Merge branch 'main' into fix_scheduled

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.goshawk
 Title: Longitudinal Visualization `teal` Modules
-Version: 0.2.0.9021
-Date: 2025-01-15
+Version: 0.2.0.9022
+Date: 2025-01-21
 Authors@R: c(
     person("Nick", "Paszty", , "[email protected]", role = c("aut", "cre")),
     person("Dawid", "Kaledkowski", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,4 @@
-# teal.goshawk 0.2.0.9021
+# teal.goshawk 0.2.0.9022
 
 # teal.goshawk 0.2.0
 

R/tm_g_gh_boxplot.R

@@ -37,6 +37,7 @@
 #' @param alpha numeric vector to define transparency of plotted points.
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #'
 #' @author Jeff Tomlinson (tomlinsj) [email protected]
 #' @author Balazs Toth (tothb2) [email protected]
@@ -168,7 +169,8 @@ tm_g_gh_boxplot <- function(label,
                             dot_size = c(2, 1, 12),
                             alpha = c(0.8, 0.0, 1.0),
                             pre_output = NULL,
-                            post_output = NULL) {
+                            post_output = NULL,
+                            transformators = list()) {
   message("Initializing tm_g_gh_boxplot")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
@@ -212,7 +214,8 @@ tm_g_gh_boxplot <- function(label,
       module_args = args
     ),
     ui = ui_g_boxplot,
-    ui_args = args
+    ui_args = args,
+    transformators = transformators
   )
 }
 

R/tm_g_gh_correlationplot.R

@@ -3,6 +3,7 @@
 #' @description Scatter Plot Teal Module For Biomarker Analysis
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @param label menu item label of the module in the teal app.
 #' @param dataname analysis data passed to the data argument of \code{\link[teal]{init}}. E.g. `ADaM` structured
 #' laboratory data frame \code{ADLB}.
@@ -220,7 +221,8 @@ tm_g_gh_correlationplot <- function(label,
                                     dot_size = c(1, 1, 12),
                                     reg_text_size = c(3, 3, 10),
                                     pre_output = NULL,
-                                    post_output = NULL) {
+                                    post_output = NULL,
+                                    transformators = list()) {
   message("Initializing tm_g_gh_correlationplot")
   checkmate::assert_class(xaxis_param, "choices_selected")
   checkmate::assert_class(yaxis_param, "choices_selected")
@@ -264,7 +266,8 @@ tm_g_gh_correlationplot <- function(label,
       module_args = args
     ),
     ui = ui_g_correlationplot,
-    ui_args = args
+    ui_args = args,
+    transformators = transformators
   )
 }
 

R/tm_g_gh_density_distribution_plot.R

@@ -23,6 +23,7 @@
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams tm_g_gh_scatterplot
+#' @inheritParams teal::module
 #'
 #'
 #' @author Nick Paszty (npaszty) [email protected]
@@ -129,7 +130,8 @@ tm_g_gh_density_distribution_plot <- function(label, # nolint
                                               comb_line = TRUE,
                                               rotate_xlab = FALSE,
                                               pre_output = NULL,
-                                              post_output = NULL) {
+                                              post_output = NULL,
+                                              transformators = list()) {
   message("Initializing tm_g_gh_density_distribution_plot")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
@@ -168,7 +170,8 @@ tm_g_gh_density_distribution_plot <- function(label, # nolint
       module_args = args
     ),
     ui = ui_g_density_distribution_plot,
-    ui_args = args
+    ui_args = args,
+    transformators = transformators
   )
 }
 

R/tm_g_gh_lineplot.R

@@ -3,6 +3,7 @@
 #' This teal module renders the UI and calls the function that creates a line plot.
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @param label menu item label of the module in the teal app.
 #' @param dataname analysis data passed to the data argument of \code{\link[teal]{init}}. E.g. `ADaM` structured
 #' laboratory data frame `ADLB`.
@@ -155,7 +156,8 @@ tm_g_gh_lineplot <- function(label,
                              count_threshold = 0,
                              table_font_size = c(12, 4, 20),
                              dot_size = c(2, 1, 12),
-                             plot_relative_height_value = 1000) {
+                             plot_relative_height_value = 1000,
+                             transformators = list()) {
   message("Initializing tm_g_gh_lineplot")
   # Validate string inputs
   checkmate::assert_string(label)
@@ -220,6 +222,7 @@ tm_g_gh_lineplot <- function(label,
     ),
     ui = ui_lineplot,
     ui_args = args,
+    transformators = transformators,
     datanames = dataname
   )
 }

R/tm_g_gh_scatterplot.R

@@ -7,6 +7,7 @@
 #'   instead.
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @param label menu item label of the module in the teal app.
 #' @param dataname analysis data passed to the data argument of \code{\link[teal]{init}}. E.g. `ADaM` structured
 #' laboratory data frame \code{ADLB}.
@@ -138,7 +139,8 @@ tm_g_gh_scatterplot <- function(label,
                                 dot_size = c(1, 1, 12),
                                 reg_text_size = c(3, 3, 10),
                                 pre_output = NULL,
-                                post_output = NULL) {
+                                post_output = NULL,
+                                transformators = list()) {
   lifecycle::deprecate_soft(
     when = "0.1.15",
     what = "tm_g_gh_scatterplot()",
@@ -178,7 +180,8 @@ tm_g_gh_scatterplot <- function(label,
       module_args = args
     ),
     ui = ui_g_scatterplot,
-    ui_args = args
+    ui_args = args,
+    transformators = transformators
   )
 }
 

R/tm_g_gh_spaghettiplot.R

@@ -46,6 +46,7 @@
 #' @param hline_vars_colors a character vector naming the colors for the additional horizontal lines.
 #' @param hline_vars_labels a character vector naming the labels for the additional horizontal lines that will appear
 #'  in the legend.
+#' @inheritParams teal::module
 #' @inheritParams teal.widgets::standard_layout
 #'
 #' @author Wenyi Liu (luiw2) [email protected]
@@ -188,7 +189,8 @@ tm_g_gh_spaghettiplot <- function(label,
                                   hline_vars_colors = "green",
                                   hline_vars_labels = hline_vars,
                                   pre_output = NULL,
-                                  post_output = NULL) {
+                                  post_output = NULL,
+                                  transformators = list()) {
   message("Initializing tm_g_gh_spaghettiplot")
 
   # Validate string inputs
@@ -258,6 +260,7 @@ tm_g_gh_spaghettiplot <- function(label,
     ),
     ui = g_ui_spaghettiplot,
     ui_args = args,
+    transformators = transformators,
     datanames = dataname
   )
 }