From d2d4e1a827c79aaf7c0702f75676fcaa32d350ce 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, 10 Apr 2024 15:18:20 +0200
Subject: [PATCH 01/25] feat: support for e2e tests in PCA module

---
 R/tm_a_pca.R                              |   2 +-
 tests/testthat/test-shinytest2-tm_a_pca.R | 155 ++++++++++++++++++++++
 2 files changed, 156 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/test-shinytest2-tm_a_pca.R

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 42261b2f0..20e2c1cb9 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -264,7 +264,7 @@ ui_a_pca <- function(id, ...) {
             collapsed = TRUE,
             conditionalPanel(
               condition = sprintf(
-                "input['%s'] == 'Elbow Plot' || input['%s'] == 'Eigenvector plot'",
+                "input['%s'] == 'Elbow plot' || input['%s'] == 'Eigenvector plot'",
                 ns("plot_type"),
                 ns("plot_type")
               ),
diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
new file mode 100644
index 000000000..71a4b34ef
--- /dev/null
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -0,0 +1,155 @@
+testthat::test_that("e2e - tm_a_pca: data extract changes output", {
+  skip_if_too_deep(5)
+
+  require(shinytest2)
+
+  data <- within(teal_data(), {
+    require(nestcolor)
+    require(ggplot2)
+
+    USArrests <- USArrests
+  })
+  datanames(data) <- "USArrests"
+
+
+  app <- TealAppDriver$new(
+    data = data,
+    modules = tm_a_pca(
+      dat = data_extract_spec(
+        dataname = "USArrests",
+        select = select_spec(
+          choices = variable_choices(
+            data = data[["USArrests"]],
+            c("Murder", "Assault", "UrbanPop", "Rape")
+          ),
+          selected = c("Murder", "Assault"),
+          multiple = TRUE
+        )
+      )
+    )
+  )
+
+  # Data selection (adds rows to tables)
+  app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"))
+  app$expect_no_validation_error()
+
+  testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "Assault")
+
+  testthat::expect_failure(
+    testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "UrbanPop")
+  )
+
+  app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
+  app$expect_no_validation_error()
+
+  testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "UrbanPop")
+
+  app$stop()
+})
+
+testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
+  skip_if_too_deep(5)
+
+  require(shinytest2)
+
+  data <- within(teal_data(), {
+    require(nestcolor)
+
+    USArrests <- USArrests
+  })
+  datanames(data) <- "USArrests"
+
+  app <- TealAppDriver$new(
+    data = data,
+    modules = tm_a_pca(
+      dat = data_extract_spec(
+        dataname = "USArrests",
+        select = select_spec(
+          choices = variable_choices(
+            data = data[["USArrests"]],
+            c("Murder", "Assault", "UrbanPop", "Rape")
+          ),
+          selected = c("Murder", "Assault"),
+          multiple = TRUE
+        )
+      )
+    )
+  )
+
+  app$view()
+  browser()
+  # Display section (hides tables)
+
+  app$set_module_input("tables_display", c())
+  app$expect_no_validation_error()
+
+  testthat::expect_type(app$get_active_module_output("tbl_importance"), "list")
+  testthat::expect_setequal(names(app$get_active_module_output("tbl_importance")), c("message", "call", "type"))
+
+  testthat::expect_type(app$get_active_module_output("tbl_eigenvector"), "list")
+  testthat::expect_setequal(names(app$get_active_module_output("tbl_eigenvector")), c("message", "call", "type"))
+
+  # Plot type (select each)
+
+  # Changing input will trigger an output change
+  app$set_module_input("plot_type", "Circle plot")
+  app$expect_no_validation_error()
+
+  app$set_module_input("plot_type", "Biplot")
+  app$expect_no_validation_error()
+
+  app$set_module_input("plot_type", "Eigenvector plot")
+  app$expect_no_validation_error()
+
+  app$set_module_input("plot_type", "Elbow plot") # Initial value
+  app$expect_no_validation_error()
+
+  # Pre-processing
+
+  app$set_module_input("standardization", "center")
+  app$set_module_input("standardization", "center_scale")
+  app$set_module_input("standardization", "none") # Initial value
+
+  # NA Action
+
+  app$set_module_input("na_action", "drop")
+  app$set_module_input("na_action", "none")
+
+  # Selected plot specific settings is not visible for Elbow plot
+  no_plot_settings_selector <- sprintf("#%s-%s %s", app$active_module_ns(), "plot_settings", "span.help-block")
+  x_axis_selector <- sprintf("#%s-%s", app$active_module_ns(), "x_axis")
+  color_by_selector <- sprintf("#%s-%s", app$active_module_ns(), "response-dataset_USArrests_singleextract-select_input")
+
+  app$set_module_input("plot_type", "Elbow plot", wait = FALSE)
+  testthat::expect_true(app$is_visible(no_plot_settings_selector))
+  testthat::expect_false(app$is_visible(x_axis_selector))
+  testthat::expect_false(app$is_visible(color_by_selector))
+
+  app$set_module_input("plot_type", "Circle plot", wait = FALSE)
+  testthat::expect_true(app$is_visible(x_axis_selector))
+
+  app$set_module_input("plot_type", "Biplot", wait = FALSE)
+  testthat::expect_true(app$is_visible(color_by_selector))
+
+  # Theme
+
+  app$set_module_input("ggtheme-selectized", "bw")
+  app$expect_no_validation_error()
+  app$set_module_input("ggtheme-selectized", "light")
+  app$expect_no_validation_error()
+  app$set_module_input("ggtheme-selectized", "dark")
+  app$expect_no_validation_error()
+
+  # Font size
+
+  app$set_module_input("font_size", "8")
+  app$expect_no_validation_error()
+
+  app$set_module_input("font_size", "20")
+  app$expect_no_validation_error()
+
+  app$set_module_input("font_size", "15")
+  app$expect_no_validation_error()
+
+  app$stop()
+})

From a20da5a9c41aed4c65cdbc7ffa53f83714a13564 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, 10 Apr 2024 15:39:48 +0200
Subject: [PATCH 02/25] fix: remove app view expressions

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 71a4b34ef..b93907f7e 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -76,8 +76,6 @@ testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
     )
   )
 
-  app$view()
-  browser()
   # Display section (hides tables)
 
   app$set_module_input("tables_display", c())

From a1a0c94c68f1711206fbf553f84c78bc1b606210 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, 10 Apr 2024 17:28:20 +0200
Subject: [PATCH 03/25] e2e feat: add remaining data extract input

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index b93907f7e..fa451dde3 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -44,6 +44,18 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
 
   testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "UrbanPop")
 
+  # Original Coordinate
+  app$set_module_input("plot_type", "Biplot")
+  app$set_module_input("variables", c("Murder"))
+  app$expect_no_validation_error()
+
+  # Color by
+  app$set_module_input("response-dataset_USArrests_singleextract-select", c("Assault"))
+  app$expect_no_validation_error()
+
+  app$set_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
+  app$expect_validation_error()
+
   app$stop()
 })
 

From 5fb88858d1adb75bc238f028f8e5058a15aaf67b 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, 11 Apr 2024 10:56:57 +0200
Subject: [PATCH 04/25] fix: linter errors

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index fa451dde3..ba4d497d7 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -7,11 +7,10 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
     require(nestcolor)
     require(ggplot2)
 
-    USArrests <- USArrests
+    USArrests <- USArrests # nolint: object_name.
   })
   datanames(data) <- "USArrests"
 
-
   app <- TealAppDriver$new(
     data = data,
     modules = tm_a_pca(
@@ -67,7 +66,7 @@ testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
   data <- within(teal_data(), {
     require(nestcolor)
 
-    USArrests <- USArrests
+    USArrests <- USArrests # nolint: object_name.
   })
   datanames(data) <- "USArrests"
 
@@ -125,10 +124,14 @@ testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
   app$set_module_input("na_action", "drop")
   app$set_module_input("na_action", "none")
 
-  # Selected plot specific settings is not visible for Elbow plot
+  # Selected plot's specific settings is not visible
   no_plot_settings_selector <- sprintf("#%s-%s %s", app$active_module_ns(), "plot_settings", "span.help-block")
   x_axis_selector <- sprintf("#%s-%s", app$active_module_ns(), "x_axis")
-  color_by_selector <- sprintf("#%s-%s", app$active_module_ns(), "response-dataset_USArrests_singleextract-select_input")
+  color_by_selector <- sprintf(
+    "#%s-%s",
+    app$active_module_ns(),
+    "response-dataset_USArrests_singleextract-select_input"
+  )
 
   app$set_module_input("plot_type", "Elbow plot", wait = FALSE)
   testthat::expect_true(app$is_visible(no_plot_settings_selector))
@@ -136,9 +139,12 @@ testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
   testthat::expect_false(app$is_visible(color_by_selector))
 
   app$set_module_input("plot_type", "Circle plot", wait = FALSE)
+  testthat::expect_false(app$is_visible(no_plot_settings_selector))
   testthat::expect_true(app$is_visible(x_axis_selector))
 
   app$set_module_input("plot_type", "Biplot", wait = FALSE)
+  testthat::expect_false(app$is_visible(no_plot_settings_selector))
+  testthat::expect_true(app$is_visible(x_axis_selector))
   testthat::expect_true(app$is_visible(color_by_selector))
 
   # Theme

From 08292fdce1ba08d8c4a6c534fd9671d2ad18e960 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, 11 Apr 2024 11:09:52 +0200
Subject: [PATCH 05/25] fix: adds ggplot2 prefix to all calls

---
 R/tm_a_pca.R | 87 +++++++++++++++++++++++++++-------------------------
 1 file changed, 45 insertions(+), 42 deletions(-)

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 20e2c1cb9..4dccb1323 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -520,12 +520,12 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         theme = list(
           legend.position = "right",
           legend.spacing.y = quote(grid::unit(-5, "pt")),
-          legend.title = quote(element_text(vjust = 25)),
+          legend.title = quote(ggplot2::element_text(vjust = 25)),
           axis.text.x = substitute(
-            element_text(angle = angle_value, hjust = hjust_value),
+            ggplot2::element_text(angle = angle_value, hjust = hjust_value),
             list(angle_value = angle_value, hjust_value = hjust_value)
           ),
-          text = substitute(element_text(size = font_size), list(font_size = font_size))
+          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size))
         )
       )
 
@@ -550,24 +550,24 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               )
 
             cols <- c(getOption("ggplot2.discrete.colour"), c("lightblue", "darkred", "black"))[1:3]
-            g <- ggplot(mapping = aes_string(x = "component", y = "value")) +
-              geom_bar(
-                aes(fill = "Single variance"),
+            g <- ggplot2::ggplot(mapping = ggplot2::aes_string(x = "component", y = "value")) +
+              ggplot2::geom_bar(
+                ggplot2::aes(fill = "Single variance"),
                 data = dplyr::filter(elb_dat, metric == "Proportion of Variance"),
                 color = "black",
                 stat = "identity"
               ) +
-              geom_point(
-                aes(color = "Cumulative variance"),
+              ggplot2::geom_point(
+                ggplot2::aes(color = "Cumulative variance"),
                 data = dplyr::filter(elb_dat, metric == "Cumulative Proportion")
               ) +
-              geom_line(
-                aes(group = 1, color = "Cumulative variance"),
+              ggplot2::geom_line(
+                ggplot2::aes(group = 1, color = "Cumulative variance"),
                 data = dplyr::filter(elb_dat, metric == "Cumulative Proportion")
               ) +
               labs +
-              scale_color_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[3])) +
-              scale_fill_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[1])) +
+              ggplot2::scale_color_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[3])) +
+              ggplot2::scale_fill_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[1])) +
               ggthemes +
               themes
 
@@ -597,9 +597,9 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       dev_ggplot2_args <- teal.widgets::ggplot2_args(
         theme = list(
-          text = substitute(element_text(size = font_size), list(font_size = font_size)),
+          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size)),
           axis.text.x = substitute(
-            element_text(angle = angle_val, hjust = hjust_val),
+            ggplot2::element_text(angle = angle_val, hjust = hjust_val),
             list(angle_val = angle, hjust_val = hjust)
           )
         )
@@ -629,15 +629,15 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               y = sin(seq(0, 2 * pi, length.out = 100))
             )
 
-            g <- ggplot(pca_rot) +
-              geom_point(aes_string(x = x_axis, y = y_axis)) +
-              geom_label(
-                aes_string(x = x_axis, y = y_axis, label = "label"),
+            g <- ggplot2::ggplot(pca_rot) +
+              ggplot2::geom_point(ggplot2::aes_string(x = x_axis, y = y_axis)) +
+              ggplot2::geom_label(
+                ggplot2::aes_string(x = x_axis, y = y_axis, label = "label"),
                 nudge_x = 0.1, nudge_y = 0.05,
                 fontface = "bold"
               ) +
-              geom_path(aes(x, y, group = 1), data = circle_data) +
-              geom_point(aes(x = x, y = y), data = data.frame(x = 0, y = 0), shape = "x", size = 5) +
+              ggplot2::geom_path(ggplot2::aes(x, y, group = 1), data = circle_data) +
+              ggplot2::geom_point(ggplot2::aes(x = x, y = y), data = data.frame(x = 0, y = 0), shape = "x", size = 5) +
               labs +
               ggthemes +
               themes
@@ -648,7 +648,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             y_axis = y_axis,
             variables = variables,
             ggthemes = parsed_ggplot2_args$ggtheme,
-            labs = `if`(is.null(parsed_ggplot2_args$labs), quote(labs()), parsed_ggplot2_args$labs),
+            labs = `if`(is.null(parsed_ggplot2_args$labs), quote(ggplot2::labs()), parsed_ggplot2_args$labs),
             themes = parsed_ggplot2_args$theme
           )
         )
@@ -726,13 +726,16 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
           )
       }
 
-      pca_plot_biplot_expr <- list(quote(ggplot()))
+      pca_plot_biplot_expr <- list(quote(ggplot2::ggplot()))
 
       if (length(resp_col) == 0) {
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            geom_point(aes_string(x = x_axis, y = y_axis), data = pca_rot, alpha = alpha, size = size),
+            ggplot2::geom_point(
+              ggplot2::aes_string(x = x_axis, y = y_axis),
+              data = pca_rot, alpha = alpha, size = size
+            ),
             list(x_axis = input$x_axis, y_axis = input$y_axis, alpha = input$alpha, size = input$size)
           )
         )
@@ -743,7 +746,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         response <- ANL[[resp_col]]
 
         aes_biplot <- substitute(
-          aes_string(x = x_axis, y = y_axis, color = "response"),
+          ggplot2::aes_string(x = x_axis, y = y_axis, color = "response"),
           env = list(x_axis = x_axis, y_axis = y_axis)
         )
 
@@ -764,7 +767,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               qenv,
               quote(pca_rot$response <- as.factor(response))
             )
-            quote(scale_color_brewer(palette = "Dark2"))
+            quote(ggplot2::scale_color_brewer(palette = "Dark2"))
           } else if (inherits(response, "Date")) {
             qenv <- teal.code::eval_code(
               qenv,
@@ -772,7 +775,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             )
 
             quote(
-              scale_color_gradient(
+              ggplot2::scale_color_gradient(
                 low = c(getOption("ggplot2.discrete.colour")[2], "darkred")[1],
                 high = c(getOption("ggplot2.discrete.colour"), "lightblue")[1],
                 labels = function(x) as.Date(x, origin = "1970-01-01")
@@ -783,7 +786,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               qenv,
               quote(pca_rot$response <- response)
             )
-            quote(scale_color_gradient(
+            quote(ggplot2::scale_color_gradient(
               low = c(getOption("ggplot2.discrete.colour")[2], "darkred")[1],
               high = c(getOption("ggplot2.discrete.colour"), "lightblue")[1]
             ))
@@ -792,7 +795,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            geom_point(aes_biplot, data = pca_rot, alpha = alpha, size = size),
+            ggplot2::geom_point(aes_biplot, data = pca_rot, alpha = alpha, size = size),
             env = list(aes_biplot = aes_biplot, alpha = alpha, size = size)
           ),
           scales_biplot
@@ -803,8 +806,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            geom_segment(
-              aes_string(x = "xstart", y = "ystart", xend = x_axis, yend = y_axis),
+            ggplot2::geom_segment(
+              ggplot2::aes_string(x = "xstart", y = "ystart", xend = x_axis, yend = y_axis),
               data = rot_vars,
               lineend = "round", linejoin = "round",
               arrow = grid::arrow(length = grid::unit(0.5, "cm"))
@@ -812,8 +815,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             env = list(x_axis = x_axis, y_axis = y_axis)
           ),
           substitute(
-            geom_label(
-              aes_string(
+            ggplot2::geom_label(
+              ggplot2::aes_string(
                 x = x_axis,
                 y = y_axis,
                 label = "label"
@@ -824,7 +827,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             ),
             env = list(x_axis = x_axis, y_axis = y_axis)
           ),
-          quote(geom_point(aes(x = xstart, y = ystart), data = rot_vars, shape = "x", size = 5))
+          quote(ggplot2::geom_point(ggplot2::aes(x = xstart, y = ystart), data = rot_vars, shape = "x", size = 5))
         )
       }
 
@@ -834,9 +837,9 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       dev_ggplot2_args <- teal.widgets::ggplot2_args(
         labs = dev_labs,
         theme = list(
-          text = substitute(element_text(size = font_size), list(font_size = font_size)),
+          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size)),
           axis.text.x = substitute(
-            element_text(angle = angle_val, hjust = hjust_val),
+            ggplot2::element_text(angle = angle_val, hjust = hjust_val),
             list(angle_val = angle, hjust_val = hjust)
           )
         )
@@ -885,9 +888,9 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       dev_ggplot2_args <- teal.widgets::ggplot2_args(
         theme = list(
-          text = substitute(element_text(size = font_size), list(font_size = font_size)),
+          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size)),
           axis.text.x = substitute(
-            element_text(angle = angle_val, hjust = hjust_val),
+            ggplot2::element_text(angle = angle_val, hjust = hjust_val),
             list(angle_val = angle, hjust_val = hjust)
           )
         )
@@ -906,10 +909,10 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       ggplot_exprs <- c(
         list(
-          quote(ggplot(pca_rot)),
+          quote(ggplot2::ggplot(pca_rot)),
           substitute(
-            geom_bar(
-              aes_string(x = "Variable", y = pc),
+            ggplot2::geom_bar(
+              ggplot2::aes_string(x = "Variable", y = pc),
               stat = "identity",
               color = "black",
               fill = c(getOption("ggplot2.discrete.colour"), "lightblue")[1]
@@ -917,8 +920,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             env = list(pc = pc)
           ),
           substitute(
-            geom_text(
-              aes(
+            ggplot2::geom_text(
+              ggplot2::aes(
                 x = Variable,
                 y = pc_name,
                 label = round(pc_name, 3),

From 7ebe92a3d9d40f77b2b68ba4c713f2da671de5d4 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, 11 Apr 2024 11:25:25 +0200
Subject: [PATCH 06/25] fix: adds prefix to missing vars() call

---
 R/tm_a_pca.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 4dccb1323..5eb1f1e26 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -694,7 +694,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
               rot_vars <- pca$rotation[, c(x_axis, y_axis)] %>%
                 dplyr::as_tibble(rownames = "label") %>%
-                dplyr::mutate_at(vars(c(x_axis, y_axis)), function(x) r * x / sqrt(max(v_scale)))
+                dplyr::mutate_at(ggplot2::vars(c(x_axis, y_axis)), function(x) r * x / sqrt(max(v_scale)))
             },
             env = list(x_axis = x_axis, y_axis = y_axis)
           )

From 3cbee3f4fd332dc57b99a6c4f2784433db7e1d50 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, 11 Apr 2024 14:08:30 +0200
Subject: [PATCH 07/25] fix: remove requirement for loading shinytest2 and adds
 wait

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index ba4d497d7..2a711d47a 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,11 +1,8 @@
 testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   skip_if_too_deep(5)
 
-  require(shinytest2)
-
   data <- within(teal_data(), {
     require(nestcolor)
-    require(ggplot2)
 
     USArrests <- USArrests # nolint: object_name.
   })
@@ -29,7 +26,8 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   )
 
   # Data selection (adds rows to tables)
-  app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"))
+  app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
+  app$wait_for_idle()
   app$expect_no_validation_error()
 
   testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "Assault")
@@ -39,6 +37,7 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   )
 
   app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
+  app$wait_for_idle()
   app$expect_no_validation_error()
 
   testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "UrbanPop")
@@ -46,13 +45,16 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   # Original Coordinate
   app$set_module_input("plot_type", "Biplot")
   app$set_module_input("variables", c("Murder"))
+  app$wait_for_idle()
   app$expect_no_validation_error()
 
   # Color by
   app$set_module_input("response-dataset_USArrests_singleextract-select", c("Assault"))
+  app$wait_for_idle()
   app$expect_no_validation_error()
 
   app$set_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
+  app$wait_for_idle()
   app$expect_validation_error()
 
   app$stop()

From ebb00ebaf9d8aa0a3a19b1ee803dc689dbb31b73 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, 11 Apr 2024 14:29:43 +0200
Subject: [PATCH 08/25] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
---
 tests/testthat/test-shinytest2-tm_a_pca.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 2a711d47a..ff86a5e55 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,7 +1,7 @@
 testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   skip_if_too_deep(5)
 
-  data <- within(teal_data(), {
+  data <- within(teal.data::teal_data(), {
     require(nestcolor)
 
     USArrests <- USArrests # nolint: object_name.
@@ -11,10 +11,10 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   app <- TealAppDriver$new(
     data = data,
     modules = tm_a_pca(
-      dat = data_extract_spec(
+      dat = teal.transform::data_extract_spec(
         dataname = "USArrests",
-        select = select_spec(
-          choices = variable_choices(
+        select = teal.transform::select_spec(
+          choices = teal.transform::variable_choices(
             data = data[["USArrests"]],
             c("Murder", "Assault", "UrbanPop", "Rape")
           ),

From e5c37835b2f4e6bd85755a48c374564a98f9f70e 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, 11 Apr 2024 14:32:02 +0200
Subject: [PATCH 09/25] feat: move app driver initialization to helper

---
 tests/testthat/helper-functions.R         |  28 ++++
 tests/testthat/test-shinytest2-tm_a_pca.R | 182 ++++++++--------------
 2 files changed, 96 insertions(+), 114 deletions(-)

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 1bc8546bb..ed66eb661 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -10,3 +10,31 @@ mock_data_extract_spec <- function(dataname = "MOCK_DATASET",
     )
   )
 }
+
+# Based on example
+local_app_tm_a_pca <- function() {
+  data <- within(teal.data::teal_data(), {
+    require(nestcolor)
+
+    USArrests <- USArrests # nolint: object_name.
+  })
+  datanames(data) <- "USArrests"
+
+
+  TealAppDriver$new(
+    data = data,
+    modules = tm_a_pca(
+      dat = teal.transform::data_extract_spec(
+        dataname = "USArrests",
+        select = teal.transform::select_spec(
+          choices = teal.transform::variable_choices(
+            data = data[["USArrests"]],
+            c("Murder", "Assault", "UrbanPop", "Rape")
+          ),
+          selected = c("Murder", "Assault"),
+          multiple = TRUE
+        )
+      )
+    )
+  )
+}
diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index ff86a5e55..d8a67ebfd 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,173 +1,127 @@
 testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   skip_if_too_deep(5)
 
-  data <- within(teal.data::teal_data(), {
-    require(nestcolor)
-
-    USArrests <- USArrests # nolint: object_name.
-  })
-  datanames(data) <- "USArrests"
-
-  app <- TealAppDriver$new(
-    data = data,
-    modules = tm_a_pca(
-      dat = teal.transform::data_extract_spec(
-        dataname = "USArrests",
-        select = teal.transform::select_spec(
-          choices = teal.transform::variable_choices(
-            data = data[["USArrests"]],
-            c("Murder", "Assault", "UrbanPop", "Rape")
-          ),
-          selected = c("Murder", "Assault"),
-          multiple = TRUE
-        )
-      )
-    )
-  )
+  app_driver <- local_app_tm_a_pca()
 
   # Data selection (adds rows to tables)
-  app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
-  app$wait_for_idle()
-  app$expect_no_validation_error()
+  app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
+  app_driver$wait_for_idle()
+  app_driver$expect_no_validation_error()
 
-  testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "Assault")
+  testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Assault")
 
   testthat::expect_failure(
-    testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "UrbanPop")
+    testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
   )
 
-  app$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
-  app$wait_for_idle()
-  app$expect_no_validation_error()
+  app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
+  app_driver$wait_for_idle()
+  app_driver$expect_no_validation_error()
 
-  testthat::expect_match(app$get_active_module_output("tbl_eigenvector"), "UrbanPop")
+  testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
 
   # Original Coordinate
-  app$set_module_input("plot_type", "Biplot")
-  app$set_module_input("variables", c("Murder"))
-  app$wait_for_idle()
-  app$expect_no_validation_error()
+  app_driver$set_module_input("plot_type", "Biplot")
+  app_driver$set_module_input("variables", c("Murder"))
+  app_driver$wait_for_idle()
+  app_driver$expect_no_validation_error()
 
   # Color by
-  app$set_module_input("response-dataset_USArrests_singleextract-select", c("Assault"))
-  app$wait_for_idle()
-  app$expect_no_validation_error()
+  app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("Assault"))
+  app_driver$wait_for_idle()
+  app_driver$expect_no_validation_error()
 
-  app$set_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
-  app$wait_for_idle()
-  app$expect_validation_error()
+  app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
+  app_driver$wait_for_idle()
+  app_driver$expect_validation_error()
 
-  app$stop()
+  app_driver$stop()
 })
 
 testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
   skip_if_too_deep(5)
 
-  require(shinytest2)
-
-  data <- within(teal_data(), {
-    require(nestcolor)
-
-    USArrests <- USArrests # nolint: object_name.
-  })
-  datanames(data) <- "USArrests"
-
-  app <- TealAppDriver$new(
-    data = data,
-    modules = tm_a_pca(
-      dat = data_extract_spec(
-        dataname = "USArrests",
-        select = select_spec(
-          choices = variable_choices(
-            data = data[["USArrests"]],
-            c("Murder", "Assault", "UrbanPop", "Rape")
-          ),
-          selected = c("Murder", "Assault"),
-          multiple = TRUE
-        )
-      )
-    )
-  )
+  app_driver <- local_app_tm_a_pca()
 
   # Display section (hides tables)
 
-  app$set_module_input("tables_display", c())
-  app$expect_no_validation_error()
+  app_driver$set_module_input("tables_display", c())
+  app_driver$expect_no_validation_error()
 
-  testthat::expect_type(app$get_active_module_output("tbl_importance"), "list")
-  testthat::expect_setequal(names(app$get_active_module_output("tbl_importance")), c("message", "call", "type"))
+  testthat::expect_type(app_driver$get_active_module_output("tbl_importance"), "list")
+  testthat::expect_setequal(names(app_driver$get_active_module_output("tbl_importance")), c("message", "call", "type"))
 
-  testthat::expect_type(app$get_active_module_output("tbl_eigenvector"), "list")
-  testthat::expect_setequal(names(app$get_active_module_output("tbl_eigenvector")), c("message", "call", "type"))
+  testthat::expect_type(app_driver$get_active_module_output("tbl_eigenvector"), "list")
+  testthat::expect_setequal(names(app_driver$get_active_module_output("tbl_eigenvector")), c("message", "call", "type"))
 
   # Plot type (select each)
 
   # Changing input will trigger an output change
-  app$set_module_input("plot_type", "Circle plot")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("plot_type", "Circle plot")
+  app_driver$expect_no_validation_error()
 
-  app$set_module_input("plot_type", "Biplot")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("plot_type", "Biplot")
+  app_driver$expect_no_validation_error()
 
-  app$set_module_input("plot_type", "Eigenvector plot")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("plot_type", "Eigenvector plot")
+  app_driver$expect_no_validation_error()
 
-  app$set_module_input("plot_type", "Elbow plot") # Initial value
-  app$expect_no_validation_error()
+  app_driver$set_module_input("plot_type", "Elbow plot") # Initial value
+  app_driver$expect_no_validation_error()
 
   # Pre-processing
 
-  app$set_module_input("standardization", "center")
-  app$set_module_input("standardization", "center_scale")
-  app$set_module_input("standardization", "none") # Initial value
+  app_driver$set_module_input("standardization", "center")
+  app_driver$set_module_input("standardization", "center_scale")
+  app_driver$set_module_input("standardization", "none") # Initial value
 
   # NA Action
 
-  app$set_module_input("na_action", "drop")
-  app$set_module_input("na_action", "none")
+  app_driver$set_module_input("na_action", "drop")
+  app_driver$set_module_input("na_action", "none")
 
   # Selected plot's specific settings is not visible
-  no_plot_settings_selector <- sprintf("#%s-%s %s", app$active_module_ns(), "plot_settings", "span.help-block")
-  x_axis_selector <- sprintf("#%s-%s", app$active_module_ns(), "x_axis")
+  no_plot_settings_selector <- sprintf("#%s-%s %s", app_driver$active_module_ns(), "plot_settings", "span.help-block")
+  x_axis_selector <- sprintf("#%s-%s", app_driver$active_module_ns(), "x_axis")
   color_by_selector <- sprintf(
     "#%s-%s",
-    app$active_module_ns(),
+    app_driver$active_module_ns(),
     "response-dataset_USArrests_singleextract-select_input"
   )
 
-  app$set_module_input("plot_type", "Elbow plot", wait = FALSE)
-  testthat::expect_true(app$is_visible(no_plot_settings_selector))
-  testthat::expect_false(app$is_visible(x_axis_selector))
-  testthat::expect_false(app$is_visible(color_by_selector))
+  app_driver$set_module_input("plot_type", "Elbow plot", wait = FALSE)
+  testthat::expect_true(app_driver$is_visible(no_plot_settings_selector))
+  testthat::expect_false(app_driver$is_visible(x_axis_selector))
+  testthat::expect_false(app_driver$is_visible(color_by_selector))
 
-  app$set_module_input("plot_type", "Circle plot", wait = FALSE)
-  testthat::expect_false(app$is_visible(no_plot_settings_selector))
-  testthat::expect_true(app$is_visible(x_axis_selector))
+  app_driver$set_module_input("plot_type", "Circle plot", wait = FALSE)
+  testthat::expect_false(app_driver$is_visible(no_plot_settings_selector))
+  testthat::expect_true(app_driver$is_visible(x_axis_selector))
 
-  app$set_module_input("plot_type", "Biplot", wait = FALSE)
-  testthat::expect_false(app$is_visible(no_plot_settings_selector))
-  testthat::expect_true(app$is_visible(x_axis_selector))
-  testthat::expect_true(app$is_visible(color_by_selector))
+  app_driver$set_module_input("plot_type", "Biplot", wait = FALSE)
+  testthat::expect_false(app_driver$is_visible(no_plot_settings_selector))
+  testthat::expect_true(app_driver$is_visible(x_axis_selector))
+  testthat::expect_true(app_driver$is_visible(color_by_selector))
 
   # Theme
 
-  app$set_module_input("ggtheme-selectized", "bw")
-  app$expect_no_validation_error()
-  app$set_module_input("ggtheme-selectized", "light")
-  app$expect_no_validation_error()
-  app$set_module_input("ggtheme-selectized", "dark")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("ggtheme-selectized", "bw")
+  app_driver$expect_no_validation_error()
+  app_driver$set_module_input("ggtheme-selectized", "light")
+  app_driver$expect_no_validation_error()
+  app_driver$set_module_input("ggtheme-selectized", "dark")
+  app_driver$expect_no_validation_error()
 
   # Font size
 
-  app$set_module_input("font_size", "8")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("font_size", "8")
+  app_driver$expect_no_validation_error()
 
-  app$set_module_input("font_size", "20")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("font_size", "20")
+  app_driver$expect_no_validation_error()
 
-  app$set_module_input("font_size", "15")
-  app$expect_no_validation_error()
+  app_driver$set_module_input("font_size", "15")
+  app_driver$expect_no_validation_error()
 
-  app$stop()
+  app_driver$stop()
 })

From f578c62898678d3144f0b2413f1fd4059327c277 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, 11 Apr 2024 14:48:39 +0200
Subject: [PATCH 10/25] feat: split complex test into smaller tests

---
 tests/testthat/helper-TealAppDriver.R     | 33 ++++++++++++++++++++++-
 tests/testthat/helper-functions.R         | 28 -------------------
 tests/testthat/test-shinytest2-tm_a_pca.R | 26 +++++++++++++-----
 3 files changed, 51 insertions(+), 36 deletions(-)

diff --git a/tests/testthat/helper-TealAppDriver.R b/tests/testthat/helper-TealAppDriver.R
index 39e5c28d9..726628b57 100644
--- a/tests/testthat/helper-TealAppDriver.R
+++ b/tests/testthat/helper-TealAppDriver.R
@@ -1,7 +1,7 @@
 # Import non-exported TealAppDriver from `teal` package
 TealAppDriver <- getFromNamespace("TealAppDriver", "teal") # nolint: object_name.
 
-# Helper function
+# Data helper functions for reusable datasets ---------------------------------
 simple_teal_data <- function() {
   data <- within(teal.data::teal_data(), {
     require(nestcolor)
@@ -27,3 +27,34 @@ simple_cdisc_data <- function(datasets = c("ADSL", "ADRS", "ADTTE")) {
   teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datasets]
   data
 }
+
+# local app drivers for module testing ----------------------------------------
+# based on examples
+
+local_app_tm_a_pca <- function() {
+  # Dataset only used once
+  data <- within(teal.data::teal_data(), {
+    require(nestcolor)
+
+    USArrests <- USArrests # nolint: object_name.
+  })
+  teal.data::datanames(data) <- "USArrests"
+
+
+  TealAppDriver$new(
+    data = data,
+    modules = tm_a_pca(
+      dat = teal.transform::data_extract_spec(
+        dataname = "USArrests",
+        select = teal.transform::select_spec(
+          choices = teal.transform::variable_choices(
+            data = data[["USArrests"]],
+            c("Murder", "Assault", "UrbanPop", "Rape")
+          ),
+          selected = c("Murder", "Assault"),
+          multiple = TRUE
+        )
+      )
+    )
+  )
+}
diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index ed66eb661..1bc8546bb 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -10,31 +10,3 @@ mock_data_extract_spec <- function(dataname = "MOCK_DATASET",
     )
   )
 }
-
-# Based on example
-local_app_tm_a_pca <- function() {
-  data <- within(teal.data::teal_data(), {
-    require(nestcolor)
-
-    USArrests <- USArrests # nolint: object_name.
-  })
-  datanames(data) <- "USArrests"
-
-
-  TealAppDriver$new(
-    data = data,
-    modules = tm_a_pca(
-      dat = teal.transform::data_extract_spec(
-        dataname = "USArrests",
-        select = teal.transform::select_spec(
-          choices = teal.transform::variable_choices(
-            data = data[["USArrests"]],
-            c("Murder", "Assault", "UrbanPop", "Rape")
-          ),
-          selected = c("Murder", "Assault"),
-          multiple = TRUE
-        )
-      )
-    )
-  )
-}
diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index d8a67ebfd..08b47e9ce 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,4 +1,4 @@
-testthat::test_that("e2e - tm_a_pca: data extract changes output", {
+testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigenvector table", {
   skip_if_too_deep(5)
 
   app_driver <- local_app_tm_a_pca()
@@ -13,21 +13,33 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   testthat::expect_failure(
     testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
   )
+})
+
+testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes output of plot", {
+  skip_if_too_deep(5)
+
+  app_driver <- local_app_tm_a_pca()
+
+  app_driver$set_module_input("plot_type", "Circle plot")
+  app_driver$wait_for_idle()
 
   app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
   app_driver$wait_for_idle()
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
+})
+
+testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be from non-selected variable set", {
+  skip_if_too_deep(5)
+
+  app_driver <- local_app_tm_a_pca()
 
-  # Original Coordinate
   app_driver$set_module_input("plot_type", "Biplot")
-  app_driver$set_module_input("variables", c("Murder"))
   app_driver$wait_for_idle()
-  app_driver$expect_no_validation_error()
 
-  # Color by
-  app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("Assault"))
+  # Change colors of data points
+  app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("UrbanPop"))
   app_driver$wait_for_idle()
   app_driver$expect_no_validation_error()
 
@@ -38,7 +50,7 @@ testthat::test_that("e2e - tm_a_pca: data extract changes output", {
   app_driver$stop()
 })
 
-testthat::test_that("e2e - tm_a_pca: encodings update main panel", {
+testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate errors", {
   skip_if_too_deep(5)
 
   app_driver <- local_app_tm_a_pca()

From 119db66a81aaf8b6c1ccece09416b6b94715d299 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, 12 Apr 2024 10:46:15 +0200
Subject: [PATCH 11/25] chore: rename helper name

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

diff --git a/tests/testthat/helper-TealAppDriver.R b/tests/testthat/helper-TealAppDriver.R
index 726628b57..99db5d797 100644
--- a/tests/testthat/helper-TealAppDriver.R
+++ b/tests/testthat/helper-TealAppDriver.R
@@ -31,7 +31,7 @@ simple_cdisc_data <- function(datasets = c("ADSL", "ADRS", "ADTTE")) {
 # local app drivers for module testing ----------------------------------------
 # based on examples
 
-local_app_tm_a_pca <- function() {
+app_driver_tm_a_pca <- function() {
   # Dataset only used once
   data <- within(teal.data::teal_data(), {
     require(nestcolor)

From 59594fdb31644718b73bf0e59a8ada1889d5d67f 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, 12 Apr 2024 10:47:42 +0200
Subject: [PATCH 12/25] chore: remove wait_for_idle as it was implementd
 upstream

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 08b47e9ce..923bd9c93 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -5,7 +5,6 @@ testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigen
 
   # Data selection (adds rows to tables)
   app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
-  app_driver$wait_for_idle()
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Assault")
@@ -21,10 +20,8 @@ testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes
   app_driver <- local_app_tm_a_pca()
 
   app_driver$set_module_input("plot_type", "Circle plot")
-  app_driver$wait_for_idle()
 
   app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
-  app_driver$wait_for_idle()
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
@@ -36,15 +33,12 @@ testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be fro
   app_driver <- local_app_tm_a_pca()
 
   app_driver$set_module_input("plot_type", "Biplot")
-  app_driver$wait_for_idle()
 
   # Change colors of data points
   app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("UrbanPop"))
-  app_driver$wait_for_idle()
   app_driver$expect_no_validation_error()
 
   app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
-  app_driver$wait_for_idle()
   app_driver$expect_validation_error()
 
   app_driver$stop()

From e7d14b587becb97774f79700fd95c7d06b76e59b 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, 12 Apr 2024 12:46:08 +0200
Subject: [PATCH 13/25] fix: rename missing instances

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 923bd9c93..afc2661f9 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,7 +1,7 @@
 testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigenvector table", {
   skip_if_too_deep(5)
 
-  app_driver <- local_app_tm_a_pca()
+  app_driver <- app_tm_a_pca()
 
   # Data selection (adds rows to tables)
   app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
@@ -17,7 +17,7 @@ testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigen
 testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes output of plot", {
   skip_if_too_deep(5)
 
-  app_driver <- local_app_tm_a_pca()
+  app_driver <- app_tm_a_pca()
 
   app_driver$set_module_input("plot_type", "Circle plot")
 
@@ -30,7 +30,7 @@ testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes
 testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be from non-selected variable set", {
   skip_if_too_deep(5)
 
-  app_driver <- local_app_tm_a_pca()
+  app_driver <- app_tm_a_pca()
 
   app_driver$set_module_input("plot_type", "Biplot")
 
@@ -47,7 +47,7 @@ testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be fro
 testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate errors", {
   skip_if_too_deep(5)
 
-  app_driver <- local_app_tm_a_pca()
+  app_driver <- app_tm_a_pca()
 
   # Display section (hides tables)
 

From c5fe9e54c4d73a8d4dde7ffa270f13240120673c 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, 12 Apr 2024 17:09:02 +0200
Subject: [PATCH 14/25] fix: missing _driver on call

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index afc2661f9..4c33e1c3d 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,7 +1,7 @@
 testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigenvector table", {
   skip_if_too_deep(5)
 
-  app_driver <- app_tm_a_pca()
+  app_driver <- app_driver_tm_a_pca()
 
   # Data selection (adds rows to tables)
   app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
@@ -17,7 +17,7 @@ testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigen
 testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes output of plot", {
   skip_if_too_deep(5)
 
-  app_driver <- app_tm_a_pca()
+  app_driver <- app_driver_tm_a_pca()
 
   app_driver$set_module_input("plot_type", "Circle plot")
 
@@ -30,7 +30,7 @@ testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes
 testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be from non-selected variable set", {
   skip_if_too_deep(5)
 
-  app_driver <- app_tm_a_pca()
+  app_driver <- app_driver_tm_a_pca()
 
   app_driver$set_module_input("plot_type", "Biplot")
 
@@ -47,7 +47,7 @@ testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be fro
 testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate errors", {
   skip_if_too_deep(5)
 
-  app_driver <- app_tm_a_pca()
+  app_driver <- app_driver_tm_a_pca()
 
   # Display section (hides tables)
 

From 1791583cdd635e4cd16d36f0a07a1656a63d48fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 15 Apr 2024 12:57:37 +0200
Subject: [PATCH 15/25] fix: move helper to test file

---
 tests/testthat/helper-TealAppDriver.R     | 31 -----------------------
 tests/testthat/test-shinytest2-tm_a_pca.R | 28 ++++++++++++++++++++
 2 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/tests/testthat/helper-TealAppDriver.R b/tests/testthat/helper-TealAppDriver.R
index 99db5d797..d2dc7fc70 100644
--- a/tests/testthat/helper-TealAppDriver.R
+++ b/tests/testthat/helper-TealAppDriver.R
@@ -27,34 +27,3 @@ simple_cdisc_data <- function(datasets = c("ADSL", "ADRS", "ADTTE")) {
   teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datasets]
   data
 }
-
-# local app drivers for module testing ----------------------------------------
-# based on examples
-
-app_driver_tm_a_pca <- function() {
-  # Dataset only used once
-  data <- within(teal.data::teal_data(), {
-    require(nestcolor)
-
-    USArrests <- USArrests # nolint: object_name.
-  })
-  teal.data::datanames(data) <- "USArrests"
-
-
-  TealAppDriver$new(
-    data = data,
-    modules = tm_a_pca(
-      dat = teal.transform::data_extract_spec(
-        dataname = "USArrests",
-        select = teal.transform::select_spec(
-          choices = teal.transform::variable_choices(
-            data = data[["USArrests"]],
-            c("Murder", "Assault", "UrbanPop", "Rape")
-          ),
-          selected = c("Murder", "Assault"),
-          multiple = TRUE
-        )
-      )
-    )
-  )
-}
diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 4c33e1c3d..0a23b83a0 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -1,3 +1,31 @@
+app_driver_tm_a_pca <- function() {
+  # Dataset only used once
+  data <- within(teal.data::teal_data(), {
+    require(nestcolor)
+
+    USArrests <- USArrests # nolint: object_name.
+  })
+  teal.data::datanames(data) <- "USArrests"
+
+
+  TealAppDriver$new(
+    data = data,
+    modules = tm_a_pca(
+      dat = teal.transform::data_extract_spec(
+        dataname = "USArrests",
+        select = teal.transform::select_spec(
+          choices = teal.transform::variable_choices(
+            data = data[["USArrests"]],
+            c("Murder", "Assault", "UrbanPop", "Rape")
+          ),
+          selected = c("Murder", "Assault"),
+          multiple = TRUE
+        )
+      )
+    )
+  )
+}
+
 testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigenvector table", {
   skip_if_too_deep(5)
 

From c7af8ca63a75fbb70d42d06383c685e61b4e7f8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 15 Apr 2024 13:00:36 +0200
Subject: [PATCH 16/25] adds some expect_no_validation_error

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 0a23b83a0..3e932547d 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -106,8 +106,11 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
   # Pre-processing
 
   app_driver$set_module_input("standardization", "center")
+  app_driver$expect_no_validation_error
   app_driver$set_module_input("standardization", "center_scale")
+  app_driver$expect_no_validation_error
   app_driver$set_module_input("standardization", "none") # Initial value
+  app_driver$expect_no_validation_error
 
   # NA Action
 

From 4356c729f113e7021ed494eb3836020030afa2ba 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, 17 Apr 2024 10:09:16 +0200
Subject: [PATCH 17/25] docs: revert prefixes

---
 R/tm_a_pca.R | 88 ++++++++++++++++++++++++++--------------------------
 1 file changed, 44 insertions(+), 44 deletions(-)

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 5eb1f1e26..6fe0bd34f 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -520,12 +520,12 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         theme = list(
           legend.position = "right",
           legend.spacing.y = quote(grid::unit(-5, "pt")),
-          legend.title = quote(ggplot2::element_text(vjust = 25)),
+          legend.title = quote(element_text(vjust = 25)),
           axis.text.x = substitute(
-            ggplot2::element_text(angle = angle_value, hjust = hjust_value),
+            element_text(angle = angle_value, hjust = hjust_value),
             list(angle_value = angle_value, hjust_value = hjust_value)
           ),
-          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size))
+          text = substitute(element_text(size = font_size), list(font_size = font_size))
         )
       )
 
@@ -550,24 +550,24 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               )
 
             cols <- c(getOption("ggplot2.discrete.colour"), c("lightblue", "darkred", "black"))[1:3]
-            g <- ggplot2::ggplot(mapping = ggplot2::aes_string(x = "component", y = "value")) +
-              ggplot2::geom_bar(
-                ggplot2::aes(fill = "Single variance"),
+            g <- ggplot(mapping = aes_string(x = "component", y = "value")) +
+              geom_bar(
+                aes(fill = "Single variance"),
                 data = dplyr::filter(elb_dat, metric == "Proportion of Variance"),
                 color = "black",
                 stat = "identity"
               ) +
-              ggplot2::geom_point(
-                ggplot2::aes(color = "Cumulative variance"),
+              geom_point(
+                aes(color = "Cumulative variance"),
                 data = dplyr::filter(elb_dat, metric == "Cumulative Proportion")
               ) +
-              ggplot2::geom_line(
-                ggplot2::aes(group = 1, color = "Cumulative variance"),
+              geom_line(
+                aes(group = 1, color = "Cumulative variance"),
                 data = dplyr::filter(elb_dat, metric == "Cumulative Proportion")
               ) +
               labs +
-              ggplot2::scale_color_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[3])) +
-              ggplot2::scale_fill_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[1])) +
+              scale_color_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[3])) +
+              scale_fill_manual(values = c("Cumulative variance" = cols[2], "Single variance" = cols[1])) +
               ggthemes +
               themes
 
@@ -597,9 +597,9 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       dev_ggplot2_args <- teal.widgets::ggplot2_args(
         theme = list(
-          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size)),
+          text = substitute(element_text(size = font_size), list(font_size = font_size)),
           axis.text.x = substitute(
-            ggplot2::element_text(angle = angle_val, hjust = hjust_val),
+            element_text(angle = angle_val, hjust = hjust_val),
             list(angle_val = angle, hjust_val = hjust)
           )
         )
@@ -629,15 +629,15 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               y = sin(seq(0, 2 * pi, length.out = 100))
             )
 
-            g <- ggplot2::ggplot(pca_rot) +
-              ggplot2::geom_point(ggplot2::aes_string(x = x_axis, y = y_axis)) +
-              ggplot2::geom_label(
-                ggplot2::aes_string(x = x_axis, y = y_axis, label = "label"),
+            g <- ggplot(pca_rot) +
+              geom_point(aes_string(x = x_axis, y = y_axis)) +
+              geom_label(
+                aes_string(x = x_axis, y = y_axis, label = "label"),
                 nudge_x = 0.1, nudge_y = 0.05,
                 fontface = "bold"
               ) +
-              ggplot2::geom_path(ggplot2::aes(x, y, group = 1), data = circle_data) +
-              ggplot2::geom_point(ggplot2::aes(x = x, y = y), data = data.frame(x = 0, y = 0), shape = "x", size = 5) +
+              geom_path(aes(x, y, group = 1), data = circle_data) +
+              geom_point(aes(x = x, y = y), data = data.frame(x = 0, y = 0), shape = "x", size = 5) +
               labs +
               ggthemes +
               themes
@@ -648,7 +648,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             y_axis = y_axis,
             variables = variables,
             ggthemes = parsed_ggplot2_args$ggtheme,
-            labs = `if`(is.null(parsed_ggplot2_args$labs), quote(ggplot2::labs()), parsed_ggplot2_args$labs),
+            labs = `if`(is.null(parsed_ggplot2_args$labs), quote(labs()), parsed_ggplot2_args$labs),
             themes = parsed_ggplot2_args$theme
           )
         )
@@ -694,7 +694,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
               rot_vars <- pca$rotation[, c(x_axis, y_axis)] %>%
                 dplyr::as_tibble(rownames = "label") %>%
-                dplyr::mutate_at(ggplot2::vars(c(x_axis, y_axis)), function(x) r * x / sqrt(max(v_scale)))
+                dplyr::mutate_at(vars(c(x_axis, y_axis)), function(x) r * x / sqrt(max(v_scale)))
             },
             env = list(x_axis = x_axis, y_axis = y_axis)
           )
@@ -726,14 +726,14 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
           )
       }
 
-      pca_plot_biplot_expr <- list(quote(ggplot2::ggplot()))
+      pca_plot_biplot_expr <- list(quote(ggplot()))
 
       if (length(resp_col) == 0) {
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            ggplot2::geom_point(
-              ggplot2::aes_string(x = x_axis, y = y_axis),
+            geom_point(
+              aes_string(x = x_axis, y = y_axis),
               data = pca_rot, alpha = alpha, size = size
             ),
             list(x_axis = input$x_axis, y_axis = input$y_axis, alpha = input$alpha, size = input$size)
@@ -746,7 +746,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         response <- ANL[[resp_col]]
 
         aes_biplot <- substitute(
-          ggplot2::aes_string(x = x_axis, y = y_axis, color = "response"),
+          aes_string(x = x_axis, y = y_axis, color = "response"),
           env = list(x_axis = x_axis, y_axis = y_axis)
         )
 
@@ -767,7 +767,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               qenv,
               quote(pca_rot$response <- as.factor(response))
             )
-            quote(ggplot2::scale_color_brewer(palette = "Dark2"))
+            quote(scale_color_brewer(palette = "Dark2"))
           } else if (inherits(response, "Date")) {
             qenv <- teal.code::eval_code(
               qenv,
@@ -775,7 +775,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             )
 
             quote(
-              ggplot2::scale_color_gradient(
+              scale_color_gradient(
                 low = c(getOption("ggplot2.discrete.colour")[2], "darkred")[1],
                 high = c(getOption("ggplot2.discrete.colour"), "lightblue")[1],
                 labels = function(x) as.Date(x, origin = "1970-01-01")
@@ -786,7 +786,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
               qenv,
               quote(pca_rot$response <- response)
             )
-            quote(ggplot2::scale_color_gradient(
+            quote(scale_color_gradient(
               low = c(getOption("ggplot2.discrete.colour")[2], "darkred")[1],
               high = c(getOption("ggplot2.discrete.colour"), "lightblue")[1]
             ))
@@ -795,7 +795,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            ggplot2::geom_point(aes_biplot, data = pca_rot, alpha = alpha, size = size),
+            geom_point(aes_biplot, data = pca_rot, alpha = alpha, size = size),
             env = list(aes_biplot = aes_biplot, alpha = alpha, size = size)
           ),
           scales_biplot
@@ -806,8 +806,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            ggplot2::geom_segment(
-              ggplot2::aes_string(x = "xstart", y = "ystart", xend = x_axis, yend = y_axis),
+            geom_segment(
+              aes_string(x = "xstart", y = "ystart", xend = x_axis, yend = y_axis),
               data = rot_vars,
               lineend = "round", linejoin = "round",
               arrow = grid::arrow(length = grid::unit(0.5, "cm"))
@@ -815,8 +815,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             env = list(x_axis = x_axis, y_axis = y_axis)
           ),
           substitute(
-            ggplot2::geom_label(
-              ggplot2::aes_string(
+            geom_label(
+              aes_string(
                 x = x_axis,
                 y = y_axis,
                 label = "label"
@@ -827,7 +827,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             ),
             env = list(x_axis = x_axis, y_axis = y_axis)
           ),
-          quote(ggplot2::geom_point(ggplot2::aes(x = xstart, y = ystart), data = rot_vars, shape = "x", size = 5))
+          quote(geom_point(aes(x = xstart, y = ystart), data = rot_vars, shape = "x", size = 5))
         )
       }
 
@@ -837,9 +837,9 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       dev_ggplot2_args <- teal.widgets::ggplot2_args(
         labs = dev_labs,
         theme = list(
-          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size)),
+          text = substitute(element_text(size = font_size), list(font_size = font_size)),
           axis.text.x = substitute(
-            ggplot2::element_text(angle = angle_val, hjust = hjust_val),
+            element_text(angle = angle_val, hjust = hjust_val),
             list(angle_val = angle, hjust_val = hjust)
           )
         )
@@ -888,9 +888,9 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       dev_ggplot2_args <- teal.widgets::ggplot2_args(
         theme = list(
-          text = substitute(ggplot2::element_text(size = font_size), list(font_size = font_size)),
+          text = substitute(element_text(size = font_size), list(font_size = font_size)),
           axis.text.x = substitute(
-            ggplot2::element_text(angle = angle_val, hjust = hjust_val),
+            element_text(angle = angle_val, hjust = hjust_val),
             list(angle_val = angle, hjust_val = hjust)
           )
         )
@@ -909,10 +909,10 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       ggplot_exprs <- c(
         list(
-          quote(ggplot2::ggplot(pca_rot)),
+          quote(ggplot(pca_rot)),
           substitute(
-            ggplot2::geom_bar(
-              ggplot2::aes_string(x = "Variable", y = pc),
+            geom_bar(
+              aes_string(x = "Variable", y = pc),
               stat = "identity",
               color = "black",
               fill = c(getOption("ggplot2.discrete.colour"), "lightblue")[1]
@@ -920,8 +920,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
             env = list(pc = pc)
           ),
           substitute(
-            ggplot2::geom_text(
-              ggplot2::aes(
+            geom_text(
+              aes(
                 x = Variable,
                 y = pc_name,
                 label = round(pc_name, 3),

From 2abbd29e3c8802071b08f3216dc74ff0b6df839b 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, 17 Apr 2024 10:10:49 +0200
Subject: [PATCH 18/25] chore: revert multiline to single line

---
 R/tm_a_pca.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
index 6fe0bd34f..20e2c1cb9 100644
--- a/R/tm_a_pca.R
+++ b/R/tm_a_pca.R
@@ -732,10 +732,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         pca_plot_biplot_expr <- c(
           pca_plot_biplot_expr,
           substitute(
-            geom_point(
-              aes_string(x = x_axis, y = y_axis),
-              data = pca_rot, alpha = alpha, size = size
-            ),
+            geom_point(aes_string(x = x_axis, y = y_axis), data = pca_rot, alpha = alpha, size = size),
             list(x_axis = input$x_axis, y_axis = input$y_axis, alpha = input$alpha, size = input$size)
           )
         )

From 65eab4e94ecfece2c1a71c3ef6a095e5cb527742 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, 17 Apr 2024 10:11:47 +0200
Subject: [PATCH 19/25] chore: revert change in comment

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

diff --git a/tests/testthat/helper-TealAppDriver.R b/tests/testthat/helper-TealAppDriver.R
index d2dc7fc70..39e5c28d9 100644
--- a/tests/testthat/helper-TealAppDriver.R
+++ b/tests/testthat/helper-TealAppDriver.R
@@ -1,7 +1,7 @@
 # Import non-exported TealAppDriver from `teal` package
 TealAppDriver <- getFromNamespace("TealAppDriver", "teal") # nolint: object_name.
 
-# Data helper functions for reusable datasets ---------------------------------
+# Helper function
 simple_teal_data <- function() {
   data <- within(teal.data::teal_data(), {
     require(nestcolor)

From a51e7450342c70a6297e3a76da52d2275f9a91b8 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, 17 Apr 2024 10:12:58 +0200
Subject: [PATCH 20/25] Apply suggestions from @m7pr on
 `set_active_module_input` rename
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
---
 tests/testthat/test-shinytest2-tm_a_pca.R | 50 +++++++++++------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 3e932547d..b329ef8af 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -32,7 +32,7 @@ testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigen
   app_driver <- app_driver_tm_a_pca()
 
   # Data selection (adds rows to tables)
-  app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
+  app_driver$set_active_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "Assault"), wait = FALSE)
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Assault")
@@ -47,9 +47,9 @@ testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes
 
   app_driver <- app_driver_tm_a_pca()
 
-  app_driver$set_module_input("plot_type", "Circle plot")
+  app_driver$set_active_module_input("plot_type", "Circle plot")
 
-  app_driver$set_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
+  app_driver$set_active_module_input("dat-dataset_USArrests_singleextract-select", c("Murder", "UrbanPop"))
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
@@ -60,13 +60,13 @@ testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be fro
 
   app_driver <- app_driver_tm_a_pca()
 
-  app_driver$set_module_input("plot_type", "Biplot")
+  app_driver$set_active_module_input("plot_type", "Biplot")
 
   # Change colors of data points
-  app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("UrbanPop"))
+  app_driver$set_active_module_input("response-dataset_USArrests_singleextract-select", c("UrbanPop"))
   app_driver$expect_no_validation_error()
 
-  app_driver$set_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
+  app_driver$set_active_module_input("response-dataset_USArrests_singleextract-select", c("Murder"))
   app_driver$expect_validation_error()
 
   app_driver$stop()
@@ -79,7 +79,7 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
 
   # Display section (hides tables)
 
-  app_driver$set_module_input("tables_display", c())
+  app_driver$set_active_module_input("tables_display", c())
   app_driver$expect_no_validation_error()
 
   testthat::expect_type(app_driver$get_active_module_output("tbl_importance"), "list")
@@ -91,31 +91,31 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
   # Plot type (select each)
 
   # Changing input will trigger an output change
-  app_driver$set_module_input("plot_type", "Circle plot")
+  app_driver$set_active_module_input("plot_type", "Circle plot")
   app_driver$expect_no_validation_error()
 
-  app_driver$set_module_input("plot_type", "Biplot")
+  app_driver$set_active_module_input("plot_type", "Biplot")
   app_driver$expect_no_validation_error()
 
-  app_driver$set_module_input("plot_type", "Eigenvector plot")
+  app_driver$set_active_module_input("plot_type", "Eigenvector plot")
   app_driver$expect_no_validation_error()
 
-  app_driver$set_module_input("plot_type", "Elbow plot") # Initial value
+  app_driver$set_active_module_input("plot_type", "Elbow plot") # Initial value
   app_driver$expect_no_validation_error()
 
   # Pre-processing
 
-  app_driver$set_module_input("standardization", "center")
+  app_driver$set_active_module_input("standardization", "center")
   app_driver$expect_no_validation_error
-  app_driver$set_module_input("standardization", "center_scale")
+  app_driver$set_active_module_input("standardization", "center_scale")
   app_driver$expect_no_validation_error
-  app_driver$set_module_input("standardization", "none") # Initial value
+  app_driver$set_active_module_input("standardization", "none") # Initial value
   app_driver$expect_no_validation_error
 
   # NA Action
 
-  app_driver$set_module_input("na_action", "drop")
-  app_driver$set_module_input("na_action", "none")
+  app_driver$set_active_module_input("na_action", "drop")
+  app_driver$set_active_module_input("na_action", "none")
 
   # Selected plot's specific settings is not visible
   no_plot_settings_selector <- sprintf("#%s-%s %s", app_driver$active_module_ns(), "plot_settings", "span.help-block")
@@ -126,38 +126,38 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
     "response-dataset_USArrests_singleextract-select_input"
   )
 
-  app_driver$set_module_input("plot_type", "Elbow plot", wait = FALSE)
+  app_driver$set_active_module_input("plot_type", "Elbow plot", wait = FALSE)
   testthat::expect_true(app_driver$is_visible(no_plot_settings_selector))
   testthat::expect_false(app_driver$is_visible(x_axis_selector))
   testthat::expect_false(app_driver$is_visible(color_by_selector))
 
-  app_driver$set_module_input("plot_type", "Circle plot", wait = FALSE)
+  app_driver$set_active_module_input("plot_type", "Circle plot", wait = FALSE)
   testthat::expect_false(app_driver$is_visible(no_plot_settings_selector))
   testthat::expect_true(app_driver$is_visible(x_axis_selector))
 
-  app_driver$set_module_input("plot_type", "Biplot", wait = FALSE)
+  app_driver$set_active_module_input("plot_type", "Biplot", wait = FALSE)
   testthat::expect_false(app_driver$is_visible(no_plot_settings_selector))
   testthat::expect_true(app_driver$is_visible(x_axis_selector))
   testthat::expect_true(app_driver$is_visible(color_by_selector))
 
   # Theme
 
-  app_driver$set_module_input("ggtheme-selectized", "bw")
+  app_driver$set_active_module_input("ggtheme-selectized", "bw")
   app_driver$expect_no_validation_error()
-  app_driver$set_module_input("ggtheme-selectized", "light")
+  app_driver$set_active_module_input("ggtheme-selectized", "light")
   app_driver$expect_no_validation_error()
-  app_driver$set_module_input("ggtheme-selectized", "dark")
+  app_driver$set_active_module_input("ggtheme-selectized", "dark")
   app_driver$expect_no_validation_error()
 
   # Font size
 
-  app_driver$set_module_input("font_size", "8")
+  app_driver$set_active_module_input("font_size", "8")
   app_driver$expect_no_validation_error()
 
-  app_driver$set_module_input("font_size", "20")
+  app_driver$set_active_module_input("font_size", "20")
   app_driver$expect_no_validation_error()
 
-  app_driver$set_module_input("font_size", "15")
+  app_driver$set_active_module_input("font_size", "15")
   app_driver$expect_no_validation_error()
 
   app_driver$stop()

From ce2a06eea1443206800d2b519e370e55efca742d 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, 17 Apr 2024 10:29:42 +0200
Subject: [PATCH 21/25] fix: replace TealAppDriver with init_teal_app_driver

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index b329ef8af..e537446b6 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -8,7 +8,7 @@ app_driver_tm_a_pca <- function() {
   teal.data::datanames(data) <- "USArrests"
 
 
-  TealAppDriver$new(
+  init_teal_app_driver(
     data = data,
     modules = tm_a_pca(
       dat = teal.transform::data_extract_spec(

From 98751d4d7c66e0e3e3817f4f7c6e66d1927b241e 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, 18 Apr 2024 13:59:53 +0200
Subject: [PATCH 22/25] Update tests/testthat/test-shinytest2-tm_a_pca.R
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-shinytest2-tm_a_pca.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index e537446b6..5bc15fee9 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -37,9 +37,7 @@ testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigen
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Assault")
 
-  testthat::expect_failure(
-    testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
-  )
+  testthat::expect_no_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
 })
 
 testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes output of plot", {

From 01b4b3b8cdfcce30d2b0e3feaff49595d8a33314 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, 18 Apr 2024 14:10:45 +0200
Subject: [PATCH 23/25] chore: split tests into multiple

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 89 ++++++++++++++++++++++-
 1 file changed, 85 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 5bc15fee9..073e8ae28 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -21,12 +21,45 @@ app_driver_tm_a_pca <- function() {
           selected = c("Murder", "Assault"),
           multiple = TRUE
         )
-      )
+      ),
+      size = c(3, 1, 5),
+      alpha = c(.5, 0, 1),
+      font_size = c(10, 8, 15),
+      ggtheme = "light",
+      rotate_xaxis_labels = TRUE,
+      pre_output = shiny::tags$div(id = "unique_id_pre", "A pre output"),
+      post_output = shiny::tags$div(id = "unique_id_post", "A post output")
     )
   )
 }
 
-testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigenvector table", {
+testthat::test_that("e2e - tm_a_pca: module is initialised with the specified defaults in function call", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
+
+  app_driver$expect_no_shiny_error()
+
+  testthat::expect_setequal(
+    app_driver$get_active_module_input("dat-dataset_USArrests_singleextract-select"),
+    c("Murder", "Assault")
+  )
+
+  module_parent_id <- gsub("-module$", "", app_driver$active_module_ns())
+  testthat::expect_equal(app_driver$get_text(sprintf("#%s %s", module_parent_id, "#unique_id_pre")), "A pre output")
+  testthat::expect_equal(app_driver$get_text(sprintf("#%s %s", module_parent_id, "#unique_id_post")), "A post output")
+
+  # Plot options that can be changed in call
+  testthat::expect_equal(app_driver$get_active_module_input("rotate_xaxis_labels"))
+  testthat::expect_equal(app_driver$get_active_module_input("ggtheme"), "light")
+  testthat::expect_equal(app_driver$get_active_module_input("font_size"), 10)
+
+  app_driver$stop()
+})
+
+# Data extract ----------------------------------------------------------------
+
+testthat::test_that("e2e - tm_a_pca: Eigenvector table should have data extract selection Murder/Assault on header", {
   skip_if_too_deep(5)
 
   app_driver <- app_driver_tm_a_pca()
@@ -36,11 +69,12 @@ testthat::test_that("e2e - tm_a_pca: Data selection (data_extract) changes eigen
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Assault")
+  testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Murder")
 
   testthat::expect_no_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
 })
 
-testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes output of plot", {
+testthat::test_that("e2e - tm_a_pca: Eigenvector table should have data extract selection Murder/UrbanPop on header", {
   skip_if_too_deep(5)
 
   app_driver <- app_driver_tm_a_pca()
@@ -51,6 +85,8 @@ testthat::test_that("e2e - tm_a_pca: Original coordinates (data_extract) changes
   app_driver$expect_no_validation_error()
 
   testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "UrbanPop")
+  testthat::expect_match(app_driver$get_active_module_output("tbl_eigenvector"), "Murder")
+  testthat::expect_no_match(app_driver$get_active_module_output("tbl_eigenvector"), "Assault")
 })
 
 testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be from non-selected variable set", {
@@ -70,21 +106,31 @@ testthat::test_that("e2e - tm_a_pca: Color by columns (data_extract) must be fro
   app_driver$stop()
 })
 
-testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate errors", {
+# Encodings -------------------------------------------------------------------
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings of tables_display does not generate errors", {
   skip_if_too_deep(5)
 
   app_driver <- app_driver_tm_a_pca()
+  app_driver$expect_no_validation_error()
 
   # Display section (hides tables)
 
   app_driver$set_active_module_input("tables_display", c())
   app_driver$expect_no_validation_error()
 
+  # Tables are removed from DOM (output should generate a silent error empty message)
   testthat::expect_type(app_driver$get_active_module_output("tbl_importance"), "list")
   testthat::expect_setequal(names(app_driver$get_active_module_output("tbl_importance")), c("message", "call", "type"))
 
   testthat::expect_type(app_driver$get_active_module_output("tbl_eigenvector"), "list")
   testthat::expect_setequal(names(app_driver$get_active_module_output("tbl_eigenvector")), c("message", "call", "type"))
+})
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings for 'plot type' does not generate errors", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
 
   # Plot type (select each)
 
@@ -100,6 +146,13 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
 
   app_driver$set_active_module_input("plot_type", "Elbow plot") # Initial value
   app_driver$expect_no_validation_error()
+})
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings of 'standardization' does not generate errors", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
+  app_driver$expect_no_validation_error()
 
   # Pre-processing
 
@@ -109,11 +162,25 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
   app_driver$expect_no_validation_error
   app_driver$set_active_module_input("standardization", "none") # Initial value
   app_driver$expect_no_validation_error
+})
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings of 'NA action' does not generate errors", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
+  app_driver$expect_no_validation_error()
 
   # NA Action
 
   app_driver$set_active_module_input("na_action", "drop")
   app_driver$set_active_module_input("na_action", "none")
+})
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings of 'plot_type' hides and shows options", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
+  app_driver$expect_no_validation_error()
 
   # Selected plot's specific settings is not visible
   no_plot_settings_selector <- sprintf("#%s-%s %s", app_driver$active_module_ns(), "plot_settings", "span.help-block")
@@ -137,6 +204,13 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
   testthat::expect_false(app_driver$is_visible(no_plot_settings_selector))
   testthat::expect_true(app_driver$is_visible(x_axis_selector))
   testthat::expect_true(app_driver$is_visible(color_by_selector))
+})
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings of 'theme' does not generate errors", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
+  app_driver$expect_no_validation_error()
 
   # Theme
 
@@ -146,6 +220,13 @@ testthat::test_that("e2e - tm_a_pca: Changing output encodings does not generate
   app_driver$expect_no_validation_error()
   app_driver$set_active_module_input("ggtheme-selectized", "dark")
   app_driver$expect_no_validation_error()
+})
+
+testthat::test_that("e2e - tm_a_pca: Changing output encodings of 'font size' does not generate errors", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_pca()
+  app_driver$expect_no_validation_error()
 
   # Font size
 

From f25df6e42629bd6ed93f4c023182af2bb402ae51 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, 18 Apr 2024 14:12:56 +0200
Subject: [PATCH 24/25] docs: adds a simple comment

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 073e8ae28..509a137e3 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -33,6 +33,8 @@ app_driver_tm_a_pca <- function() {
   )
 }
 
+# Defaults --------------------------------------------------------------------
+
 testthat::test_that("e2e - tm_a_pca: module is initialised with the specified defaults in function call", {
   skip_if_too_deep(5)
 

From 1428f582c5f1a01d0b32dd841c98636801d88842 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, 18 Apr 2024 14:50:16 +0200
Subject: [PATCH 25/25] fix: wrong expectation

---
 tests/testthat/test-shinytest2-tm_a_pca.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-shinytest2-tm_a_pca.R b/tests/testthat/test-shinytest2-tm_a_pca.R
index 509a137e3..8752a0ca9 100644
--- a/tests/testthat/test-shinytest2-tm_a_pca.R
+++ b/tests/testthat/test-shinytest2-tm_a_pca.R
@@ -52,7 +52,7 @@ testthat::test_that("e2e - tm_a_pca: module is initialised with the specified de
   testthat::expect_equal(app_driver$get_text(sprintf("#%s %s", module_parent_id, "#unique_id_post")), "A post output")
 
   # Plot options that can be changed in call
-  testthat::expect_equal(app_driver$get_active_module_input("rotate_xaxis_labels"))
+  testthat::expect_true(app_driver$get_active_module_input("rotate_xaxis_labels"))
   testthat::expect_equal(app_driver$get_active_module_input("ggtheme"), "light")
   testthat::expect_equal(app_driver$get_active_module_input("font_size"), 10)