Using teal_data in the modules instead of tdata (#344)

--------- Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Aleksander Chlebowski <[email protected]> Co-authored-by: unknown <[email protected]>
insightsengineering · Dec 8, 2023 · 6fb3af1 · 6fb3af1
1 parent a29dd97
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,7 @@ Depends:
     ggplot2,
     R (>= 3.6),
     shiny,
-    teal (>= 0.14.0.9019)
+    teal (>= 0.14.0.9027)
 Imports:
     checkmate,
     DT,
@@ -47,7 +47,7 @@ Imports:
     stats,
     stringr,
     SummarizedExperiment,
-    teal.data (>= 0.3.0.9010),
+    teal.data (>= 0.3.0.9018),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),

diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,7 @@
 ### Miscellaneous
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.
 * Disabled the select input for `assaySpec` and `adtteSpec` when there are no options available.
+* For module developers: The module gets `teal_data` object in the UI and `reactive(<teal_data>)` in the server
 
 ### Enhancements
 

diff --git a/R/adtteSpec.R b/R/adtteSpec.R
@@ -148,23 +148,27 @@ adtteSpecInput <- function(inputId, # nolint
 #' @export
 #'
 #' @examples
-#' ui <- function(id,
-#'                data) {
+#' ui <- function(id) {
 #'   ns <- NS(id)
 #'
 #'   teal.widgets::standard_layout(
-#'     encoding = div(
-#'       experimentSpecInput(ns("experiment"), data = data, mae_name = "MAE"),
-#'       assaySpecInput(ns("assay")),
-#'       geneSpecInput(ns("genes"), funs = list(Mean = colMeans)),
-#'       adtteSpecInput(ns("adtte"))
-#'     ),
+#'     encoding = uiOutput(ns("encoding_ui")),
 #'     output = verbatimTextOutput(ns("summary"))
 #'   )
 #' }
 #'
 #' server <- function(id, data, filter_panel_api) {
+#'   checkmate::assert_class(data, "reactive")
+#'   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 #'   moduleServer(id, function(input, output, session) {
+#'     output$encoding_ui <- renderUI({
+#'       div(
+#'         experimentSpecInput(session$ns("experiment"), data, mae_name = "MAE"),
+#'         assaySpecInput(session$ns("assay")),
+#'         geneSpecInput(session$ns("genes"), funs = list(Mean = colMeans)),
+#'         adtteSpecInput(session$ns("adtte"))
+#'       )
+#'     })
 #'     experiment <- experimentSpecServer(
 #'       "experiment",
 #'       data = data,
@@ -210,6 +214,7 @@ adtteSpecInput <- function(inputId, # nolint
 #' my_app <- function() {
 #'   data <- teal_data()
 #'   data <- within(data, {
+#'     ADSL <- teal.data::rADSL
 #'     ADTTE <- teal.modules.hermes::rADTTE %>%
 #'       dplyr::mutate(is_event = .data$CNSR == 0)
 #'     MAE <- hermes::multi_assay_experiment
@@ -254,6 +259,8 @@ adtteSpecServer <- function(id, # nolint
   assert_reactive(assay)
   assert_reactive(genes)
   assert_reactive(probs)
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     # Join ADTTE with gene data.
@@ -271,8 +278,8 @@ adtteSpecServer <- function(id, # nolint
         assay
       )
 
-      mae <- data[[mae_name]]()
-      adtte <- data[[adtte_name]]()
+      mae <- data()[[mae_name]]
+      adtte <- data()[[adtte_name]]
 
       mae[[experiment_name]] <- experiment_data
       h_km_mae_to_adtte(

diff --git a/R/argument_convention.R b/R/argument_convention.R
@@ -5,9 +5,9 @@
 #' The documentation to this function lists all the conventional arguments in
 #' `hermes` teal modules.
 #'
-#' @param data (`tdata`)\cr
-#'   `tdata` object which is automatically passed to the UI and server
-#'   functions, holding all the data sets provided in the app initialization.
+#' @param data (`reactive`)\cr
+#' `reactive(<teal_data>)` holding all the data sets provided
+#' during app initialization after going through the filters.
 #' @param label (`string`)\cr
 #'   menu item label of the module in the teal app.
 #' @param inputId (`string`)\cr

diff --git a/R/assaySpec.R b/R/assaySpec.R
@@ -44,27 +44,25 @@ assaySpecInput <- function(inputId, # nolint
 #' @export
 #'
 #' @examples
-#' ui <- function(id,
-#'                data) {
+#' ui <- function(id) {
 #'   ns <- NS(id)
 #'   teal.widgets::standard_layout(
-#'     encoding = div(
-#'       experimentSpecInput(
-#'         ns("experiment"),
-#'         data,
-#'         "MAE"
-#'       ),
-#'       assaySpecInput(
-#'         ns("assay"),
-#'         label_assays = "Please choose assay"
-#'       )
-#'     ),
+#'     encoding = uiOutput(ns("encoding_ui")),
 #'     output = textOutput(ns("result"))
 #'   )
 #' }
 #'
 #' server <- function(id, data, filter_panel_api) {
 #'   moduleServer(id, module = function(input, output, session) {
+#'     output$encoding_ui <- renderUI({
+#'       div(
+#'         experimentSpecInput(session$ns("experiment"), data, "MAE"),
+#'         assaySpecInput(
+#'           session$ns("assay"),
+#'           label_assays = "Please choose assay"
+#'         )
+#'       )
+#'     })
 #'     experiment <- experimentSpecServer(
 #'       id = "experiment",
 #'       data = data,

diff --git a/R/barplot.R b/R/barplot.R
@@ -66,7 +66,6 @@ tm_g_barplot <- function(label,
 #' @inheritParams module_arguments
 #' @export
 ui_g_barplot <- function(id,
-                         data,
                          mae_name,
                          summary_funs,
                          pre_output,
@@ -79,7 +78,7 @@ ui_g_barplot <- function(id,
       ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis of MAE:", tags$code(mae_name)),
-      experimentSpecInput(ns("experiment"), data, mae_name),
+      uiOutput(ns("experiment_ui")),
       assaySpecInput(ns("assay")),
       sampleVarSpecInput(ns("facet"), "Select Facet Variable"),
       geneSpecInput(ns("x"), summary_funs),
@@ -120,8 +119,12 @@ srv_g_barplot <- function(id,
                           summary_funs) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    output$experiment_ui <- renderUI({
+      experimentSpecInput(session$ns("experiment"), data, mae_name)
+    })
     experiment <- experimentSpecServer(
       "experiment",
       data = data,

diff --git a/R/boxplot.R b/R/boxplot.R
@@ -67,7 +67,6 @@ tm_g_boxplot <- function(label,
 #' @inheritParams module_arguments
 #' @export
 ui_g_boxplot <- function(id,
-                         data,
                          mae_name,
                          summary_funs,
                          pre_output,
@@ -80,7 +79,7 @@ ui_g_boxplot <- function(id,
       ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis of MAE:", tags$code(mae_name)),
-      experimentSpecInput(ns("experiment"), data, mae_name),
+      uiOutput(ns("experiment_ui")),
       assaySpecInput(ns("assay")),
       geneSpecInput(ns("genes"), summary_funs),
       tags$label("Jitter"),
@@ -116,9 +115,13 @@ srv_g_boxplot <- function(id,
                           summary_funs) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$experiment_ui <- renderUI({
+      experimentSpecInput(session$ns("experiment"), data, mae_name)
+    })
     experiment <- experimentSpecServer(
       "experiment",
       data = data,

diff --git a/R/experimentSpec.R b/R/experimentSpec.R
@@ -17,7 +17,7 @@ experimentSpecInput <- function(inputId, # nolint
   assert_string(inputId)
   assert_string(mae_name, min.chars = 1L)
   assert_string(label_experiments, min.chars = 1L)
-  mae <- data[[mae_name]]()
+  mae <- data()[[mae_name]]
   name_choices <- names(mae)
 
   ns <- NS(inputId)
@@ -210,7 +210,8 @@ experimentSpecServer <- function(id, # nolint
                                  sample_vars_as_factors = TRUE,
                                  with_mae_col_data = TRUE) {
   assert_string(id)
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
   assert_string(mae_name, min.chars = 1L)
   assert_string(name_annotation, min.chars = 1L, null.ok = TRUE)
   assert_flag(sample_vars_as_factors)
@@ -222,7 +223,7 @@ experimentSpecServer <- function(id, # nolint
     data_return <- reactive({
       name <- input$name
       req(name)
-      mae <- data[[mae_name]]()
+      mae <- data()[[mae_name]]
       orig_object <- mae[[name]]
       validate(need(
         hermes::is_hermes_data(orig_object),

diff --git a/R/forestplot.R b/R/forestplot.R
@@ -92,7 +92,6 @@ tm_g_forest_tte <- function(label,
 #' @inheritParams module_arguments
 #' @export
 ui_g_forest_tte <- function(id,
-                            data,
                             adtte_name,
                             mae_name,
                             summary_funs,
@@ -106,7 +105,7 @@ ui_g_forest_tte <- function(id,
       ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis of MAE:", tags$code(mae_name)),
-      experimentSpecInput(ns("experiment"), data, mae_name),
+      uiOutput(ns("experiment_ui")),
       assaySpecInput(ns("assay")),
       geneSpecInput(ns("genes"), summary_funs),
       helpText("Analysis of ADTTE:", tags$code(adtte_name)),
@@ -143,9 +142,13 @@ srv_g_forest_tte <- function(id,
                              plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$experiment_ui <- renderUI({
+      experimentSpecInput(session$ns("experiment"), data, mae_name)
+    })
     experiment <- experimentSpecServer(
       "experiment",
       data = data,

diff --git a/R/geneSpec.R b/R/geneSpec.R
@@ -219,9 +219,7 @@ h_parse_genes <- function(words, choices) {
 #' @export
 #'
 #' @examples
-#' ui <- function(id,
-#'                data,
-#'                funs) {
+#' ui <- function(id, funs) {
 #'   ns <- NS(id)
 #'   teal.widgets::standard_layout(
 #'     encoding = div(
@@ -237,9 +235,11 @@ h_parse_genes <- function(words, choices) {
 #' server <- function(id,
 #'                    data,
 #'                    funs) {
+#'   checkmate::assert_class(data, "reactive")
+#'   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 #'   moduleServer(id, function(input, output, session) {
 #'     gene_choices <- reactive({
-#'       mae <- data[["MAE"]]()
+#'       mae <- data()[["MAE"]]
 #'       object <- mae[[1]]
 #'       gene_ids <- rownames(object)
 #'       gene_names <- SummarizedExperiment::rowData(object)$symbol

diff --git a/R/km.R b/R/km.R
@@ -93,22 +93,20 @@ tm_g_km <- function(label,
 #' @inheritParams module_arguments
 #' @export
 ui_g_km <- function(id,
-                    data,
                     adtte_name,
                     mae_name,
                     summary_funs,
                     pre_output,
                     post_output) {
   ns <- NS(id)
-
   teal.widgets::standard_layout(
     encoding = div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis of MAE:", tags$code(mae_name)),
-      experimentSpecInput(ns("experiment"), data, mae_name),
+      uiOutput(ns("experiment_ui")),
       assaySpecInput(ns("assay")),
       geneSpecInput(ns("genes"), summary_funs),
       helpText("Analysis of ADTTE:", tags$code(adtte_name)),
@@ -149,9 +147,13 @@ srv_g_km <- function(id,
                      exclude_assays) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$experiment_ui <- renderUI({
+      experimentSpecInput(session$ns("experiment"), data, mae_name)
+    })
     experiment <- experimentSpecServer(
       "experiment",
       data = data,

diff --git a/R/pca.R b/R/pca.R
@@ -57,13 +57,10 @@ tm_g_pca <- function(label,
 #' @inheritParams module_arguments
 #' @export
 ui_g_pca <- function(id,
-                     data,
                      mae_name,
                      pre_output,
                      post_output) {
   ns <- NS(id)
-  mae <- data[[mae_name]]()
-  experiment_name_choices <- names(mae)
 
   tagList(
     teal.widgets::standard_layout(
@@ -74,7 +71,7 @@ ui_g_pca <- function(id,
         ###
         tags$label("Encodings", class = "text-primary"),
         helpText("Analysis of MAE:", tags$code(mae_name)),
-        experimentSpecInput(ns("experiment"), data, mae_name),
+        uiOutput(ns("experiment_ui")),
         assaySpecInput(ns("assay")),
         conditionalPanel(
           condition = "input.tab_selected == 'PCA'",
@@ -160,9 +157,13 @@ srv_g_pca <- function(id,
                       exclude_assays) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$experiment_ui <- renderUI({
+      experimentSpecInput(session$ns("experiment"), data, mae_name)
+    })
     experiment <- experimentSpecServer(
       "experiment",
       data = data,

diff --git a/R/quality.R b/R/quality.R
@@ -111,7 +111,6 @@ tm_g_quality <- function(label,
 #' @inheritParams module_arguments
 #' @export
 ui_g_quality <- function(id,
-                         data,
                          mae_name,
                          pre_output,
                          post_output) {
@@ -123,7 +122,7 @@ ui_g_quality <- function(id,
       ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis of MAE:", tags$code(mae_name)),
-      experimentSpecInput(ns("experiment"), data, mae_name),
+      uiOutput(ns("experiment_ui")),
       selectInput(
         ns("plot_type"),
         "Plot Type",
@@ -200,9 +199,13 @@ srv_g_quality <- function(id,
                           exclude_assays) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
-  assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$experiment_ui <- renderUI({
+      experimentSpecInput(session$ns("experiment"), data, mae_name)
+    })
     experiment <- experimentSpecServer(
       "experiment",
       data = data,