From 4e945a756c207d146e5c5c4c53a0fd14231c9924 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, 27 Feb 2024 11:39:34 +0100
Subject: [PATCH 01/19] feat: ordering and add missing assertions

---
 R/tm_a_pca.R                | 46 ++++++++++++---------
 R/tm_data_table.R           | 10 ++++-
 R/tm_file_viewer.R          | 18 ++++-----
 R/tm_front_page.R           |  6 ++-
 R/tm_g_association.R        | 13 ++++++
 R/tm_g_bivariate.R          | 79 +++++++++++++++++++++----------------
 R/tm_g_distribution.R       | 36 +++++++++++++----
 R/tm_g_response.R           | 23 +++++++----
 R/tm_g_scatterplot.R        | 45 ++++++++++++---------
 R/tm_g_scatterplotmatrix.R  | 12 ++++++
 R/tm_missing_data.R         | 16 +++++++-
 R/tm_outliers.R             | 21 +++++++++-
 R/tm_t_crosstable.R         | 15 +++++--
 R/tm_variable_browser.R     |  8 ++++
 R/utils.R                   | 12 ++++++
 tests/testthat/test-utils.R | 22 +++++++++++
 16 files changed, 277 insertions(+), 105 deletions(-)
 create mode 100644 tests/testthat/test-utils.R

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index f5cf694ff..4e341bb41 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -110,14 +110,38 @@ tm_a_pca <- function(label = "Principal Component Analysis",
                      pre_output = NULL,
                      post_output = NULL) {
   logger::log_info("Initializing tm_a_pca")
+
+  # Normalizing data types
   if (inherits(dat, "data_extract_spec")) dat <- list(dat)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_list(dat, types = "data_extract_spec")
+
+  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+  )
+
   ggtheme <- match.arg(ggtheme)
+
+  plot_choices <- c("Elbow plot", "Circle plot", "Biplot", "Eigenvector plot")
+  checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
+  checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
+
   checkmate::assert_flag(rotate_xaxis_labels)
 
+  if (length(font_size) == 1) {
+    checkmate::assert_numeric(font_size, any.missing = FALSE, finite = TRUE, lower = 8, upper = 20)
+  } else {
+    checkmate::assert_numeric(font_size, len = 3, any.missing = FALSE, finite = TRUE, lower = 8, upper = 20)
+    checkmate::assert_numeric(font_size[1], lower = font_size[2], upper = font_size[3], .var.name = "font_size")
+  }
+
   if (length(alpha) == 1) {
     checkmate::assert_numeric(alpha, any.missing = FALSE, finite = TRUE, lower = 0, upper = 1)
   } else {
@@ -132,25 +156,11 @@ tm_a_pca <- function(label = "Principal Component Analysis",
     checkmate::assert_numeric(size[1], lower = size[2], upper = size[3], .var.name = "size")
   }
 
-  if (length(font_size) == 1) {
-    checkmate::assert_numeric(font_size, any.missing = FALSE, finite = TRUE, lower = 8, upper = 20)
-  } else {
-    checkmate::assert_numeric(font_size, len = 3, any.missing = FALSE, finite = TRUE, lower = 8, upper = 20)
-    checkmate::assert_numeric(font_size[1], lower = font_size[2], upper = font_size[3], .var.name = "font_size")
-  }
-
-  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
-  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
-  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
-  checkmate::assert_numeric(
-    plot_width[1],
-    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
-  )
-
-  plot_choices <- c("Elbow plot", "Circle plot", "Biplot", "Eigenvector plot")
-  checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
-  checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
 
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(dat = dat)
diff --git a/R/tm_data_table.R b/R/tm_data_table.R
index 9d6cd866c..3a5f47180 100644
--- a/R/tm_data_table.R
+++ b/R/tm_data_table.R
@@ -89,7 +89,10 @@ tm_data_table <- function(label = "Data Table",
                           pre_output = NULL,
                           post_output = NULL) {
   logger::log_info("Initializing tm_data_table")
+
+  # Start of assertions
   checkmate::assert_string(label)
+
   checkmate::assert_list(variables_selected, min.len = 0, types = "character", names = "named")
   if (length(variables_selected) > 0) {
     lapply(seq_along(variables_selected), function(i) {
@@ -99,14 +102,17 @@ tm_data_table <- function(label = "Data Table",
       }
     })
   }
+
   checkmate::assert_character(datasets_selected, min.len = 0, min.chars = 1)
-  checkmate::assert_list(dt_options, names = "named")
   checkmate::assert(
     checkmate::check_list(dt_args, len = 0),
     checkmate::check_subset(names(dt_args), choices = names(formals(DT::datatable)))
   )
-
+  checkmate::assert_list(dt_options, names = "named")
   checkmate::assert_flag(server_rendering)
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
 
   module(
     label,
diff --git a/R/tm_file_viewer.R b/R/tm_file_viewer.R
index 8be167330..e46d6154f 100644
--- a/R/tm_file_viewer.R
+++ b/R/tm_file_viewer.R
@@ -39,25 +39,24 @@
 tm_file_viewer <- function(label = "File Viewer Module",
                            input_path = list("Current Working Directory" = ".")) {
   logger::log_info("Initializing tm_file_viewer")
-  if (length(label) == 0 || identical(label, "")) {
-    label <- " "
-  }
-  if (length(input_path) == 0 || identical(input_path, "")) {
-    input_path <- list()
-  }
 
+  # Normalize the parameters
+  if (length(label) == 0 || identical(label, "")) label <- " "
+  if (length(input_path) == 0 || identical(input_path, "")) input_path <- list()
+
+  # Start of assertions
   checkmate::assert_string(label)
+
   checkmate::assert(
     checkmate::check_list(input_path, types = "character", min.len = 0),
     checkmate::check_character(input_path, min.len = 1)
   )
-
   if (length(input_path) > 0) {
     valid_url <- function(url_input, timeout = 2) {
       con <- try(url(url_input), silent = TRUE)
       check <- suppressWarnings(try(open.connection(con, open = "rt", timeout = timeout), silent = TRUE)[1])
       try(close.connection(con), silent = TRUE)
-      ifelse(is.null(check), TRUE, FALSE)
+      is.null(check)
     }
     idx <- vapply(input_path, function(x) file.exists(x) || valid_url(x), logical(1))
 
@@ -75,8 +74,9 @@ tm_file_viewer <- function(label = "File Viewer Module",
       "No file or url paths were provided."
     )
   }
+  # End of assertions
 
-
+  # Send ui args
   args <- as.list(environment())
 
   module(
diff --git a/R/tm_front_page.R b/R/tm_front_page.R
index c10ef2bd0..54ada504e 100644
--- a/R/tm_front_page.R
+++ b/R/tm_front_page.R
@@ -67,14 +67,18 @@ tm_front_page <- function(label = "Front page",
                           additional_tags = tagList(),
                           footnotes = character(0),
                           show_metadata = FALSE) {
+  logger::log_info("Initializing tm_front_page")
+
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_character(header_text, min.len = 0, any.missing = FALSE)
   checkmate::assert_list(tables, types = "data.frame", names = "named", any.missing = FALSE)
   checkmate::assert_multi_class(additional_tags, classes = c("shiny.tag.list", "html"))
   checkmate::assert_character(footnotes, min.len = 0, any.missing = FALSE)
   checkmate::assert_flag(show_metadata)
+  # End of assertions
 
-  logger::log_info("Initializing tm_front_page")
+  # Send ui args
   args <- as.list(environment())
 
   module(
diff --git a/R/tm_g_association.R b/R/tm_g_association.R
index 1ee28d45a..8768ec8ed 100644
--- a/R/tm_g_association.R
+++ b/R/tm_g_association.R
@@ -131,17 +131,23 @@ tm_g_association <- function(label = "Association",
                              post_output = NULL,
                              ggplot2_args = teal.widgets::ggplot2_args()) {
   logger::log_info("Initializing tm_g_association")
+
+  # Normalize the parameters
   if (inherits(ref, "data_extract_spec")) ref <- list(ref)
   if (inherits(vars, "data_extract_spec")) vars <- list(vars)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
+  # Start of assertions
   checkmate::assert_string(label)
+
   checkmate::assert_list(ref, types = "data_extract_spec")
   if (!all(vapply(ref, function(x) !x$select$multiple, logical(1)))) {
     stop("'ref' should not allow multiple selection")
   }
+
   checkmate::assert_list(vars, types = "data_extract_spec")
   checkmate::assert_flag(show_association)
+
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
@@ -149,12 +155,19 @@ tm_g_association <- function(label = "Association",
     plot_width[1],
     lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
   )
+
   distribution_theme <- match.arg(distribution_theme)
   association_theme <- match.arg(association_theme)
+
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+
   plot_choices <- c("Bivariate1", "Bivariate2")
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
+  # End of assertions
 
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 99fa167f4..1d2d7d62a 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -192,6 +192,8 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
                            pre_output = NULL,
                            post_output = NULL) {
   logger::log_info("Initializing tm_g_bivariate")
+
+  # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)
   if (inherits(row_facet, "data_extract_spec")) row_facet <- list(row_facet)
@@ -200,52 +202,37 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   if (inherits(fill, "data_extract_spec")) fill <- list(fill)
   if (inherits(size, "data_extract_spec")) size <- list(size)
 
+  # Start of assertions
+  checkmate::assert_string(label)
+
   checkmate::assert_list(x, types = "data_extract_spec")
-  if (!all(vapply(x, function(x) !x$select$multiple, logical(1)))) {
-    stop("'x' should not allow multiple selection")
-  }
+  assert_single_selection(x)
+
   checkmate::assert_list(y, types = "data_extract_spec")
-  if (!all(vapply(y, function(x) !x$select$multiple, logical(1)))) {
-    stop("'y' should not allow multiple selection")
-  }
+  assert_single_selection(y)
+
   checkmate::assert_list(row_facet, types = "data_extract_spec", null.ok = TRUE)
-  if (!all(vapply(row_facet, function(x) !x$select$multiple, logical(1)))) {
-    stop("'row_facet' should not allow multiple selection")
-  }
+  assert_single_selection(row_facet)
+
   checkmate::assert_list(col_facet, types = "data_extract_spec", null.ok = TRUE)
-  if (!all(vapply(col_facet, function(x) !x$select$multiple, logical(1)))) {
-    stop("'col_facet' should not allow multiple selection")
-  }
+  assert_single_selection(col_facet)
+
   checkmate::assert_list(color, types = "data_extract_spec", null.ok = TRUE)
-  if (!all(vapply(color, function(x) !x$select$multiple, logical(1)))) {
-    stop("'color' should not allow multiple selection")
-  }
+  assert_single_selection(color)
+
   checkmate::assert_list(fill, types = "data_extract_spec", null.ok = TRUE)
-  if (!all(vapply(fill, function(x) !x$select$multiple, logical(1)))) {
-    stop("'fill' should not allow multiple selection")
-  }
+  assert_single_selection(fill)
+
   checkmate::assert_list(size, types = "data_extract_spec", null.ok = TRUE)
-  if (!all(vapply(size, function(x) !x$select$multiple, logical(1)))) {
-    stop("'size' should not allow multiple selection")
-  }
+  assert_single_selection(size)
 
-  ggtheme <- match.arg(ggtheme)
-  checkmate::assert_string(label)
-  checkmate::assert_flag(use_density)
-  checkmate::assert_flag(color_settings)
-  checkmate::assert_flag(free_x_scales)
-  checkmate::assert_flag(free_y_scales)
+  checkmate::assert_flag(facet)
   checkmate::assert_flag(rotate_xaxis_labels)
   checkmate::assert_flag(swap_axes)
-  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
-  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
-  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
-  checkmate::assert_numeric(
-    plot_width[1],
-    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
-  )
-  checkmate::assert_class(ggplot2_args, "ggplot2_args")
+  checkmate::assert_flag(use_density)
 
+  # Determines color, fill & size if they are not explicitly set
+  checkmate::assert_flag(color_settings)
   if (color_settings) {
     if (is.null(color)) {
       color <- x
@@ -265,6 +252,28 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
     }
   }
 
+  checkmate::assert_flag(free_x_scales)
+  checkmate::assert_flag(free_y_scales)
+
+  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+  )
+
+  checkmate::assert_flag(rotate_xaxis_labels)
+  checkmate::assert_flag(swap_axes)
+
+  ggtheme <- match.arg(ggtheme)
+  checkmate::assert_class(ggplot2_args, "ggplot2_args")
+
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
+
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R
index a60d6465f..3cb0345f9 100644
--- a/R/tm_g_distribution.R
+++ b/R/tm_g_distribution.R
@@ -119,6 +119,7 @@ tm_g_distribution <- function(label = "Distribution Module",
                               post_output = NULL) {
   logger::log_info("Initializing tm_g_distribution")
 
+  # Requires Suggested packages
   extra_packages <- c("ggpmisc", "ggpp", "goftest", "MASS", "broom")
   missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
   if (length(missing_packages) > 0L) {
@@ -128,28 +129,47 @@ tm_g_distribution <- function(label = "Distribution Module",
     ))
   }
 
+  # Normalize the parameters
   if (inherits(dist_var, "data_extract_spec")) dist_var <- list(dist_var)
   if (inherits(strata_var, "data_extract_spec")) strata_var <- list(strata_var)
   if (inherits(group_var, "data_extract_spec")) group_var <- list(group_var)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
-  ggtheme <- match.arg(ggtheme)
-  if (length(bins) == 1) {
-    checkmate::assert_numeric(bins, any.missing = FALSE, lower = 1)
-  } else {
-    checkmate::assert_numeric(bins, len = 3, any.missing = FALSE, lower = 1)
-    checkmate::assert_numeric(bins[1], lower = bins[2], upper = bins[3], .var.name = "bins")
-  }
+  # Start of assertions
   checkmate::assert_string(label)
+
   checkmate::assert_list(dist_var, "data_extract_spec")
-  checkmate::assert_false(dist_var[[1]]$select$multiple)
+  checkmate::assert_false(dist_var[[1L]]$select$multiple)
+
   checkmate::assert_list(strata_var, types = "data_extract_spec", null.ok = TRUE)
   checkmate::assert_list(group_var, types = "data_extract_spec", null.ok = TRUE)
   checkmate::assert_flag(freq)
+  ggtheme <- match.arg(ggtheme)
+
   plot_choices <- c("Histogram", "QQplot")
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
 
+  if (length(bins) == 1) {
+    checkmate::assert_numeric(bins, any.missing = FALSE, lower = 1)
+  } else {
+    checkmate::assert_numeric(bins, len = 3, any.missing = FALSE, lower = 1)
+    checkmate::assert_numeric(bins[1], lower = bins[2], upper = bins[3], .var.name = "bins")
+  }
+
+  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+  )
+
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
+
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_response.R b/R/tm_g_response.R
index 52c221e7e..55dcebcd5 100644
--- a/R/tm_g_response.R
+++ b/R/tm_g_response.R
@@ -152,32 +152,35 @@ tm_g_response <- function(label = "Response Plot",
                           pre_output = NULL,
                           post_output = NULL) {
   logger::log_info("Initializing tm_g_response")
+
+  # Normalize the parameters
   if (inherits(response, "data_extract_spec")) response <- list(response)
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(row_facet, "data_extract_spec")) row_facet <- list(row_facet)
   if (inherits(col_facet, "data_extract_spec")) col_facet <- list(col_facet)
+
+  # Start of assertions
   checkmate::assert_string(label)
-  ggtheme <- match.arg(ggtheme)
+
   checkmate::assert_list(response, types = "data_extract_spec")
   if (!all(vapply(response, function(x) !("" %in% x$select$choices), logical(1)))) {
     stop("'response' should not allow empty values")
   }
-  if (!all(vapply(response, function(x) !x$select$multiple, logical(1)))) {
-    stop("'response' should not allow multiple selection")
-  }
+  assert_single_selection(response)
+
   checkmate::assert_list(x, types = "data_extract_spec")
   if (!all(vapply(x, function(x) !("" %in% x$select$choices), logical(1)))) {
     stop("'x' should not allow empty values")
   }
-  if (!all(vapply(x, function(x) !x$select$multiple, logical(1)))) {
-    stop("'x' should not allow multiple selection")
-  }
+  assert_single_selection(x)
+
   checkmate::assert_list(row_facet, types = "data_extract_spec", null.ok = TRUE)
   checkmate::assert_list(col_facet, types = "data_extract_spec", null.ok = TRUE)
   checkmate::assert_flag(coord_flip)
   checkmate::assert_flag(count_labels)
   checkmate::assert_flag(rotate_xaxis_labels)
   checkmate::assert_flag(freq)
+
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
@@ -186,8 +189,14 @@ tm_g_response <- function(label = "Response Plot",
     lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
   )
 
+  ggtheme <- match.arg(ggtheme)
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
 
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
+
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R
index 2bed23a61..0e96eab2c 100644
--- a/R/tm_g_scatterplot.R
+++ b/R/tm_g_scatterplot.R
@@ -233,6 +233,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
                              ggplot2_args = teal.widgets::ggplot2_args()) {
   logger::log_info("Initializing tm_g_scatterplot")
 
+  # Requires Suggested packages
   extra_packages <- c("ggpmisc", "ggExtra", "colourpicker")
   missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
   if (length(missing_packages) > 0L) {
@@ -242,6 +243,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
     ))
   }
 
+  # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)
   if (inherits(color_by, "data_extract_spec")) color_by <- list(color_by)
@@ -250,26 +252,27 @@ tm_g_scatterplot <- function(label = "Scatterplot",
   if (inherits(col_facet, "data_extract_spec")) col_facet <- list(col_facet)
   if (is.double(max_deg)) max_deg <- as.integer(max_deg)
 
-  ggtheme <- match.arg(ggtheme)
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_list(x, types = "data_extract_spec")
   checkmate::assert_list(y, types = "data_extract_spec")
   checkmate::assert_list(color_by, types = "data_extract_spec", null.ok = TRUE)
   checkmate::assert_list(size_by, types = "data_extract_spec", null.ok = TRUE)
+
   checkmate::assert_list(row_facet, types = "data_extract_spec", null.ok = TRUE)
+  assert_single_selection(row_facet)
+
   checkmate::assert_list(col_facet, types = "data_extract_spec", null.ok = TRUE)
-  checkmate::assert_list(row_facet, types = "data_extract_spec", null.ok = TRUE)
-  if (!all(vapply(row_facet, function(x) !x$select$multiple, logical(1)))) {
-    stop("'row_facet' should not allow multiple selection")
-  }
-  if (!all(vapply(col_facet, function(x) !x$select$multiple, logical(1)))) {
-    stop("'col_facet' should not allow multiple selection")
-  }
-  checkmate::assert_character(shape)
+  assert_single_selection(col_facet)
+
+  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+  )
 
-  checkmate::assert_int(max_deg, lower = 1L)
-  checkmate::assert_scalar(table_dec)
-  checkmate::assert_flag(rotate_xaxis_labels)
   if (length(alpha) == 1) {
     checkmate::assert_numeric(alpha, any.missing = FALSE, finite = TRUE)
   } else {
@@ -277,6 +280,8 @@ tm_g_scatterplot <- function(label = "Scatterplot",
     checkmate::assert_numeric(alpha[1], lower = alpha[2], upper = alpha[3], .var.name = "alpha")
   }
 
+  checkmate::assert_character(shape)
+
   if (length(size) == 1) {
     checkmate::assert_numeric(size, any.missing = FALSE, finite = TRUE)
   } else {
@@ -284,16 +289,18 @@ tm_g_scatterplot <- function(label = "Scatterplot",
     checkmate::assert_numeric(size[1], lower = size[2], upper = size[3], .var.name = "size")
   }
 
-  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
-  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
-  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
-  checkmate::assert_numeric(
-    plot_width[1],
-    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
-  )
+  checkmate::assert_int(max_deg, lower = 1L)
+  checkmate::assert_flag(rotate_xaxis_labels)
+  ggtheme <- match.arg(ggtheme)
 
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+
+  checkmate::assert_scalar(table_dec)
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
+  # End of assertions
 
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R
index a334686cd..01a19fda9 100644
--- a/R/tm_g_scatterplotmatrix.R
+++ b/R/tm_g_scatterplotmatrix.R
@@ -161,13 +161,19 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
                                    pre_output = NULL,
                                    post_output = NULL) {
   logger::log_info("Initializing tm_g_scatterplotmatrix")
+
+  # Requires Suggested packages
   if (!requireNamespace("lattice", quietly = TRUE)) {
     stop("Cannot load lattice - please install the package or restart your session.")
   }
+
+  # Normalize the parameters
   if (inherits(variables, "data_extract_spec")) variables <- list(variables)
 
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_list(variables, types = "data_extract_spec")
+
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
@@ -176,7 +182,13 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
     lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
   )
 
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
+
+  # Send ui args
   args <- as.list(environment())
+
   module(
     label = label,
     server = srv_g_scatterplotmatrix,
diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R
index ce4240ded..8c2235583 100644
--- a/R/tm_missing_data.R
+++ b/R/tm_missing_data.R
@@ -87,17 +87,22 @@ tm_missing_data <- function(label = "Missing data",
                             ),
                             pre_output = NULL,
                             post_output = NULL) {
+  logger::log_info("Initializing tm_missing_data")
+
+  # Requires Suggested packages
   if (!requireNamespace("gridExtra", quietly = TRUE)) {
     stop("Cannot load gridExtra - please install the package or restart your session.")
   }
   if (!requireNamespace("rlang", quietly = TRUE)) {
     stop("Cannot load rlang - please install the package or restart your session.")
   }
-  logger::log_info("Initializing tm_missing_data")
+
+  # Normalize the parameters
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
+  # Start of assertions
   checkmate::assert_string(label)
-  checkmate::assert_character(parent_dataname, min.len = 0, max.len = 1)
+
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
@@ -105,11 +110,18 @@ tm_missing_data <- function(label = "Missing data",
     plot_width[1],
     lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
   )
+
+  checkmate::assert_character(parent_dataname, min.len = 0, max.len = 1)
   ggtheme <- match.arg(ggtheme)
+
   plot_choices <- c("Summary Obs", "Summary Patients", "Combinations Main", "Combinations Hist", "By Subject")
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
 
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
+
   module(
     label,
     server = srv_page_missing_data,
diff --git a/R/tm_outliers.R b/R/tm_outliers.R
index 34cccf2b2..bbbf95797 100644
--- a/R/tm_outliers.R
+++ b/R/tm_outliers.R
@@ -130,13 +130,16 @@ tm_outliers <- function(label = "Outliers Module",
                         pre_output = NULL,
                         post_output = NULL) {
   logger::log_info("Initializing tm_outliers")
+
+  # Normalize the parameters
   if (inherits(outlier_var, "data_extract_spec")) outlier_var <- list(outlier_var)
   if (inherits(categorical_var, "data_extract_spec")) categorical_var <- list(categorical_var)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
-  ggtheme <- match.arg(ggtheme)
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_list(outlier_var, types = "data_extract_spec")
+
   checkmate::assert_list(categorical_var, types = "data_extract_spec", null.ok = TRUE)
   if (is.list(categorical_var)) {
     lapply(categorical_var, function(x) {
@@ -145,10 +148,26 @@ tm_outliers <- function(label = "Outliers Module",
       }
     })
   }
+
+  ggtheme <- match.arg(ggtheme)
+
   plot_choices <- c("Boxplot", "Density Plot", "Cumulative Distribution Plot")
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
 
+  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+  )
+
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  # End of assertions
+
+  # Send ui args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_t_crosstable.R b/R/tm_t_crosstable.R
index 8fdc090e6..a41ba1133 100644
--- a/R/tm_t_crosstable.R
+++ b/R/tm_t_crosstable.R
@@ -139,22 +139,31 @@ tm_t_crosstable <- function(label = "Cross Table",
                             post_output = NULL,
                             basic_table_args = teal.widgets::basic_table_args()) {
   logger::log_info("Initializing tm_t_crosstable")
+
+  # Requires Suggested packages
   if (!requireNamespace("rtables", quietly = TRUE)) {
     stop("Cannot load rtables - please install the package or restart your session.")
   }
+
+  # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)
 
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_list(x, types = "data_extract_spec")
+
   checkmate::assert_list(y, types = "data_extract_spec")
-  if (any(vapply(y, function(x) x$select$multiple, logical(1)))) {
-    stop("'y' should not allow multiple selection")
-  }
+  assert_single_selection(y)
+
   checkmate::assert_flag(show_percentage)
   checkmate::assert_flag(show_total)
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_class(basic_table_args, classes = "basic_table_args")
+  # End of assertions
 
+  # Send ui args
   ui_args <- as.list(environment())
 
   server_args <- list(
diff --git a/R/tm_variable_browser.R b/R/tm_variable_browser.R
index bc8bd03d7..930c37005 100644
--- a/R/tm_variable_browser.R
+++ b/R/tm_variable_browser.R
@@ -75,6 +75,8 @@ tm_variable_browser <- function(label = "Variable Browser",
                                 post_output = NULL,
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
   logger::log_info("Initializing tm_variable_browser")
+
+  # Requires Suggested packages
   if (!requireNamespace("sparkline", quietly = TRUE)) {
     stop("Cannot load sparkline - please install the package or restart your session.")
   }
@@ -84,10 +86,16 @@ tm_variable_browser <- function(label = "Variable Browser",
   if (!requireNamespace("jsonlite", quietly = TRUE)) {
     stop("Cannot load jsonlite - please install the package or restart your session.")
   }
+
+  # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_character(datasets_selected)
   checkmate::assert_character(parent_dataname, min.len = 0, max.len = 1)
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
+  # End of assertions
+
   datasets_selected <- unique(datasets_selected)
 
   module(
diff --git a/R/utils.R b/R/utils.R
index cdcb4ece7..b4c94da6f 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -285,3 +285,15 @@ is_tab_active_js <- function(id, name) {
     id, name
   )
 }
+
+#' Assert single selection on `data_extract_spec` object
+#' Helper to reduce code in assertions
+#' @noRd
+#'
+assert_single_selection <- function(x,
+                                    .var.name = checkmate::vname(x)) { # nolint: object_name.
+  if (any(vapply(x, function(.x) .x$select$multiple, logical(1)))) {
+    stop("'", .var.name, "' should not allow multiple selection")
+  }
+  invisible(TRUE)
+}
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
new file mode 100644
index 000000000..fe402f4ee
--- /dev/null
+++ b/tests/testthat/test-utils.R
@@ -0,0 +1,22 @@
+testthat::test_that("assert_single_selection will pass if all elements have multiple choices disabled", {
+  mock_spec <- list(select = list(multiple = FALSE))
+
+  testthat::expect_true(assert_single_selection(list(mock_spec)))
+  testthat::expect_true(assert_single_selection(list(mock_spec, mock_spec)))
+})
+
+testthat::test_that("assert_single_selection fails when multiple selection is selected in any of the specs", {
+  mock_spec <- list(select = list(multiple = TRUE))
+  mock_spec2 <- list(select = list(multiple = FALSE))
+
+  x <- list(mock_spec)
+
+  testthat::expect_error(
+    assert_single_selection(x),
+    "'x' should not allow multiple selection"
+  )
+  testthat::expect_error(
+    assert_single_selection(list(mock_spec2, mock_spec), .var.name = "x"),
+    "'x' should not allow multiple selection"
+  )
+})

From cdf949d2a1ddffa209f6c6c616a5aa870d1e55af 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, 28 Feb 2024 13:25:27 +0100
Subject: [PATCH 02/19] chore: replace "Send ui args" with "Make UI args"

---
 R/tm_a_pca.R               | 2 +-
 R/tm_file_viewer.R         | 2 +-
 R/tm_front_page.R          | 2 +-
 R/tm_g_association.R       | 2 +-
 R/tm_g_bivariate.R         | 2 +-
 R/tm_g_distribution.R      | 2 +-
 R/tm_g_response.R          | 2 +-
 R/tm_g_scatterplot.R       | 2 +-
 R/tm_g_scatterplotmatrix.R | 2 +-
 R/tm_outliers.R            | 2 +-
 R/tm_t_crosstable.R        | 2 +-
 11 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 4e341bb41..134ea6556 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -160,7 +160,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(dat = dat)
diff --git a/R/tm_file_viewer.R b/R/tm_file_viewer.R
index e46d6154f..bf16a287c 100644
--- a/R/tm_file_viewer.R
+++ b/R/tm_file_viewer.R
@@ -76,7 +76,7 @@ tm_file_viewer <- function(label = "File Viewer Module",
   }
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   module(
diff --git a/R/tm_front_page.R b/R/tm_front_page.R
index 54ada504e..f8bf83d0f 100644
--- a/R/tm_front_page.R
+++ b/R/tm_front_page.R
@@ -78,7 +78,7 @@ tm_front_page <- function(label = "Front page",
   checkmate::assert_flag(show_metadata)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   module(
diff --git a/R/tm_g_association.R b/R/tm_g_association.R
index 8768ec8ed..009654212 100644
--- a/R/tm_g_association.R
+++ b/R/tm_g_association.R
@@ -167,7 +167,7 @@ tm_g_association <- function(label = "Association",
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 1d2d7d62a..6aa7d6b22 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -273,7 +273,7 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R
index 3cb0345f9..624de3cd9 100644
--- a/R/tm_g_distribution.R
+++ b/R/tm_g_distribution.R
@@ -169,7 +169,7 @@ tm_g_distribution <- function(label = "Distribution Module",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_response.R b/R/tm_g_response.R
index 55dcebcd5..64640640a 100644
--- a/R/tm_g_response.R
+++ b/R/tm_g_response.R
@@ -196,7 +196,7 @@ tm_g_response <- function(label = "Response Plot",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R
index 0e96eab2c..f739453ca 100644
--- a/R/tm_g_scatterplot.R
+++ b/R/tm_g_scatterplot.R
@@ -300,7 +300,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R
index 01a19fda9..3cbf05e4f 100644
--- a/R/tm_g_scatterplotmatrix.R
+++ b/R/tm_g_scatterplotmatrix.R
@@ -186,7 +186,7 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   module(
diff --git a/R/tm_outliers.R b/R/tm_outliers.R
index bbbf95797..6ca76f986 100644
--- a/R/tm_outliers.R
+++ b/R/tm_outliers.R
@@ -167,7 +167,7 @@ tm_outliers <- function(label = "Outliers Module",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   args <- as.list(environment())
 
   data_extract_list <- list(
diff --git a/R/tm_t_crosstable.R b/R/tm_t_crosstable.R
index a41ba1133..f7ad03136 100644
--- a/R/tm_t_crosstable.R
+++ b/R/tm_t_crosstable.R
@@ -163,7 +163,7 @@ tm_t_crosstable <- function(label = "Cross Table",
   checkmate::assert_class(basic_table_args, classes = "basic_table_args")
   # End of assertions
 
-  # Send ui args
+  # Make UI args
   ui_args <- as.list(environment())
 
   server_args <- list(

From 928eca25ac5a0b28019ef06c866d6b5fbd92c6ba 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, 28 Feb 2024 13:26:05 +0100
Subject: [PATCH 03/19] feat: reorder assertions and add necessary

---
 R/tm_a_regression.R | 47 +++++++++++++++++++++++++++++++++------------
 1 file changed, 35 insertions(+), 12 deletions(-)

diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R
index e3dd0bfd3..6e0dbc1fa 100644
--- a/R/tm_a_regression.R
+++ b/R/tm_a_regression.R
@@ -143,33 +143,56 @@ tm_a_regression <- function(label = "Regression Analysis",
                             default_plot_type = 1,
                             default_outlier_label = "USUBJID") {
   logger::log_info("Initializing tm_a_regression")
+
+  # Normalizing data types
   if (inherits(regressor, "data_extract_spec")) regressor <- list(regressor)
   if (inherits(response, "data_extract_spec")) response <- list(response)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
+  # Start of assertions
   checkmate::assert_string(label)
+  checkmate::assert_list(regressor, types = "data_extract_spec")
   checkmate::assert_list(response, types = "data_extract_spec")
-  if (!all(vapply(response, function(x) !(x$select$multiple), logical(1)))) {
-    stop("'response' should not allow multiple selection")
+  assert_single_selection(response)
+
+  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
+  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
+  checkmate::assert_numeric(
+    plot_width[1],
+    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+  )
+
+  if (length(alpha) == 1) {
+    checkmate::assert_numeric(alpha, any.missing = FALSE, finite = TRUE)
+  } else {
+    checkmate::assert_numeric(alpha, len = 3, any.missing = FALSE, finite = TRUE)
+    checkmate::assert_numeric(alpha[1], lower = alpha[2], upper = alpha[3], .var.name = "alpha")
   }
-  checkmate::assert_list(regressor, types = "data_extract_spec")
+
+  if (length(size) == 1) {
+    checkmate::assert_numeric(size, any.missing = FALSE, finite = TRUE)
+  } else {
+    checkmate::assert_numeric(size, len = 3, any.missing = FALSE, finite = TRUE)
+    checkmate::assert_numeric(size[1], lower = size[2], upper = size[3], .var.name = "size")
+  }
+
   ggtheme <- match.arg(ggtheme)
-  checkmate::assert_string(default_outlier_label)
+
   plot_choices <- c(
     "Response vs Regressor", "Residuals vs Fitted", "Normal Q-Q", "Scale-Location",
     "Cook's distance", "Residuals vs Leverage", "Cook's dist vs Leverage"
   )
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
-  checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
-  checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
-  checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
-  checkmate::assert_numeric(
-    plot_width[1],
-    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
-  )
 
-  # Send ui args
+  checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
+  checkmate::assert_choice(default_plot_type, seq.int(1, length(plot_choices)))
+  checkmate::assert_string(default_outlier_label)
+  # End of assertions
+
+  # Make UI args
   args <- as.list(environment())
   args[["plot_choices"]] <- plot_choices
   data_extract_list <- list(

From 48c96c3e80e18062c9aeda48714d53b01fe1b5d5 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, 28 Feb 2024 13:28:49 +0100
Subject: [PATCH 04/19] fix: remove duplicated assertion

---
 R/tm_g_bivariate.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
index 6aa7d6b22..5e72316b2 100644
--- a/R/tm_g_bivariate.R
+++ b/R/tm_g_bivariate.R
@@ -217,6 +217,8 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   checkmate::assert_list(col_facet, types = "data_extract_spec", null.ok = TRUE)
   assert_single_selection(col_facet)
 
+  checkmate::assert_flag(facet)
+
   checkmate::assert_list(color, types = "data_extract_spec", null.ok = TRUE)
   assert_single_selection(color)
 
@@ -226,9 +228,6 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   checkmate::assert_list(size, types = "data_extract_spec", null.ok = TRUE)
   assert_single_selection(size)
 
-  checkmate::assert_flag(facet)
-  checkmate::assert_flag(rotate_xaxis_labels)
-  checkmate::assert_flag(swap_axes)
   checkmate::assert_flag(use_density)
 
   # Determines color, fill & size if they are not explicitly set

From b43aecf06a6c19cce5b20f910fcc8d58a0628536 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, 28 Feb 2024 13:58:13 +0100
Subject: [PATCH 05/19] tests: expand tests of assert_single_selection to
 include public API

---
 tests/testthat/test-utils.R | 62 ++++++++++++++++++++++++++++++++++---
 1 file changed, 58 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index fe402f4ee..4e29bf409 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -1,13 +1,22 @@
-testthat::test_that("assert_single_selection will pass if all elements have multiple choices disabled", {
-  mock_spec <- list(select = list(multiple = FALSE))
+testthat::test_that("assert_single_selection succeeds if all elements have multiple choices disabled", {
+  mock_spec <- data_extract_spec(
+    dataname = "MOCK_DATASET",
+    select = teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
+  )
 
   testthat::expect_true(assert_single_selection(list(mock_spec)))
   testthat::expect_true(assert_single_selection(list(mock_spec, mock_spec)))
 })
 
 testthat::test_that("assert_single_selection fails when multiple selection is selected in any of the specs", {
-  mock_spec <- list(select = list(multiple = TRUE))
-  mock_spec2 <- list(select = list(multiple = FALSE))
+  mock_spec <- data_extract_spec(
+    dataname = "MOCK_DATASET",
+    select = teal.transform::select_spec(choices = c("A", "B"), multiple = TRUE)
+  )
+  mock_spec2 <- data_extract_spec(
+    dataname = "MOCK_DATASET",
+    select = teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
+  )
 
   x <- list(mock_spec)
 
@@ -20,3 +29,48 @@ testthat::test_that("assert_single_selection fails when multiple selection is se
     "'x' should not allow multiple selection"
   )
 })
+
+testthat::test_that("assert_single_selection fails when multiple selection is enabled", {
+  mock_spec <- data_extract_spec(
+    dataname = "MOCK_DATASET",
+    select = teal.transform::select_spec(choices = c("A", "B"), multiple = TRUE)
+  )
+
+  # Suppress logger messages
+  logger::with_log_threshold(
+    testthat::expect_error(
+      tm_g_bivariate(
+        "a label",
+        mock_spec,
+        mock_spec
+      ),
+      "'x' should not allow multiple selection"
+    ),
+    threshold = logger::FATAL,
+    namespace = "teal.modules.general"
+  )
+})
+
+testthat::test_that("assert_single_selection succeeds when multiple selection is disabled", {
+  mock_spec <- data_extract_spec(
+    dataname = "ADSL",
+    select = teal.transform::select_spec(
+      choices = c("USUBJID", "AGE"),
+      multiple = FALSE
+    )
+  )
+
+  # Suppress logger messages
+  logger::with_log_threshold(
+    testthat::expect_s3_class(
+      tm_g_bivariate(
+        "a label",
+        mock_spec,
+        mock_spec
+      ),
+      "teal_module"
+    ),
+    threshold = logger::FATAL,
+    namespace = "teal.modules.general"
+  )
+})

From c5294bbc4133d128d0d60e3c57b3ea9428cf6e2a 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, 28 Feb 2024 14:14:10 +0100
Subject: [PATCH 06/19] tests: only use public functions

---
 tests/testthat/helper-functions.R |  9 +++
 tests/testthat/test-utils.R       | 92 +++++++++++++++----------------
 2 files changed, 52 insertions(+), 49 deletions(-)
 create mode 100644 tests/testthat/helper-functions.R

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
new file mode 100644
index 000000000..5887b60f2
--- /dev/null
+++ b/tests/testthat/helper-functions.R
@@ -0,0 +1,9 @@
+local_logger_threshold <- function(threshold, envir = parent.frame()) {
+  old <- logger::log_threshold(namespace = "teal.modules.general")
+  if (!requireNamespace("withr", quietly = FALSE)) {
+    return(invisible(old))
+  }
+  withr::defer(logger::log_threshold(old, namespace = "teal.modules.general"), envir = envir)
+  logger::log_threshold(threshold, namespace = "teal.modules.general")
+  invisible(old)
+}
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 4e29bf409..8d0a14ce8 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -1,14 +1,44 @@
 testthat::test_that("assert_single_selection succeeds if all elements have multiple choices disabled", {
+  # Suppress logger messages
+  local_logger_threshold(logger::FATAL)
+
   mock_spec <- data_extract_spec(
     dataname = "MOCK_DATASET",
     select = teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
   )
 
-  testthat::expect_true(assert_single_selection(list(mock_spec)))
-  testthat::expect_true(assert_single_selection(list(mock_spec, mock_spec)))
+  testthat::expect_s3_class(
+    tm_g_bivariate(
+      "a label",
+      mock_spec,
+      mock_spec
+    ),
+    "teal_module"
+  )
+
+  testthat::expect_s3_class(
+    tm_g_bivariate(
+      "a label",
+      list(mock_spec),
+      mock_spec
+    ),
+    "teal_module"
+  )
+
+  testthat::expect_s3_class(
+    tm_g_bivariate(
+      "a label",
+      list(mock_spec, mock_spec),
+      mock_spec
+    ),
+    "teal_module"
+  )
 })
 
 testthat::test_that("assert_single_selection fails when multiple selection is selected in any of the specs", {
+  # Suppress logger messages
+  local_logger_threshold(logger::FATAL)
+
   mock_spec <- data_extract_spec(
     dataname = "MOCK_DATASET",
     select = teal.transform::select_spec(choices = c("A", "B"), multiple = TRUE)
@@ -21,56 +51,20 @@ testthat::test_that("assert_single_selection fails when multiple selection is se
   x <- list(mock_spec)
 
   testthat::expect_error(
-    assert_single_selection(x),
-    "'x' should not allow multiple selection"
-  )
-  testthat::expect_error(
-    assert_single_selection(list(mock_spec2, mock_spec), .var.name = "x"),
-    "'x' should not allow multiple selection"
-  )
-})
-
-testthat::test_that("assert_single_selection fails when multiple selection is enabled", {
-  mock_spec <- data_extract_spec(
-    dataname = "MOCK_DATASET",
-    select = teal.transform::select_spec(choices = c("A", "B"), multiple = TRUE)
-  )
-
-  # Suppress logger messages
-  logger::with_log_threshold(
-    testthat::expect_error(
-      tm_g_bivariate(
-        "a label",
-        mock_spec,
-        mock_spec
-      ),
-      "'x' should not allow multiple selection"
+    tm_g_bivariate(
+      "a label",
+      x,
+      x
     ),
-    threshold = logger::FATAL,
-    namespace = "teal.modules.general"
-  )
-})
-
-testthat::test_that("assert_single_selection succeeds when multiple selection is disabled", {
-  mock_spec <- data_extract_spec(
-    dataname = "ADSL",
-    select = teal.transform::select_spec(
-      choices = c("USUBJID", "AGE"),
-      multiple = FALSE
-    )
+    "'x' should not allow multiple selection"
   )
 
-  # Suppress logger messages
-  logger::with_log_threshold(
-    testthat::expect_s3_class(
-      tm_g_bivariate(
-        "a label",
-        mock_spec,
-        mock_spec
-      ),
-      "teal_module"
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      list(mock_spec2, mock_spec, data_extract_spec("EMPTY")),
+      x
     ),
-    threshold = logger::FATAL,
-    namespace = "teal.modules.general"
+    "'x' should not allow multiple selection"
   )
 })

From edc1d275922dd2b2e9edf6e43279d8212a3ece40 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, 28 Feb 2024 14:17:34 +0100
Subject: [PATCH 07/19] tests: add default spec failure test

---
 tests/testthat/test-utils.R | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 8d0a14ce8..810df7fb7 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -54,7 +54,7 @@ testthat::test_that("assert_single_selection fails when multiple selection is se
     tm_g_bivariate(
       "a label",
       x,
-      x
+      mock_spec2
     ),
     "'x' should not allow multiple selection"
   )
@@ -62,8 +62,25 @@ testthat::test_that("assert_single_selection fails when multiple selection is se
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
-      list(mock_spec2, mock_spec, data_extract_spec("EMPTY")),
-      x
+      list(mock_spec2, mock_spec),
+      mock_spec2
+    ),
+    "'x' should not allow multiple selection"
+  )
+})
+
+testthat::test_that("assert_single_selection fails when with default spec", {
+  # Suppress logger messages
+  local_logger_threshold(logger::FATAL)
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      data_extract_spec("DEFAULT"),
+      data_extract_spec(
+        "VALID",
+        teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
+      )
     ),
     "'x' should not allow multiple selection"
   )

From 4e3f7fcf8074c7b6e23da61a0cd74de58699c902 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, 28 Feb 2024 14:23:59 +0100
Subject: [PATCH 08/19] Merge pre-release

---
 R/tm_a_pca.R           |   2 +-
 R/tm_a_regression.R    | 103 +++++++++++++++++++++++++++++++++--------
 man/tm_a_regression.Rd |  38 ++++++++-------
 3 files changed, 107 insertions(+), 36 deletions(-)

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 134ea6556..4da38b6d6 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -111,7 +111,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
                      post_output = NULL) {
   logger::log_info("Initializing tm_a_pca")
 
-  # Normalizing data types
+  # Normalize the parameters
   if (inherits(dat, "data_extract_spec")) dat <- list(dat)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R
index 6e0dbc1fa..3f2a45e5d 100644
--- a/R/tm_a_regression.R
+++ b/R/tm_a_regression.R
@@ -1,4 +1,4 @@
-#' Scatterplot and regression model
+#' `teal` module: Scatterplot and regression analysis
 #'
 #' Module for visualizing regression analysis, including scatterplots and
 #' various regression diagnostics plots.
@@ -14,14 +14,6 @@
 #' Regressor variables from an incoming dataset with filtering and selecting.
 #' @param response (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #' Response variables from an incoming dataset with filtering and selecting.
-#' @param alpha (`integer(1)` or `integer(3)`, optional) Specifies point opacity.
-#' - When the length of `alpha` is one: the plot points will have a fixed opacity.
-#' - When the length of `alpha` is three: the plot points opacity are dynamically adjusted based on
-#' vector of `value`, `min`, and `max`.
-#' @param size (`integer(1)` or `integer(3)`, optional) Specifies point size.
-#' - When the length of `size` is one: the plot point sizes will have a fixed size.
-#' - When the length of `size` is three: the plot points size are dynamically adjusted based on
-#' vector of `value`, `min`, and `max`.
 #' @param default_outlier_label (`character`, optional) The default column selected to label outliers.
 #' @param default_plot_type (`numeric`, optional) Defaults to Response vs Regressor.
 #' 1. Response vs Regressor
@@ -31,10 +23,25 @@
 #' 5. Cook's distance
 #' 6. Residuals vs Leverage
 #' 7. Cook's dist vs Leverage
+#' @param label_segment_threshold (`numeric(1)` or `numeric(3)`)
+#' Minimum distance between label and point on the plot that triggers the creation of
+#' a line segment between the two.
+#' This may happen when the label cannot be placed next to the point as it overlaps another
+#' label or point.
+#' The value is used as the `min.segment.length` parameter to the [ggrepel::geom_text_repel()] function.
+#'
+#' It can take the following forms:
+#' - `numeric(1)`: Fixed value used for the minimum distance and the slider is not presented in the UI.
+#' - `numeric(3)`: A slider is presented in the UI (under "Plot settings") to adjust the minimum distance dynamically.
+#'
+#'     It takes the form of `c(value, min, max)` and it is passed to the `value_min_max`
+#'     argument in `teal.widgets::optionalSliderInputValMinMax`.
 #'
 #' @templateVar ggnames `r regression_names`
 #' @template ggplot2_args_multi
 #'
+#' @inherit shared_params return
+#'
 #' @examples
 #' # general data example
 #' library(teal.widgets)
@@ -141,10 +148,11 @@ tm_a_regression <- function(label = "Regression Analysis",
                             pre_output = NULL,
                             post_output = NULL,
                             default_plot_type = 1,
-                            default_outlier_label = "USUBJID") {
+                            default_outlier_label = "USUBJID",
+                            label_segment_threshold = c(0.5, 0, 10)) {
   logger::log_info("Initializing tm_a_regression")
 
-  # Normalizing data types
+  # Normalize the parameters
   if (inherits(regressor, "data_extract_spec")) regressor <- list(regressor)
   if (inherits(response, "data_extract_spec")) response <- list(response)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
@@ -152,15 +160,20 @@ tm_a_regression <- function(label = "Regression Analysis",
   # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_list(regressor, types = "data_extract_spec")
+
   checkmate::assert_list(response, types = "data_extract_spec")
   assert_single_selection(response)
 
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
+
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
   checkmate::assert_numeric(
     plot_width[1],
-    lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
+    lower = plot_width[2],
+    upper = plot_width[3],
+    null.ok = TRUE,
+    .var.name = "plot_width"
   )
 
   if (length(alpha) == 1) {
@@ -188,8 +201,20 @@ tm_a_regression <- function(label = "Regression Analysis",
 
   checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
-  checkmate::assert_choice(default_plot_type, seq.int(1, length(plot_choices)))
+  checkmate::assert_choice(default_plot_type, seq.int(1L, length(plot_choices)))
   checkmate::assert_string(default_outlier_label)
+
+  if (length(label_segment_threshold) == 1) {
+    checkmate::assert_numeric(label_segment_threshold, any.missing = FALSE, finite = TRUE)
+  } else {
+    checkmate::assert_numeric(label_segment_threshold, len = 3, any.missing = FALSE, finite = TRUE)
+    checkmate::assert_numeric(
+      label_segment_threshold[1],
+      lower = label_segment_threshold[2],
+      upper = label_segment_threshold[3],
+      .var.name = "label_segment_threshold"
+    )
+  }
   # End of assertions
 
   # Make UI args
@@ -287,6 +312,29 @@ ui_a_regression <- function(id, ...) {
           title = "Plot settings",
           teal.widgets::optionalSliderInputValMinMax(ns("alpha"), "Opacity:", args$alpha, ticks = FALSE),
           teal.widgets::optionalSliderInputValMinMax(ns("size"), "Points size:", args$size, ticks = FALSE),
+          teal.widgets::optionalSliderInputValMinMax(
+            inputId = ns("label_min_segment"),
+            label = div(
+              class = "teal-tooltip",
+              tagList(
+                "Label min. segment:",
+                icon("circle-info"),
+                span(
+                  class = "tooltiptext",
+                  paste(
+                    "Use the slider to choose the cut-off value to define minimum distance between label and point",
+                    "that generates a line segment.",
+                    "It's only valid when 'Display outlier labels' is checked."
+                  )
+                )
+              )
+            ),
+            value_min_max = args$label_segment_threshold,
+            # Extra parameters to sliderInput
+            ticks = FALSE,
+            step = .1,
+            round = FALSE
+          ),
           selectInput(
             inputId = ns("ggtheme"),
             label = "Theme (by ggplot):",
@@ -467,10 +515,23 @@ srv_a_regression <- function(id,
       )
     })
 
+    label_min_segment <- reactive({
+      input$label_min_segment
+    })
+
     outlier_label <- reactive({
       substitute(
-        expr = geom_text(label = label_col, hjust = 0, vjust = 1, color = "red"),
-        env = list(label_col = label_col())
+        expr = ggrepel::geom_text_repel(
+          label = label_col,
+          color = "red",
+          hjust = 0,
+          vjust = 1,
+          max.overlaps = Inf,
+          min.segment.length = label_min_segment,
+          segment.alpha = 0.5,
+          seed = 123
+        ),
+        env = list(label_col = label_col(), label_min_segment = label_min_segment())
       )
     })
 
@@ -638,16 +699,20 @@ srv_a_regression <- function(id,
           plot <- substitute(
             expr = plot +
               stat_qq(
-                geom = "text",
+                geom = ggrepel::GeomTextRepel,
                 label = label_col %>%
                   data.frame(label = .) %>%
                   dplyr::filter(label != "cooksd == NaN") %>%
                   unlist(),
+                color = "red",
                 hjust = 0,
-                vjust = 1,
-                color = "red"
+                vjust = 0,
+                max.overlaps = Inf,
+                min.segment.length = label_min_segment,
+                segment.alpha = .5,
+                seed = 123
               ),
-            env = list(plot = plot, label_col = label_col())
+            env = list(plot = plot, label_col = label_col(), label_min_segment = label_min_segment())
           )
         }
 
diff --git a/man/tm_a_regression.Rd b/man/tm_a_regression.Rd
index 5d539d163..99aed7d27 100644
--- a/man/tm_a_regression.Rd
+++ b/man/tm_a_regression.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/tm_a_regression.R
 \name{tm_a_regression}
 \alias{tm_a_regression}
-\title{Scatterplot and regression model}
+\title{\code{teal} module: Scatterplot and regression analysis}
 \usage{
 tm_a_regression(
   label = "Regression Analysis",
@@ -17,7 +17,8 @@ tm_a_regression(
   pre_output = NULL,
   post_output = NULL,
   default_plot_type = 1,
-  default_outlier_label = "USUBJID"
+  default_outlier_label = "USUBJID",
+  label_segment_threshold = c(0.5, 0, 10)
 )
 }
 \arguments{
@@ -36,20 +37,6 @@ Response variables from an incoming dataset with filtering and selecting.}
 \item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of
 \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.}
 
-\item{alpha}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point opacity.
-\itemize{
-\item When the length of \code{alpha} is one: the plot points will have a fixed opacity.
-\item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on
-vector of \code{value}, \code{min}, and \code{max}.
-}}
-
-\item{size}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point size.
-\itemize{
-\item When the length of \code{size} is one: the plot point sizes will have a fixed size.
-\item When the length of \code{size} is three: the plot points size are dynamically adjusted based on
-vector of \code{value}, \code{min}, and \code{max}.
-}}
-
 \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.}
 
 \item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
@@ -79,6 +66,25 @@ adding context or further instructions. Elements like \code{shiny::helpText()} a
 }}
 
 \item{default_outlier_label}{(\code{character}, optional) The default column selected to label outliers.}
+
+\item{label_segment_threshold}{(\code{numeric(1)} or \code{numeric(3)})
+Minimum distance between label and point on the plot that triggers the creation of
+a line segment between the two.
+This may happen when the label cannot be placed next to the point as it overlaps another
+label or point.
+The value is used as the \code{min.segment.length} parameter to the \code{\link[ggrepel:geom_text_repel]{ggrepel::geom_text_repel()}} function.
+
+It can take the following forms:
+\itemize{
+\item \code{numeric(1)}: Fixed value used for the minimum distance and the slider is not presented in the UI.
+\item \code{numeric(3)}: A slider is presented in the UI (under "Plot settings") to adjust the minimum distance dynamically.
+
+It takes the form of \code{c(value, min, max)} and it is passed to the \code{value_min_max}
+argument in \code{teal.widgets::optionalSliderInputValMinMax}.
+}}
+}
+\value{
+Object of class \code{teal_module} to be used in \code{teal} applications.
 }
 \description{
 Module for visualizing regression analysis, including scatterplots and

From 8af721c1d518f0aa8c7ce64333806ae1572de476 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, 29 Feb 2024 13:15:40 +0100
Subject: [PATCH 09/19] chore: rename tests file

---
 tests/testthat/{test-utils.R => test-tm_g_bivariate.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tests/testthat/{test-utils.R => test-tm_g_bivariate.R} (100%)

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-tm_g_bivariate.R
similarity index 100%
rename from tests/testthat/test-utils.R
rename to tests/testthat/test-tm_g_bivariate.R

From e98f7b0b124087f20c2ba69daab9fe297d276528 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, 29 Feb 2024 14:04:23 +0100
Subject: [PATCH 10/19] tests: testing tm_g_bivariate

---
 tests/testthat/helper-functions.R    |  13 ++
 tests/testthat/test-tm_g_bivariate.R | 211 ++++++++++++++++++++++-----
 2 files changed, 188 insertions(+), 36 deletions(-)

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 5887b60f2..8992327f4 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -7,3 +7,16 @@ local_logger_threshold <- function(threshold, envir = parent.frame()) {
   logger::log_threshold(threshold, namespace = "teal.modules.general")
   invisible(old)
 }
+
+# Create a mock data extact spec for tests
+mock_data_extract_spec <- function(dataname = "MOCK_DATASET",
+                                   select_choices = sample(LETTERS, sample(2:10, 1)),
+                                   select_multiple = FALSE) {
+  teal.transform::data_extract_spec(
+    dataname = dataname,
+    select = teal.transform::select_spec(
+      choices = select_choices,
+      multiple = select_multiple
+    )
+  )
+}
diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index 810df7fb7..5d84e936d 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -1,87 +1,226 @@
-testthat::test_that("assert_single_selection succeeds if all elements have multiple choices disabled", {
-  # Suppress logger messages
-  local_logger_threshold(logger::FATAL)
-
-  mock_spec <- data_extract_spec(
-    dataname = "MOCK_DATASET",
-    select = teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
-  )
+testthat::test_that("tm_g_bivariate creates a `teal_module` object", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   testthat::expect_s3_class(
     tm_g_bivariate(
       "a label",
-      mock_spec,
-      mock_spec
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_height = c(400, 100, 600),
+      plot_width = c(600, 100, 600)
     ),
     "teal_module"
   )
+})
+
+testthat::test_that("tm_g_bivariate creates a `teal_module` object with default options", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   testthat::expect_s3_class(
     tm_g_bivariate(
       "a label",
-      list(mock_spec),
-      mock_spec
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE)
     ),
     "teal_module"
   )
+})
+
+testthat::test_that("tm_g_bivariate creates a `teal_module` object with multiple data extract specs", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   testthat::expect_s3_class(
     tm_g_bivariate(
       "a label",
-      list(mock_spec, mock_spec),
-      mock_spec
+      list(mock_data_extract_spec(select_multiple = FALSE), mock_data_extract_spec(select_multiple = FALSE)),
+      list(mock_data_extract_spec(select_multiple = FALSE), mock_data_extract_spec(select_multiple = FALSE)),
+      plot_height = c(400, 100, 600),
+      plot_width = c(600, 100, 600)
     ),
     "teal_module"
   )
 })
 
-testthat::test_that("assert_single_selection fails when multiple selection is selected in any of the specs", {
-  # Suppress logger messages
-  local_logger_threshold(logger::FATAL)
+testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have all arguments of function", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  mod <- tm_g_bivariate(
+    "a label",
+    mock_data_extract_spec(select_multiple = FALSE),
+    mock_data_extract_spec(select_multiple = FALSE)
+  )
+
+  expect_contains(
+    names(mod$ui_args),
+    names(formals(tm_g_bivariate))
+  )
+})
+
+testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have all arguments of function", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
-  mock_spec <- data_extract_spec(
-    dataname = "MOCK_DATASET",
-    select = teal.transform::select_spec(choices = c("A", "B"), multiple = TRUE)
+  mod <- tm_g_bivariate(
+    "a label",
+    list(
+      mock_data_extract_spec(dataname = "A", select_multiple = FALSE),
+      mock_data_extract_spec(dataname = "B", select_multiple = FALSE)
+    ),
+    mock_data_extract_spec(dataname = "C", select_multiple = FALSE)
   )
-  mock_spec2 <- data_extract_spec(
-    dataname = "MOCK_DATASET",
-    select = teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
+
+  expect_setequal(
+    mod$datanames,
+    c("A", "B", "C")
   )
+})
 
-  x <- list(mock_spec)
+# Test `x` and `y` arguments with invalid data_extract_spec
+
+testthat::test_that("tm_g_bivariate fails when `x` contains a spec with multiple selection", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
-      x,
-      mock_spec2
+      list(
+        mock_data_extract_spec(select_multiple = TRUE)
+      ),
+      list()
     ),
     "'x' should not allow multiple selection"
   )
+})
+
+testthat::test_that("tm_g_bivariate fails when `x` contains multiple spec with (at least one ) multiple selection", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
-      list(mock_spec2, mock_spec),
-      mock_spec2
+      list(
+        mock_data_extract_spec(select_multiple = FALSE),
+        mock_data_extract_spec(select_multiple = TRUE)
+      ),
+      list(mock_data_extract_spec(select_multiple = FALSE))
     ),
     "'x' should not allow multiple selection"
   )
 })
 
-testthat::test_that("assert_single_selection fails when with default spec", {
-  # Suppress logger messages
-  local_logger_threshold(logger::FATAL)
+testthat::test_that("tm_g_bivariate fails when `x` contains multiple spec with (at least one ) multiple selection", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
-      data_extract_spec("DEFAULT"),
-      data_extract_spec(
-        "VALID",
-        teal.transform::select_spec(choices = c("A", "B"), multiple = FALSE)
+      mock_data_extract_spec(select_multiple = FALSE),
+      list(
+        mock_data_extract_spec(select_multiple = FALSE),
+        mock_data_extract_spec(select_multiple = TRUE)
       )
     ),
-    "'x' should not allow multiple selection"
+    "'y' should not allow multiple selection"
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `y` contains multiple spec with (at least one ) multiple selection", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      list(
+        mock_data_extract_spec(select_multiple = FALSE),
+        mock_data_extract_spec(select_multiple = TRUE)
+      )
+    ),
+    "'y' should not allow multiple selection"
+  )
+})
+
+# Test `plot_height` and `plot_width` arguments
+
+testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_height = c(100, 10, 20)
+    ),
+    "Assertion on 'plot_height' failed: Element 1 is not <= 20"
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_height = c(1, 10, 20)
+    ),
+    "Assertion on 'plot_height' failed: Element 1 is not >= 10"
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_height = 100
+    ),
+    "Assertion on 'plot_height' failed: Must have length 3, but has length 1"
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_width = c(100, 10, 20)
+    ),
+    "Assertion on 'plot_width' failed: Element 1 is not <= 20"
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_width = c(1, 10, 20)
+    ),
+    "Assertion on 'plot_width' failed: Element 1 is not >= 10"
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      plot_width = 100
+    ),
+    "Assertion on 'plot_width' failed: Must have length 3, but has length 1"
   )
 })

From 9483f20122d48957b4f71d39e6663eccb8c8e402 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, 29 Feb 2024 14:27:13 +0100
Subject: [PATCH 11/19] tests: color_settings

---
 tests/testthat/test-tm_g_bivariate.R | 67 ++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index 5d84e936d..c347442b0 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -224,3 +224,70 @@ testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
     "Assertion on 'plot_width' failed: Must have length 3, but has length 1"
   )
 })
+
+# Test `color_settings` argument
+
+testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `color` is supplied", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      color_setting = FALSE,
+      color = mock_data_extract_spec()
+    ),
+    "'color_settings' argument needs to be set to TRUE if 'color', 'fill', and/or 'size' is/are supplied."
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `size` is supplied", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      color_setting = FALSE,
+      size = mock_data_extract_spec()
+    ),
+    "'color_settings' argument needs to be set to TRUE if 'color', 'fill', and/or 'size' is/are supplied."
+  )
+})
+
+testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `fill` is supplied", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  testthat::expect_error(
+    tm_g_bivariate(
+      "a label",
+      mock_data_extract_spec(select_multiple = FALSE),
+      mock_data_extract_spec(select_multiple = FALSE),
+      color_setting = FALSE,
+      fill = mock_data_extract_spec()
+    ),
+    "'color_settings' argument needs to be set to TRUE if 'color', 'fill', and/or 'size' is/are supplied."
+  )
+})
+
+testthat::test_that("tm_g_bivariate determines `color`, `size` and `fill` when `color_setting` is TRUE", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  mod <- tm_g_bivariate(
+    "a label",
+    mock_data_extract_spec(select_multiple = FALSE),
+    mock_data_extract_spec(select_multiple = FALSE),
+    color_setting = TRUE
+  )
+
+  expect_contains(
+    vapply(
+      unlist(mod$ui_args[c("color", "size", "fill")], recursive = FALSE),
+      class,
+      character(1)
+    ),
+    "data_extract_spec"
+  )
+})

From 9b78c18622c70eb1b7ac1e4c90ba4cef92de91cb 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, 29 Feb 2024 14:30:12 +0100
Subject: [PATCH 12/19] chore: missing testthat prefix

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

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index c347442b0..928ee69ba 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -282,7 +282,7 @@ testthat::test_that("tm_g_bivariate determines `color`, `size` and `fill` when `
     color_setting = TRUE
   )
 
-  expect_contains(
+  testthat::expect_contains(
     vapply(
       unlist(mod$ui_args[c("color", "size", "fill")], recursive = FALSE),
       class,

From 407df25df17625dd088ef73fa065fc0c1e6d54d5 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, 29 Feb 2024 14:30:40 +0100
Subject: [PATCH 13/19] chore: missing testthat prefix

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

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index 928ee69ba..f86c8279a 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -50,7 +50,7 @@ testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have al
     mock_data_extract_spec(select_multiple = FALSE)
   )
 
-  expect_contains(
+  testthat::expect_contains(
     names(mod$ui_args),
     names(formals(tm_g_bivariate))
   )

From b71252d64c0ea72cc79862c4a9209f0a2b73c24a 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, 29 Feb 2024 14:36:27 +0100
Subject: [PATCH 14/19] tests: add extra arguments to non-default test

---
 tests/testthat/test-tm_g_bivariate.R | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index f86c8279a..5babd384a 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -6,8 +6,17 @@ testthat::test_that("tm_g_bivariate creates a `teal_module` object", {
       "a label",
       mock_data_extract_spec(select_multiple = FALSE),
       mock_data_extract_spec(select_multiple = FALSE),
+      row_facet = mock_data_extract_spec(select_multiple = FALSE),
+      col_facet = mock_data_extract_spec(select_multiple = FALSE),
+      facet = TRUE,
+      color_setting = TRUE,
+      use_density = TRUE,
+      free_x_scales = TRUE,
+      free_y_scales = TRUE,
       plot_height = c(400, 100, 600),
-      plot_width = c(600, 100, 600)
+      plot_width = c(600, 100, 600),
+      rotate_xaxis_labels = TRUE,
+      swap_axes = TRUE
     ),
     "teal_module"
   )

From 6bc23002e7eba35c3ede18cee2830c8dd013e90f 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, 29 Feb 2024 14:51:44 +0100
Subject: [PATCH 15/19] tests: adds superficial tests on UI and server merged
 dataset

---
 tests/testthat/test-tm_g_bivariate.R | 85 ++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index 5babd384a..eab907bf3 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -83,6 +83,91 @@ testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have al
   )
 })
 
+testthat::test_that("tm_g_bivariate module UI function creates a shiny tag", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  mod <- tm_g_bivariate(
+    "a label",
+    mock_data_extract_spec(select_multiple = FALSE),
+    mock_data_extract_spec(select_multiple = FALSE)
+  )
+
+  testthat::expect_class(
+    do.call(
+      mod$ui,
+      c(list("a_id"), mod$ui_args)
+    ),
+    "shiny.tag"
+  )
+})
+
+testthat::test_that("tm_g_bivariate module server", {
+  local_logger_threshold(logger::FATAL) # Suppress logger messages
+
+  data <- teal_data()
+  data <- within(data, {
+    require(nestcolor)
+    CO2 <- data.frame(CO2)
+  })
+  datanames(data) <- c("CO2")
+  join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+
+  mod <- tm_g_bivariate(
+    x = data_extract_spec(
+      dataname = "CO2",
+      select = select_spec(
+        label = "Select variable:",
+        choices = variable_choices(data[["CO2"]]),
+        selected = "conc",
+        multiple = FALSE,
+        fixed = FALSE
+      )
+    ),
+    y = data_extract_spec(
+      dataname = "CO2",
+      select = select_spec(
+        label = "Select variable:",
+        choices = variable_choices(data[["CO2"]]),
+        selected = "uptake",
+        multiple = FALSE,
+        fixed = FALSE
+      )
+    ),
+    row_facet = data_extract_spec(
+      dataname = "CO2",
+      select = select_spec(
+        label = "Select variable:",
+        choices = variable_choices(data[["CO2"]]),
+        selected = "Type",
+        fixed = FALSE
+      )
+    ),
+    col_facet = data_extract_spec(
+      dataname = "CO2",
+      select = select_spec(
+        label = "Select variable:",
+        choices = variable_choices(data[["CO2"]]),
+        selected = "Treatment",
+        fixed = FALSE
+      )
+    ),
+    ggplot2_args = ggplot2_args(
+      labs = list(subtitle = "Plot generated by Bivariate Module")
+    )
+  )
+
+  shiny::testServer(
+    mod$server,
+    args = c(mod$server_args, data = shiny::reactive(data)),
+    expr = {
+      checkmate::expect_data_frame(
+        anl_merged_q()[["ANL"]],
+        min.rows = 1
+      )
+    }
+  )
+})
+
 # Test `x` and `y` arguments with invalid data_extract_spec
 
 testthat::test_that("tm_g_bivariate fails when `x` contains a spec with multiple selection", {

From 30457d8df91461387362a681a01c5eaa4419eb55 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, 29 Feb 2024 14:52:29 +0100
Subject: [PATCH 16/19] tests: minor correction

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

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index eab907bf3..7470d7cbf 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -92,7 +92,7 @@ testthat::test_that("tm_g_bivariate module UI function creates a shiny tag", {
     mock_data_extract_spec(select_multiple = FALSE)
   )
 
-  testthat::expect_class(
+  testthat::expect_s3_class(
     do.call(
       mod$ui,
       c(list("a_id"), mod$ui_args)

From edbef9064557f09a62513824ae7da63b0663d20d 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, 29 Feb 2024 14:54:06 +0100
Subject: [PATCH 17/19] tests: simplify server test

---
 tests/testthat/test-tm_g_bivariate.R | 27 ++-------------------------
 1 file changed, 2 insertions(+), 25 deletions(-)

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index 7470d7cbf..4806e761b 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -101,16 +101,14 @@ testthat::test_that("tm_g_bivariate module UI function creates a shiny tag", {
   )
 })
 
-testthat::test_that("tm_g_bivariate module server", {
+testthat::test_that("tm_g_bivariate module server builds merged datasets", {
   local_logger_threshold(logger::FATAL) # Suppress logger messages
 
-  data <- teal_data()
-  data <- within(data, {
+  data <- within(teal_data(), {
     require(nestcolor)
     CO2 <- data.frame(CO2)
   })
   datanames(data) <- c("CO2")
-  join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 
   mod <- tm_g_bivariate(
     x = data_extract_spec(
@@ -132,27 +130,6 @@ testthat::test_that("tm_g_bivariate module server", {
         multiple = FALSE,
         fixed = FALSE
       )
-    ),
-    row_facet = data_extract_spec(
-      dataname = "CO2",
-      select = select_spec(
-        label = "Select variable:",
-        choices = variable_choices(data[["CO2"]]),
-        selected = "Type",
-        fixed = FALSE
-      )
-    ),
-    col_facet = data_extract_spec(
-      dataname = "CO2",
-      select = select_spec(
-        label = "Select variable:",
-        choices = variable_choices(data[["CO2"]]),
-        selected = "Treatment",
-        fixed = FALSE
-      )
-    ),
-    ggplot2_args = ggplot2_args(
-      labs = list(subtitle = "Plot generated by Bivariate Module")
     )
   )
 

From da72fc77f7106ee67d39ddbb9cbd543d11624139 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, 1 Mar 2024 10:35:10 +0100
Subject: [PATCH 18/19] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Dawid Kałędkowski <6959016+gogonzo@users.noreply.github.com>
Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
---
 tests/testthat/test-tm_g_bivariate.R | 79 +---------------------------
 1 file changed, 1 insertion(+), 78 deletions(-)

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
index 4806e761b..1d97a37fc 100644
--- a/tests/testthat/test-tm_g_bivariate.R
+++ b/tests/testthat/test-tm_g_bivariate.R
@@ -50,22 +50,7 @@ testthat::test_that("tm_g_bivariate creates a `teal_module` object with multiple
   )
 })
 
-testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have all arguments of function", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
-  mod <- tm_g_bivariate(
-    "a label",
-    mock_data_extract_spec(select_multiple = FALSE),
-    mock_data_extract_spec(select_multiple = FALSE)
-  )
-
-  testthat::expect_contains(
-    names(mod$ui_args),
-    names(formals(tm_g_bivariate))
-  )
-})
-
-testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have all arguments of function", {
+testthat::test_that("tm_g_bivariate creates a module with datanames taken from data extracts", {
   local_logger_threshold(logger::FATAL) # Suppress logger messages
 
   mod <- tm_g_bivariate(
@@ -83,68 +68,6 @@ testthat::test_that("tm_g_bivariate creates a module with `ui_args` that have al
   )
 })
 
-testthat::test_that("tm_g_bivariate module UI function creates a shiny tag", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
-  mod <- tm_g_bivariate(
-    "a label",
-    mock_data_extract_spec(select_multiple = FALSE),
-    mock_data_extract_spec(select_multiple = FALSE)
-  )
-
-  testthat::expect_s3_class(
-    do.call(
-      mod$ui,
-      c(list("a_id"), mod$ui_args)
-    ),
-    "shiny.tag"
-  )
-})
-
-testthat::test_that("tm_g_bivariate module server builds merged datasets", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
-  data <- within(teal_data(), {
-    require(nestcolor)
-    CO2 <- data.frame(CO2)
-  })
-  datanames(data) <- c("CO2")
-
-  mod <- tm_g_bivariate(
-    x = data_extract_spec(
-      dataname = "CO2",
-      select = select_spec(
-        label = "Select variable:",
-        choices = variable_choices(data[["CO2"]]),
-        selected = "conc",
-        multiple = FALSE,
-        fixed = FALSE
-      )
-    ),
-    y = data_extract_spec(
-      dataname = "CO2",
-      select = select_spec(
-        label = "Select variable:",
-        choices = variable_choices(data[["CO2"]]),
-        selected = "uptake",
-        multiple = FALSE,
-        fixed = FALSE
-      )
-    )
-  )
-
-  shiny::testServer(
-    mod$server,
-    args = c(mod$server_args, data = shiny::reactive(data)),
-    expr = {
-      checkmate::expect_data_frame(
-        anl_merged_q()[["ANL"]],
-        min.rows = 1
-      )
-    }
-  )
-})
-
 # Test `x` and `y` arguments with invalid data_extract_spec
 
 testthat::test_that("tm_g_bivariate fails when `x` contains a spec with multiple selection", {

From c0b46c75f73f4b08f98bcd4aa4fd03439dbcb686 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, 1 Mar 2024 10:50:26 +0100
Subject: [PATCH 19/19] chore: refactor code to avoid adding withr to suggests

---
 tests/testthat/helper-functions.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 8992327f4..8ae39cb2a 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -1,9 +1,9 @@
 local_logger_threshold <- function(threshold, envir = parent.frame()) {
   old <- logger::log_threshold(namespace = "teal.modules.general")
-  if (!requireNamespace("withr", quietly = FALSE)) {
-    return(invisible(old))
-  }
-  withr::defer(logger::log_threshold(old, namespace = "teal.modules.general"), envir = envir)
+
+  # Equivalent to withr::defer
+  thunk <- as.call(list(function() logger::log_threshold(old, namespace = "teal.modules.general")))
+  do.call(base::on.exit, list(thunk, TRUE, FALSE), envir = envir)
   logger::log_threshold(threshold, namespace = "teal.modules.general")
   invisible(old)
 }