data$x <- data[, grepl("x__", colnames(data))]
     result <- .calculate_coordinates(data)
 
@@ -125,7 +113,6 @@ StatMosaic <- ggplot2::ggproto(
   )
 }
 
-#' @rdname dot-scale_x_mosaic
 #' @keywords internal
 ScaleContinuousMosaic <- ggplot2::ggproto(
   "ScaleContinuousMosaic", ggplot2::ScaleContinuousPosition,
@@ -170,20 +157,14 @@ ScaleContinuousMosaic <- ggplot2::ggproto(
 )
 is.discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
 
-#' Calculate Rectangle Coordinates for Mosaic Plot
-#'
+#' @describeIn geom_mosaic
 #' Computes the coordinates for rectangles in a mosaic plot based on combinations of `x` and `fill` variables.
 #' For each unique `x` and `fill`, calculates the proportional widths and heights, stacking rectangles within each `x` group.
 #'
-#' @param data A data frame containing at least `x` and `fill` columns.
+#' ### Value
 #'
-#' @return A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`, representing the position and size of each rectangle.
+#' A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`, representing the position and size of each rectangle.
 #'
-#' @details
-#' - Counts occurrences of each `x`/`fill` combination.
-#' - Calculates proportions within each `x` group.
-#' - Determines horizontal (`xmin`, `xmax`) and vertical (`ymin`, `ymax`) boundaries for each rectangle.
-#' - Adds small padding to each boundary for visual separation.
 #' @keywords internal
 .calculate_coordinates <- function(data) {
   # Example: compute rectangles from x and y
diff --git a/man/StatMosaic.Rd b/man/StatMosaic.Rd
deleted file mode 100644
index fd8d091de..000000000
--- a/man/StatMosaic.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/custom_mosaic.R
-\docType{data}
-\name{StatMosaic}
-\alias{StatMosaic}
-\title{Mosaic Statistic for ggplot2}
-\format{
-An object of class \code{StatMosaic} (inherits from \code{Stat}, \code{ggproto}, \code{gg}) of length 4.
-}
-\usage{
-StatMosaic
-}
-\description{
-Implements a custom statistic for mosaic plots in ggplot2,
-calculating coordinates and axis breaks/labels for categorical
-variables.
-}
-\details{
-This statistic processes input data to compute the positions
-and sizes of mosaic rectangles, as well as the appropriate
-axis breaks and labels for the plot.
-}
-\keyword{internal}
diff --git a/man/dot-calculate_coordinates.Rd b/man/dot-calculate_coordinates.Rd
deleted file mode 100644
index 0118bc49f..000000000
--- a/man/dot-calculate_coordinates.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/custom_mosaic.R
-\name{.calculate_coordinates}
-\alias{.calculate_coordinates}
-\title{Calculate Rectangle Coordinates for Mosaic Plot}
-\usage{
-.calculate_coordinates(data)
-}
-\arguments{
-\item{data}{A data frame containing at least \code{x} and \code{fill} columns.}
-}
-\value{
-A data frame with columns: \code{x}, \code{fill}, \code{xmin}, \code{xmax}, \code{ymin}, \code{ymax}, representing the position and size of each rectangle.
-}
-\description{
-Computes the coordinates for rectangles in a mosaic plot based on combinations of \code{x} and \code{fill} variables.
-For each unique \code{x} and \code{fill}, calculates the proportional widths and heights, stacking rectangles within each \code{x} group.
-}
-\details{
-\itemize{
-\item Counts occurrences of each \code{x}/\code{fill} combination.
-\item Calculates proportions within each \code{x} group.
-\item Determines horizontal (\code{xmin}, \code{xmax}) and vertical (\code{ymin}, \code{ymax}) boundaries for each rectangle.
-\item Adds small padding to each boundary for visual separation.
-}
-}
-\keyword{internal}
diff --git a/man/dot-scale_x_mosaic.Rd b/man/dot-scale_x_mosaic.Rd
index 4006a6281..d4a5397a6 100644
--- a/man/dot-scale_x_mosaic.Rd
+++ b/man/dot-scale_x_mosaic.Rd
@@ -1,13 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/custom_mosaic.R
-\docType{data}
 \name{.scale_x_mosaic}
 \alias{.scale_x_mosaic}
-\alias{ScaleContinuousMosaic}
 \title{Determining scales for mosaics}
-\format{
-An object of class \code{ScaleContinuousMosaic} (inherits from \code{ScaleContinuousPosition}, \code{ScaleContinuous}, \code{Scale}, \code{ggproto}, \code{gg}) of length 5.
-}
 \usage{
 .scale_x_mosaic(
   breaks = function(x) unique(x),
@@ -17,8 +12,6 @@ An object of class \code{ScaleContinuousMosaic} (inherits from \code{ScaleContin
   position = "bottom",
   ...
 )
-
-ScaleContinuousMosaic
 }
 \arguments{
 \item{breaks}{One of:
diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
index f122dcc8d..fdad53e46 100644
--- a/man/geom_mosaic.Rd
+++ b/man/geom_mosaic.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/custom_mosaic.R
 \name{geom_mosaic}
 \alias{geom_mosaic}
+\alias{.calculate_coordinates}
 \title{Mosaic Rectangles Layer for ggplot2}
 \usage{
 geom_mosaic(
@@ -14,6 +15,8 @@ geom_mosaic(
   show.legend = TRUE,
   inherit.aes = TRUE
 )
+
+.calculate_coordinates(data)
 }
 \arguments{
 \item{mapping}{Set of aesthetic mappings created by \code{aes()}. Must specify \code{x} and \code{fill}.}
@@ -39,9 +42,20 @@ A ggplot2 layer that adds mosaic rectangles to the plot.
 Adds a mosaic-style rectangles layer to a ggplot, visualizing the joint distribution of categorical variables.
 Each rectangle's size reflects the proportion of observations for combinations of \code{x} and \code{fill}.
 }
+\section{Functions}{
+\itemize{
+\item \code{.calculate_coordinates()}: Computes the coordinates for rectangles in a mosaic plot based on combinations of \code{x} and \code{fill} variables.
+For each unique \code{x} and \code{fill}, calculates the proportional widths and heights, stacking rectangles within each \code{x} group.
+\subsection{Value}{
+
+A data frame with columns: \code{x}, \code{fill}, \code{xmin}, \code{xmax}, \code{ymin}, \code{ymax}, representing the position and size of each rectangle.
+}
+
+}}
 \examples{
 df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 library(ggplot2)
 ggplot(df, aes(x = RACE, fill = SEX)) +
   geom_rects()
 }
+\keyword{internal}

From c06f9f99cce36f0bec2c3a0b425f3a2fc86d4407 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 26 Nov 2025 12:04:23 +0000
Subject: [PATCH 14/24] chore: lint code

---
 R/custom_mosaic.R  | 37 ++++++++++++++++++++++---------------
 man/geom_mosaic.Rd | 15 ++++++++++-----
 2 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 78ff21774..b2f02039f 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -1,7 +1,9 @@
 #' Mosaic Rectangles Layer for ggplot2
 #'
-#' Adds a mosaic-style rectangles layer to a ggplot, visualizing the joint distribution of categorical variables.
-#' Each rectangle's size reflects the proportion of observations for combinations of `x` and `fill`.
+#' Adds a mosaic-style rectangles layer to a ggplot, visualizing the
+#' joint distribution of categorical variables.
+#' Each rectangle's size reflects the proportion of observations for
+#' combinations of `x` and `fill`.
 #'
 #' @param mapping Set of aesthetic mappings created by `aes()`. Must specify `x` and `fill`.
 #' @param data The data to be displayed in this layer.
@@ -23,9 +25,9 @@
 geom_mosaic <- function(mapping = NULL, data = NULL,
                         stat = "mosaic", position = "identity",
                         ...,
-                        na.rm = FALSE,
-                        show.legend = TRUE,
-                        inherit.aes = TRUE) {
+                        na.rm = FALSE, # nolint: object_name_linter.
+                        show.legend = TRUE, # nolint: object_name_linter.
+                        inherit.aes = TRUE) { # nolint: object_name_linter.
   aes_x <- list(rlang::quo_get_expr(mapping$x))
   var_x <- sprintf("x__%s", as.character(aes_x))
   aes_fill <- rlang::quo_text(mapping$fill)
@@ -49,7 +51,7 @@ geom_mosaic <- function(mapping = NULL, data = NULL,
 }
 
 #' @keywords internal
-GeomMosaic <- ggplot2::ggproto(
+GeomMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
   "GeomMosaic", ggplot2::GeomRect,
   default_aes = ggplot2::aes(
     colour = NA, linewidth = 0.5, linetype = 1, alpha = 1, fill = "grey30"
@@ -62,7 +64,7 @@ GeomMosaic <- ggplot2::ggproto(
 )
 
 #' @keywords internal
-StatMosaic <- ggplot2::ggproto(
+StatMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
   "StatMosaic", ggplot2::Stat,
   required_aes = c("x", "fill"),
   compute_group = function(data, scales) data,
@@ -93,7 +95,7 @@ StatMosaic <- ggplot2::ggproto(
 .scale_x_mosaic <- function(breaks = function(x) unique(x),
                             minor_breaks = NULL,
                             labels = function(x) unique(x),
-                            na.value = NA_real_,
+                            na.value = NA_real_, # nolint: object_name_linter.
                             position = "bottom",
                             ...) {
   ggplot2::continuous_scale(
@@ -114,7 +116,7 @@ StatMosaic <- ggplot2::ggproto(
 }
 
 #' @keywords internal
-ScaleContinuousMosaic <- ggplot2::ggproto(
+ScaleContinuousMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
   "ScaleContinuousMosaic", ggplot2::ScaleContinuousPosition,
   train = function(self, x) {
     if (length(x) == 0) {
@@ -127,14 +129,14 @@ ScaleContinuousMosaic <- ggplot2::ggproto(
       if (is.function(self$labels)) self$labels <- as.vector(scale_x$labels)
       return(NULL)
     }
-    if (is.discrete(x)) {
+    if (is_discrete(x)) {
       self$range$train(x = c(0, 1))
       return(NULL)
     }
     self$range$train(x, call = self$call)
   },
   map = function(self, x, limits = self$get_limits()) {
-    if (is.discrete(x)) {
+    if (is_discrete(x)) {
       return(x)
     }
     if (is.list(x)) {
@@ -155,15 +157,20 @@ ScaleContinuousMosaic <- ggplot2::ggproto(
     }
   }
 )
-is.discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
+
+#' @noRd
+is_discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
 
 #' @describeIn geom_mosaic
-#' Computes the coordinates for rectangles in a mosaic plot based on combinations of `x` and `fill` variables.
-#' For each unique `x` and `fill`, calculates the proportional widths and heights, stacking rectangles within each `x` group.
+#' Computes the coordinates for rectangles in a mosaic plot based
+#' on combinations of `x` and `fill` variables.
+#' For each unique `x` and `fill`, calculates the proportional
+#' widths and heights, stacking rectangles within each `x` group.
 #'
 #' ### Value
 #'
-#' A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`, representing the position and size of each rectangle.
+#' A data frame with columns: `x`, `fill`, `xmin`, `xmax`, `ymin`, `ymax`,
+#' representing the position and size of each rectangle.
 #'
 #' @keywords internal
 .calculate_coordinates <- function(data) {
diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
index fdad53e46..63d720cbe 100644
--- a/man/geom_mosaic.Rd
+++ b/man/geom_mosaic.Rd
@@ -39,16 +39,21 @@ geom_mosaic(
 A ggplot2 layer that adds mosaic rectangles to the plot.
 }
 \description{
-Adds a mosaic-style rectangles layer to a ggplot, visualizing the joint distribution of categorical variables.
-Each rectangle's size reflects the proportion of observations for combinations of \code{x} and \code{fill}.
+Adds a mosaic-style rectangles layer to a ggplot, visualizing the
+joint distribution of categorical variables.
+Each rectangle's size reflects the proportion of observations for
+combinations of \code{x} and \code{fill}.
 }
 \section{Functions}{
 \itemize{
-\item \code{.calculate_coordinates()}: Computes the coordinates for rectangles in a mosaic plot based on combinations of \code{x} and \code{fill} variables.
-For each unique \code{x} and \code{fill}, calculates the proportional widths and heights, stacking rectangles within each \code{x} group.
+\item \code{.calculate_coordinates()}: Computes the coordinates for rectangles in a mosaic plot based
+on combinations of \code{x} and \code{fill} variables.
+For each unique \code{x} and \code{fill}, calculates the proportional
+widths and heights, stacking rectangles within each \code{x} group.
 \subsection{Value}{
 
-A data frame with columns: \code{x}, \code{fill}, \code{xmin}, \code{xmax}, \code{ymin}, \code{ymax}, representing the position and size of each rectangle.
+A data frame with columns: \code{x}, \code{fill}, \code{xmin}, \code{xmax}, \code{ymin}, \code{ymax},
+representing the position and size of each rectangle.
 }
 
 }}

From eacc78d66f916aca34b654fb54e700528b526506 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 26 Nov 2025 12:09:01 +0000
Subject: [PATCH 15/24] chore: cleanup and adds disclaimer on top

---
 R/custom_mosaic.R | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index b2f02039f..0f7b96e21 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -1,3 +1,8 @@
+# minimal implementation of ggplot2 mosaic after ggmosaic was archived in CRAN
+#
+# This was heavily inspired by github.com/haleyjeppson/ggmosaic package but
+# simplified to only support 2 categorical variables
+
 #' Mosaic Rectangles Layer for ggplot2
 #'
 #' Adds a mosaic-style rectangles layer to a ggplot, visualizing the
@@ -145,17 +150,7 @@ ScaleContinuousMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
     scaled <- as.numeric(self$oob(x, limits))
     ifelse(!is.na(scaled), scaled, self$na.value)
   },
-  dimension = function(self, expand = c(0, 0)) {
-    c(-0.05, 1.05)
-  },
-  make_title = function(..., self) {
-    title <- ggplot2::ggproto_parent(ggplot2::ScaleContinuousPosition, self)$make_title(...)
-    if (isTRUE(title %in% self$aesthetics)) {
-      title <- self$product_name
-    } else {
-      title
-    }
-  }
+  dimension = function(self, expand = c(0, 0)) c(-0.05, 1.05)
 )
 
 #' @noRd

From 296ab1505f8b48b5c5e3ae7697a63abf17b536c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 27 Nov 2025 12:54:07 +0000
Subject: [PATCH 16/24] fix: update tests with bivariate geom plot call

---
 tests/testthat/test_bivariate_ggplot_call.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test_bivariate_ggplot_call.R b/tests/testthat/test_bivariate_ggplot_call.R
index d65d122f5..618ada9e2 100644
--- a/tests/testthat/test_bivariate_ggplot_call.R
+++ b/tests/testthat/test_bivariate_ggplot_call.R
@@ -31,7 +31,7 @@ testthat::describe("bivariate_ggplot_call with arguments:", {
             bivariate_ggplot_call(x[[1]], x[[2]], data_name = "ANL", x = "x", y = "y"),
             width.cutoff = 300
           ),
-          "mosaic_data <- ",
+          "teal.modules.general::geom_mosaic",
           all = FALSE
         )
       })

From f0917e5d2dd9c30ea876ff76553569746f947276 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 27 Nov 2025 15:17:39 +0100
Subject: [PATCH 17/24] Update R/custom_mosaic.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
---
 R/custom_mosaic.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index 0f7b96e21..c1b14bacb 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -25,7 +25,7 @@
 #' df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 #' library(ggplot2)
 #' ggplot(df, aes(x = RACE, fill = SEX)) +
-#'   geom_rects()
+#'   geom_mosaic()
 #' @export
 geom_mosaic <- function(mapping = NULL, data = NULL,
                         stat = "mosaic", position = "identity",

From a05f6ddfa400563a93d8ab55fb6bd43ec416e11d Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 27 Nov 2025 14:24:18 +0000
Subject: [PATCH 18/24] [skip roxygen] [skip vbump] Roxygen Man Pages Auto
 Update

---
 man/geom_mosaic.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
index 63d720cbe..f0eb14173 100644
--- a/man/geom_mosaic.Rd
+++ b/man/geom_mosaic.Rd
@@ -61,6 +61,6 @@ representing the position and size of each rectangle.
 df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 library(ggplot2)
 ggplot(df, aes(x = RACE, fill = SEX)) +
-  geom_rects()
+  geom_mosaic()
 }
 \keyword{internal}

From dcb15072c58e61395f04f36df8186877bfed1dae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 27 Nov 2025 14:29:26 +0000
Subject: [PATCH 19/24] fix: examples

---
 R/custom_mosaic.R  | 21 ++++++++++++++-------
 man/geom_mosaic.Rd |  4 ++--
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index c1b14bacb..f2e737ce4 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -24,8 +24,8 @@
 #' @examples
 #' df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 #' library(ggplot2)
-#' ggplot(df, aes(x = RACE, fill = SEX)) +
-#'   geom_mosaic()
+#' ggplot(df) +
+#'   geom_mosaic(aes(x = RACE, fill = SEX))
 #' @export
 geom_mosaic <- function(mapping = NULL, data = NULL,
                         stat = "mosaic", position = "identity",
@@ -33,12 +33,19 @@ geom_mosaic <- function(mapping = NULL, data = NULL,
                         na.rm = FALSE, # nolint: object_name_linter.
                         show.legend = TRUE, # nolint: object_name_linter.
                         inherit.aes = TRUE) { # nolint: object_name_linter.
-  aes_x <- list(rlang::quo_get_expr(mapping$x))
-  var_x <- sprintf("x__%s", as.character(aes_x))
-  aes_fill <- rlang::quo_text(mapping$fill)
-  var_fill <- sprintf("x__fill__%s", aes_fill)
 
-  mapping[[var_x]] <- mapping$x
+  aes_x <- mapping$x
+  if (!is.null(aes_x)) {
+    aes_x <- list(rlang::quo_get_expr(mapping$x))
+    var_x <- paste0("x__", as.character(aes_x))
+    mapping[[var_x]] <- mapping$x
+  }
+
+  aes_fill <- mapping$fill
+  if (!is.null(aes_fill)) {
+    aes_fill <- rlang::quo_text(mapping$fill)
+  }
+
   mapping$x <- structure(1L)
 
   layer <- ggplot2::layer(
diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
index f0eb14173..01524681f 100644
--- a/man/geom_mosaic.Rd
+++ b/man/geom_mosaic.Rd
@@ -60,7 +60,7 @@ representing the position and size of each rectangle.
 \examples{
 df <- data.frame(RACE = c("Black", "White", "Black", "Asian"), SEX = c("M", "M", "F", "F"))
 library(ggplot2)
-ggplot(df, aes(x = RACE, fill = SEX)) +
-  geom_mosaic()
+ggplot(df) +
+  geom_mosaic(aes(x = RACE, fill = SEX))
 }
 \keyword{internal}

From 07e3ff48a5abb071ec71449566a83991645f19fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 27 Nov 2025 14:47:05 +0000
Subject: [PATCH 20/24] feat: use simpler expressions

---
 R/custom_mosaic.R | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/R/custom_mosaic.R b/R/custom_mosaic.R
index f2e737ce4..b4b65f34f 100644
--- a/R/custom_mosaic.R
+++ b/R/custom_mosaic.R
@@ -84,12 +84,8 @@ StatMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
     data$x <- data[, grepl("x__", colnames(data))]
     result <- .calculate_coordinates(data)
 
-    breaks <- result |>
-      dplyr::distinct(x, xmin, xmax) |>
-      dplyr::mutate(mid = (xmin + xmax) / 2) |>
-      dplyr::pull(mid)
-
-    labels <- dplyr::pull(dplyr::distinct(result, x))
+    breaks <- breaks <- unique(with(result, (xmin + xmax) / 2))
+    labels <- unique(result$x)
     result$x <- list(list2env(list(breaks = breaks[breaks != 0], labels = labels[breaks != 0])))
 
     result$group <- 1

From 60ee4e2b4da85e175f92da06759414629d00894c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 27 Nov 2025 15:10:49 +0000
Subject: [PATCH 21/24] chore: rename of file to better describe contents

---
 R/{custom_mosaic.R => geom_mosaic.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename R/{custom_mosaic.R => geom_mosaic.R} (100%)

diff --git a/R/custom_mosaic.R b/R/geom_mosaic.R
similarity index 100%
rename from R/custom_mosaic.R
rename to R/geom_mosaic.R

From 3eb774c71222e1b952f6b0ee0de13d1d56491517 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 27 Nov 2025 15:16:53 +0000
Subject: [PATCH 22/24] chore: update ggplot2 and dplyr versions

---
 DESCRIPTION     | 4 ++--
 R/geom_mosaic.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9ba78ad5d..e0cee387d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -23,7 +23,7 @@ URL: https://insightsengineering.github.io/teal.modules.general/,
 BugReports:
     https://github.com/insightsengineering/teal.modules.general/issues
 Depends:
-    ggplot2 (>= 3.4.0),
+    ggplot2 (>= 3.5.0),
     R (>= 4.1),
     shiny (>= 1.8.1),
     teal (>= 1.0.0.9003),
@@ -32,7 +32,7 @@ Imports:
     bslib (>= 0.8.0),
     checkmate (>= 2.1.0),
     colourpicker (>= 1.3.0),
-    dplyr (>= 1.0.5),
+    dplyr (>= 1.1.0),
     DT (>= 0.13),
     forcats (>= 1.0.0),
     generics (>= 0.1.3),
diff --git a/R/geom_mosaic.R b/R/geom_mosaic.R
index b4b65f34f..a672e500a 100644
--- a/R/geom_mosaic.R
+++ b/R/geom_mosaic.R
@@ -84,7 +84,7 @@ StatMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
     data$x <- data[, grepl("x__", colnames(data))]
     result <- .calculate_coordinates(data)
 
-    breaks <- breaks <- unique(with(result, (xmin + xmax) / 2))
+    breaks <- unique(with(result, (xmin + xmax) / 2))
     labels <- unique(result$x)
     result$x <- list(list2env(list(breaks = breaks[breaks != 0], labels = labels[breaks != 0])))
 

From e88600b730d56e4a0230102bf6c782b50260d812 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 27 Nov 2025 15:25:00 +0000
Subject: [PATCH 23/24] [skip roxygen] [skip vbump] Roxygen Man Pages Auto
 Update

---
 man/dot-scale_x_mosaic.Rd | 2 +-
 man/geom_mosaic.Rd        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/dot-scale_x_mosaic.Rd b/man/dot-scale_x_mosaic.Rd
index d4a5397a6..6e1c17c5c 100644
--- a/man/dot-scale_x_mosaic.Rd
+++ b/man/dot-scale_x_mosaic.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/custom_mosaic.R
+% Please edit documentation in R/geom_mosaic.R
 \name{.scale_x_mosaic}
 \alias{.scale_x_mosaic}
 \title{Determining scales for mosaics}
diff --git a/man/geom_mosaic.Rd b/man/geom_mosaic.Rd
index 01524681f..dadbb4902 100644
--- a/man/geom_mosaic.Rd
+++ b/man/geom_mosaic.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/custom_mosaic.R
+% Please edit documentation in R/geom_mosaic.R
 \name{geom_mosaic}
 \alias{geom_mosaic}
 \alias{.calculate_coordinates}

From 5ca3ffdb840eb97def1e1fef2d460931692a4352 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 2 Dec 2025 12:02:12 +0000
Subject: [PATCH 24/24] fix: .data pronoun and bug with breaks/labels

---
 NAMESPACE                 |  1 +
 R/geom_mosaic.R           | 62 ++++++++++++++++++++++-----------------
 R/teal.modules.general.R  |  3 +-
 R/tm_g_association.R      |  2 +-
 man/dot-scale_x_mosaic.Rd | 51 +++++++-------------------------
 5 files changed, 48 insertions(+), 71 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index b48bd9068..9a8bb56e3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -34,4 +34,5 @@ import(shiny)
 import(teal)
 import(teal.transform)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,.data)
 importFrom(lifecycle,deprecated)
diff --git a/R/geom_mosaic.R b/R/geom_mosaic.R
index a672e500a..6ecfddb4b 100644
--- a/R/geom_mosaic.R
+++ b/R/geom_mosaic.R
@@ -84,8 +84,9 @@ StatMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
     data$x <- data[, grepl("x__", colnames(data))]
     result <- .calculate_coordinates(data)
 
-    breaks <- unique(with(result, (xmin + xmax) / 2))
-    labels <- unique(result$x)
+    results_non_zero <- result[result$.n != 0, ]
+    breaks <- unique(with(results_non_zero, (xmin + xmax) / 2))
+    labels <- unique(results_non_zero$x)
     result$x <- list(list2env(list(breaks = breaks[breaks != 0], labels = labels[breaks != 0])))
 
     result$group <- 1
@@ -96,13 +97,20 @@ StatMosaic <- ggplot2::ggproto( # nolint: object_name_linter.
 
 #' Determining scales for mosaics
 #'
-#' @param name set to pseudo waiver function `product_names` by default.
+#' @param breaks,labels,minor_breaks One of:
+#' - `NULL` for no breaks / labels.
+#' - [ggplot2::waiver()] for the default breaks / labels computed by the scale.
+#' - A numeric / character vector giving the positions of the breaks / labels.
+#' - A function.
+#' See [ggplot2::scale_x_continuous()] for more details.
+#' @param na.value The value to be used for `NA` values.
+#' @param position For position scales, The position of the axis.
+#' left or right for y axes, top or bottom for x axes.
 #' @param ... other arguments passed to `continuous_scale()`.
-#' @inheritParams ggplot2::continuous_scale
 #' @keywords internal
-.scale_x_mosaic <- function(breaks = function(x) unique(x),
+.scale_x_mosaic <- function(breaks = unique,
                             minor_breaks = NULL,
-                            labels = function(x) unique(x),
+                            labels = unique,
                             na.value = NA_real_, # nolint: object_name_linter.
                             position = "bottom",
                             ...) {
@@ -175,44 +183,44 @@ is_discrete <- function(x) is.factor(x) || is.character(x) || is.logical(x)
   # Example: compute rectangles from x and y
   result <- data |>
     # Count combinations of X and Y
-    dplyr::count(x, fill, .drop = FALSE) |>
+    dplyr::count(.data$x, .data$fill, .drop = FALSE) |>
     # Compute total for each X group
     dplyr::mutate(
-      .by = x,
-      x_total = sum(n),
-      prop = n / x_total,
-      prop = dplyr::if_else(is.nan(prop), 0, prop)
+      .by = .data$x,
+      x_total = sum(.data$n),
+      prop = .data$n / .data$x_total,
+      prop = dplyr::if_else(is.nan(.data$prop), 0, .data$prop)
     ) |>
-    dplyr::arrange(dplyr::desc(x_total), x, fill) |>
+    dplyr::arrange(dplyr::desc(.data$x_total), .data$x, .data$fill) |>
     # Compute total sample size to turn counts into widths
     dplyr::mutate(
       N_total = dplyr::n(),
-      x_width = x_total / N_total
+      x_width = .data$x_total / .data$N_total
     ) |>
     # Convert counts to x widths
     dplyr::mutate(
-      .by = x,
-      x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), x_width, 0)
+      .by = .data$x,
+      x_width_last = dplyr::if_else(dplyr::row_number() == dplyr::n(), .data$x_width, 0)
     ) |>
     # Compute x-min/x-max for each group
     dplyr::mutate(
-      xmin = cumsum(dplyr::lag(x_width_last, default = 0)),
-      xmax = xmin + x_width
+      xmin = cumsum(dplyr::lag(.data$x_width_last, default = 0)),
+      xmax = .data$xmin + .data$x_width
     ) |>
     # Compute y-min/y-max for stacked proportions
     dplyr::mutate(
-      .by = x,
-      ymin = c(0, head(cumsum(prop), -1)),
-      ymax = cumsum(prop)
+      .by = .data$x,
+      ymin = c(0, utils::head(cumsum(.data$prop), -1)),
+      ymax = cumsum(.data$prop)
     ) |>
     dplyr::mutate(
-      xmin = xmin / max(xmax),
-      xmax = xmax / max(xmax),
-      xmin = dplyr::if_else(n == 0, 0, xmin + 0.005),
-      xmax = dplyr::if_else(n == 0, 0, xmax - 0.005),
-      ymin = dplyr::if_else(n == 0, 0, ymin + 0.005),
-      ymax = dplyr::if_else(n == 0, 0, ymax - 0.005)
+      xmin = .data$xmin / max(.data$xmax),
+      xmax = .data$xmax / max(.data$xmax),
+      xmin = dplyr::if_else(.data$n == 0, 0, .data$xmin + 0.005),
+      xmax = dplyr::if_else(.data$n == 0, 0, .data$xmax - 0.005),
+      ymin = dplyr::if_else(.data$n == 0, 0, .data$ymin + 0.005),
+      ymax = dplyr::if_else(.data$n == 0, 0, .data$ymax - 0.005)
     ) |>
-    dplyr::select(x, fill, xmin, xmax, ymin, ymax, .n = n)
+    dplyr::select(.data$x, .data$fill, .data$xmin, .data$xmax, .data$ymin, .data$ymax, .n = .data$n)
   result
 }
diff --git a/R/teal.modules.general.R b/R/teal.modules.general.R
index 07e7cf03c..d733f4fdc 100644
--- a/R/teal.modules.general.R
+++ b/R/teal.modules.general.R
@@ -7,8 +7,7 @@
 #' @import shiny
 #' @import teal
 #' @import teal.transform
-#' @importFrom dplyr %>%
-#'
+#' @importFrom dplyr %>% .data
 #'
 #' @name teal.modules.general
 #' @keywords internal
diff --git a/R/tm_g_association.R b/R/tm_g_association.R
index 3fbc19d2c..d4bda6fd9 100644
--- a/R/tm_g_association.R
+++ b/R/tm_g_association.R
@@ -511,7 +511,7 @@ srv_tm_g_association <- function(id,
             env = list(
               plot_calls = do.call(
                 "call",
-                c(list("list", ref_call), var_calls),
+                c(list("list", ref_call), unname(var_calls)),
                 quote = TRUE
               )
             )
diff --git a/man/dot-scale_x_mosaic.Rd b/man/dot-scale_x_mosaic.Rd
index 6e1c17c5c..610143b36 100644
--- a/man/dot-scale_x_mosaic.Rd
+++ b/man/dot-scale_x_mosaic.Rd
@@ -5,61 +5,30 @@
 \title{Determining scales for mosaics}
 \usage{
 .scale_x_mosaic(
-  breaks = function(x) unique(x),
+  breaks = unique,
   minor_breaks = NULL,
-  labels = function(x) unique(x),
+  labels = unique,
   na.value = NA_real_,
   position = "bottom",
   ...
 )
 }
 \arguments{
-\item{breaks}{One of:
+\item{breaks, labels, minor_breaks}{One of:
 \itemize{
-\item \code{NULL} for no breaks
-\item \code{waiver()} for the default breaks computed by the
-\link[scales:new_transform]{transformation object}
-\item A numeric vector of positions
-\item A function that takes the limits as input and returns breaks
-as output (e.g., a function returned by \code{\link[scales:breaks_extended]{scales::extended_breaks()}}).
-Note that for position scales, limits are provided after scale expansion.
-Also accepts rlang \link[rlang:as_function]{lambda} function notation.
+\item \code{NULL} for no breaks / labels.
+\item \code{\link[ggplot2:waiver]{ggplot2::waiver()}} for the default breaks / labels computed by the scale.
+\item A numeric / character vector giving the positions of the breaks / labels.
+\item A function.
+See \code{\link[ggplot2:scale_continuous]{ggplot2::scale_x_continuous()}} for more details.
 }}
 
-\item{minor_breaks}{One of:
-\itemize{
-\item \code{NULL} for no minor breaks
-\item \code{waiver()} for the default breaks (none for discrete, one minor break
-between each major break for continuous)
-\item A numeric vector of positions
-\item A function that given the limits returns a vector of minor breaks. Also
-accepts rlang \link[rlang:as_function]{lambda} function notation. When
-the function has two arguments, it will be given the limits and major
-break positions.
-}}
-
-\item{labels}{One of the options below. Please note that when \code{labels} is a
-vector, it is highly recommended to also set the \code{breaks} argument as a
-vector to protect against unintended mismatches.
-\itemize{
-\item \code{NULL} for no labels
-\item \code{waiver()} for the default labels computed by the
-transformation object
-\item A character vector giving labels (must be same length as \code{breaks})
-\item An expression vector (must be the same length as breaks). See ?plotmath for details.
-\item A function that takes the breaks as input and returns labels
-as output. Also accepts rlang \link[rlang:as_function]{lambda} function
-notation.
-}}
-
-\item{na.value}{Missing values will be replaced with this value.}
+\item{na.value}{The value to be used for \code{NA} values.}
 
 \item{position}{For position scales, The position of the axis.
-\code{left} or \code{right} for y axes, \code{top} or \code{bottom} for x axes.}
+left or right for y axes, top or bottom for x axes.}
 
 \item{...}{other arguments passed to \code{continuous_scale()}.}
-
-\item{name}{set to pseudo waiver function \code{product_names} by default.}
 }
 \description{
 Determining scales for mosaics