Unify plot and table namespaces

R/tm_a_gee.R

@@ -263,7 +263,7 @@ ui_gee <- function(id, ...) {
   teal.widgets::standard_layout(
     output = teal.widgets::white_small_well(
       tags$h3(textOutput(ns("gee_title"))),
-      teal.widgets::table_with_settings_ui(ns("table"))
+      tmctable_with_settings_ui()
     ),
     encoding = tags$div(
       ### Reporter
@@ -389,7 +389,7 @@ srv_gee <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     ## split_covariates ----
     observeEvent(input[[extract_input("cov_var", dataname)]],
       ignoreNULL = FALSE,
@@ -547,10 +547,7 @@ srv_gee <- function(id,
       table_q()[["result_table"]]
     })
 
-    teal.widgets::table_with_settings_srv(
-      id = "table",
-      table_r = table_r
-    )
+    tmctable_with_settings_srv(table_r = table_r)
 
     # Render R code
     teal.widgets::verbatim_popup_srv(

R/tm_a_mmrm.R

@@ -623,8 +623,8 @@ ui_mmrm <- function(id, ...) {
       output = teal.widgets::white_small_well(
         textOutput(ns("null_input_msg")),
         tags$h3(textOutput(ns("mmrm_title"))),
-        teal.widgets::table_with_settings_ui(ns("mmrm_table")),
-        teal.widgets::plot_with_settings_ui(id = ns("mmrm_plot"))
+        tmctable_with_settings_ui(),
+        tmcplot_with_settings_ui()
       ),
       encoding = tags$div(
         ### Reporter
@@ -845,7 +845,7 @@ srv_mmrm <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     # Reactive responsible for sending a disable/enable signal
     # to show R code and debug info buttons
     disable_r_code <- reactiveVal(FALSE)
@@ -1004,9 +1004,9 @@ srv_mmrm <- function(id,
       output_function <- input$output_function
       if (isTRUE(grepl("^t_", output_function))) {
         show_plot_rv(FALSE)
-        shinyjs::show("mmrm_table")
+        shinyjs::show("table")
       } else if (isTRUE(grepl("^g_", output_function))) {
-        shinyjs::hide("mmrm_table")
+        shinyjs::hide("table")
         show_plot_rv(TRUE)
       } else {
         stop("unknown output type")
@@ -1420,16 +1420,14 @@ srv_mmrm <- function(id,
       )
     })
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "mmrm_plot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width,
       show_hide_signal = reactive(show_plot_rv())
     )
 
-    teal.widgets::table_with_settings_srv(
-      id = "mmrm_table",
+    tmctable_with_settings_srv(
       table_r = table_r,
       show_hide_signal = reactive(!show_plot_rv())
     )

R/tm_g_barchart_simple.R

@@ -204,7 +204,7 @@ ui_g_barchart_simple <- function(id, ...) {
     ),
     teal.widgets::standard_layout(
       output = teal.widgets::white_small_well(
-        teal.widgets::plot_with_settings_ui(id = ns("myplot")),
+        tmcplot_with_settings_ui(),
         uiOutput(ns("table"), class = "overflow-y-scroll max-h-250")
       ),
       encoding = tags$div(
@@ -339,7 +339,8 @@ srv_g_barchart_simple <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+
+    tmc_track_shiny_input_changes(input)
     rule_dupl <- function(others) {
       function(value) {
         othervals <- lapply(
@@ -535,8 +536,7 @@ srv_g_barchart_simple <- function(id,
     }
 
     # Insert the plot into a plot with settings module from teal.widgets
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_ci.R

@@ -319,7 +319,7 @@ ui_g_ci <- function(id, ...) {
   args <- list(...)
 
   teal.widgets::standard_layout(
-    output = teal.widgets::plot_with_settings_ui(id = ns("myplot")),
+    output = tmcplot_with_settings_ui(),
     encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
@@ -382,7 +382,7 @@ srv_g_ci <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(x_var = x_var, y_var = y_var, color = color),
       datasets = data,
@@ -473,8 +473,7 @@ srv_g_ci <- function(id,
       title = label
     )
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_forest_rsp.R

@@ -398,7 +398,7 @@ ui_g_forest_rsp <- function(id, ...) {
   ns <- NS(id)
 
   teal.widgets::standard_layout(
-    output = teal.widgets::plot_with_settings_ui(id = ns("myplot")),
+    output = tmcplot_with_settings_ui(),
     encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
@@ -508,7 +508,7 @@ srv_g_forest_rsp <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     # Setup arm variable selection, default reference arms, and default
     # comparison arms for encoding panel
     iv_arm_ref <- arm_ref_comp_observer(
@@ -733,8 +733,7 @@ srv_g_forest_rsp <- function(id,
 
     plot_r <- reactive(all_q()[["p"]])
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_forest_tte.R

@@ -387,7 +387,7 @@ ui_g_forest_tte <- function(id, ...) {
   ns <- NS(id)
 
   teal.widgets::standard_layout(
-    output = teal.widgets::plot_with_settings_ui(id = ns("myplot")),
+    output = tmcplot_with_settings_ui(),
     encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
@@ -502,7 +502,7 @@ srv_g_forest_tte <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     # Setup arm variable selection, default reference arms, and default
     # comparison arms for encoding panel
     iv_arm_ref <- arm_ref_comp_observer(
@@ -658,8 +658,7 @@ srv_g_forest_tte <- function(id,
     # Outputs to render.
     plot_r <- reactive(all_q()[["p"]])
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_ipp.R

@@ -373,7 +373,7 @@ ui_g_ipp <- function(id, ...) {
   ns <- NS(id)
 
   teal.widgets::standard_layout(
-    output = teal.widgets::plot_with_settings_ui(id = ns("myplot")),
+    output = tmcplot_with_settings_ui(),
     encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
@@ -482,7 +482,7 @@ srv_g_ipp <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     selector_list <- teal.transform::data_extract_multiple_srv(
       datasets = data,
       data_extract = list(
@@ -610,8 +610,7 @@ srv_g_ipp <- function(id,
     plot_r <- reactive(all_q()[["plot"]])
 
     # Insert the plot into a plot with settings module from teal.widgets
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_km.R

@@ -435,9 +435,7 @@ ui_g_km <- function(id, ...) {
   teal.widgets::standard_layout(
     output = teal.widgets::white_small_well(
       verbatimTextOutput(outputId = ns("text")),
-      teal.widgets::plot_with_settings_ui(
-        id = ns("myplot")
-      )
+      tmcplot_with_settings_ui()
     ),
     encoding = tags$div(
       ### Reporter
@@ -637,7 +635,7 @@ srv_g_km <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     # Setup arm variable selection, default reference arms and default
     # comparison arms for encoding panel
     iv_arm_ref <- arm_ref_comp_observer(
@@ -807,8 +805,7 @@ srv_g_km <- function(id,
     plot_r <- reactive(all_q()[["plot"]])
 
     # Insert the plot into a plot with settings module from teal.widgets
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_lineplot.R

@@ -353,9 +353,7 @@ ui_g_lineplot <- function(id, ...) {
   teal.widgets::standard_layout(
     output = teal.widgets::white_small_well(
       verbatimTextOutput(outputId = ns("text")),
-      teal.widgets::plot_with_settings_ui(
-        id = ns("myplot")
-      )
+      tmcplot_with_settings_ui()
     ),
     encoding = tags$div(
       ### Reporter
@@ -516,7 +514,7 @@ srv_g_lineplot <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(x = x, y = y, strata = strata, paramcd = paramcd, y_unit = y_unit, param = param),
       datasets = data,
@@ -627,8 +625,7 @@ srv_g_lineplot <- function(id,
     plot_r <- reactive(all_q()[["plot"]])
 
     # Insert the plot into a plot with settings module from teal.widgets
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "myplot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_pp_adverse_events.R

@@ -335,7 +335,7 @@ ui_g_adverse_events <- function(id, ...) {
       htmlOutput(ns("title")),
       teal.widgets::get_dt_rows(ns("table"), ns("table_rows")),
       DT::DTOutput(outputId = ns("table")),
-      teal.widgets::plot_with_settings_ui(id = ns("chart"))
+      tmcplot_with_settings_ui()
     ),
     encoding = tags$div(
       ### Reporter
@@ -442,7 +442,7 @@ srv_g_adverse_events <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     patient_id <- reactive(input$patient_id)
 
     # Init
@@ -564,8 +564,7 @@ srv_g_adverse_events <- function(id,
       all_q()[["plot"]]
     })
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "chart",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_pp_patient_timeline.R

@@ -562,7 +562,7 @@ ui_g_patient_timeline <- function(id, ...) {
 
   ns <- NS(id)
   teal.widgets::standard_layout(
-    output = teal.widgets::plot_with_settings_ui(id = ns("patient_timeline_plot")),
+    output = tmcplot_with_settings_ui(),
     encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
@@ -713,7 +713,7 @@ srv_g_patient_timeline <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     patient_id <- reactive(input$patient_id)
 
     # Init
@@ -903,10 +903,9 @@ srv_g_patient_timeline <- function(id,
       teal.code::eval_code(object = qenv, as.expression(patient_timeline_calls))
     })
 
-    plot_r <- reactive(all_q()[["patient_timeline_plot"]])
+    plot_r <- reactive(all_q()[["tmcplot"]])
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "patient_timeline_plot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width

R/tm_g_pp_therapy.R

@@ -432,7 +432,7 @@ ui_g_therapy <- function(id, ...) {
       htmlOutput(ns("title")),
       teal.widgets::get_dt_rows(ns("therapy_table"), ns("therapy_table_rows")),
       DT::DTOutput(outputId = ns("therapy_table")),
-      teal.widgets::plot_with_settings_ui(id = ns("therapy_plot"))
+      tmcplot_with_settings_ui()
     ),
     encoding = tags$div(
       ### Reporter
@@ -557,7 +557,7 @@ srv_g_therapy <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
-    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
+    tmc_track_shiny_input_changes(input)
     patient_id <- reactive(input$patient_id)
 
     # Init
@@ -681,11 +681,10 @@ srv_g_therapy <- function(id,
 
     plot_r <- reactive({
       req(iv_r()$is_valid())
-      all_q()[["therapy_plot"]]
+      all_q()[["tmcplot"]]
     })
 
-    pws <- teal.widgets::plot_with_settings_srv(
-      id = "therapy_plot",
+    pws <- tmcplot_with_settings_srv(
       plot_r = plot_r,
       height = plot_height,
       width = plot_width