Merge branch 'main' into 495_plot_missing@main

m7pr · web-flow · commit 56020d4ab0d3 · 2025-10-08T11:45:19.000+02:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.5.0.9004
-Date: 2025-10-01
+Version: 0.5.0.9005
+Date: 2025-10-07
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.modules.general 0.5.0.9004
+# teal.modules.general 0.5.0.9005
 
 ### Enhancements
 
diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
@@ -341,9 +341,6 @@ ui_a_pca <- function(id, ...) {
           )
         )
       ),
-      forms = tagList(
-        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-      ),
       pre_output = args$pre_output,
       post_output = args$post_output
     )
@@ -1080,8 +1077,6 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
       graph_align = "center"
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)
-
     # tables ----
     output$tbl_importance <- renderTable(
       expr = {
@@ -1135,14 +1130,6 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
       )
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R Code for PCA"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q)
   })
 }
diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R
@@ -374,9 +374,6 @@ ui_a_regression <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -1021,22 +1018,12 @@ srv_a_regression <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)
-
     output$text <- renderText({
       req(iv_r()$is_valid())
       req(iv_out$is_valid())
       paste(utils::capture.output(summary(fitted()))[-1], collapse = "\n")
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R code for the regression plot",
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q)
   })
 }
diff --git a/R/tm_g_association.R b/R/tm_g_association.R
@@ -289,9 +289,6 @@ ui_tm_g_association <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -545,18 +542,8 @@ srv_tm_g_association <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_grob_q)
-
     output$title <- renderText(output_q()[["title"]])
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Association Plot"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_grob_q)
   })
 }
diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
@@ -466,9 +466,6 @@ ui_g_bivariate <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -737,18 +734,7 @@ srv_g_bivariate <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q_facets)
-
-    # Render R code.
-
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Bivariate Plot"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q_facets)
   })
 }
 
diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R
@@ -377,9 +377,6 @@ ui_distribution <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -1402,14 +1399,6 @@ srv_distribution <- function(id,
 
     output$t_stats <- DT::renderDataTable(tests_r())
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R Code for distribution"
-    )
     decorated_output_q
   })
 }
diff --git a/R/tm_g_response.R b/R/tm_g_response.R
@@ -320,9 +320,6 @@ ui_g_response <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -594,16 +591,6 @@ srv_g_response <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_plot_q)
-
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Show R Code for Response"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_plot_q)
   })
 }
diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R
@@ -495,9 +495,6 @@ ui_g_scatterplot <- function(id, ...) {
           )
         )
       ),
-      forms = tagList(
-        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-      ),
       pre_output = args$pre_output,
       post_output = args$post_output
     )
@@ -1037,8 +1034,6 @@ srv_g_scatterplot <- function(id,
       brushing = TRUE
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_plot_q)
-
     output$data_table <- DT::renderDataTable({
       plot_brush <- pws$brush()
 
@@ -1067,14 +1062,6 @@ srv_g_scatterplot <- function(id,
       }
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R Code for scatterplot"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_plot_q)
   })
 }
diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R
@@ -288,9 +288,6 @@ ui_g_scatterplotmatrix <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -479,8 +476,6 @@ srv_g_scatterplotmatrix <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)
-
     # show a message if conversion to factors took place
     output$message <- renderText({
       req(iv_r()$is_valid())
@@ -503,15 +498,7 @@ srv_g_scatterplotmatrix <- function(id,
       }
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Show R Code for Scatterplotmatrix"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q)
   })
 }
 
diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R
@@ -191,7 +191,6 @@ ui_page_missing_data <- function(id, pre_output = NULL, post_output = NULL) {
       encoding = tags$div(
         uiOutput(ns("dataset_encodings"))
       ),
-      uiOutput(ns("dataset_reporter")),
       pre_output = pre_output,
       post_output = post_output
     )
@@ -250,19 +249,6 @@ srv_page_missing_data <- function(id, data, datanames, parent_dataname,
       )
     })
 
-    output$dataset_reporter <- renderUI({
-      lapply(datanames, function(x) {
-        dataname_ns <- NS(ns(x))
-
-        conditionalPanel(
-          is_tab_active_js(ns("dataname_tab"), x),
-          tagList(
-            teal.widgets::verbatim_popup_ui(dataname_ns("rcode"), "Show R code")
-          )
-        )
-      })
-    })
-
     result <- sapply(
       datanames,
       function(x) {
@@ -728,7 +714,7 @@ srv_missing_data <- function(id,
     # Prepare qenvs for output objects
 
     summary_plot_q <- reactive({
-      req(input$summary_type == "Summary") # needed to trigger show r code update on tab change
+      req(input$summary_type == "Summary") # needed to trigger update on tab change
       teal::validate_has_data(data_r(), 1)
 
       qenv <- common_code_q()
@@ -1072,7 +1058,7 @@ srv_missing_data <- function(id,
 
     by_variable_plot_q <- reactive({
       req(
-        input$summary_type == "By Variable Levels", # needed to trigger show r code update on tab change
+        input$summary_type == "By Variable Levels", # needed to trigger update on tab change
         common_code_q()
       )
       teal::validate_has_data(data_r(), 1)
@@ -1235,7 +1221,7 @@ srv_missing_data <- function(id,
     })
 
     by_subject_plot_q <- reactive({
-      # needed to trigger show r code update on tab change
+      # needed to trigger update on tab change
       req(input$summary_type == "Grouped by Subject", common_code_q())
 
       teal::validate_has_data(data_r(), 1)
@@ -1462,14 +1448,6 @@ srv_missing_data <- function(id,
       }
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_final_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Show R Code for Missing Data"
-    )
     decorated_final_q
   })
 }
diff --git a/R/tm_outliers.R b/R/tm_outliers.R
@@ -374,9 +374,6 @@ ui_outliers <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -1336,14 +1333,6 @@ srv_outliers <- function(id, data, outlier_var,
       )
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_final_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Show R Code for Outlier"
-    )
     decorated_final_q
   })
 }
diff --git a/R/tm_t_crosstable.R b/R/tm_t_crosstable.R
@@ -264,9 +264,6 @@ ui_t_crosstable <- function(id, x, y, show_percentage, show_total, remove_zero_c
       ),
       ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(args$decorators, "table"))
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = pre_output,
     post_output = post_output
   )
@@ -482,14 +479,6 @@ srv_t_crosstable <- function(id, data, label, x, y, remove_zero_columns, basic_t
       table_r = table_r
     )
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Show R Code for Cross-Table"
-    )
     decorated_output_q
   })
 }

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# teal.modules.general 0.5.0.9004`
	`1`	`+# teal.modules.general 0.5.0.9005`
`2`	`2`
`3`	`3`	`### Enhancements`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -341,9 +341,6 @@ ui_a_pca <- function(id, ...) {`
`341`	`341`	`)`
`342`	`342`	`)`
`343`	`343`	`),`
`344`		`- forms = tagList(`
`345`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`346`		`- ),`
`347`	`344`	`pre_output = args$pre_output,`
`348`	`345`	`post_output = args$post_output`
`349`	`346`	`)`
`@@ -1080,8 +1077,6 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco`
`1080`	`1077`	`graph_align = "center"`
`1081`	`1078`	`)`
`1082`	`1079`
`1083`		`- decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)`
`1084`		`-`
`1085`	`1080`	`# tables ----`
`1086`	`1081`	`output$tbl_importance <- renderTable(`
`1087`	`1082`	`expr = {`
`@@ -1135,14 +1130,6 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco`
`1135`	`1130`	`)`
`1136`	`1131`	`})`
`1137`	`1132`
`1138`		`- # Render R code.`
`1139`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))`
`1140`		`-`
`1141`		`- teal.widgets::verbatim_popup_srv(`
`1142`		`- id = "rcode",`
`1143`		`- verbatim_content = source_code_r,`
`1144`		`- title = "R Code for PCA"`
`1145`		`- )`
`1146`		`- decorated_output_dims_q`
	`1133`	`+ set_chunk_dims(pws, decorated_output_q)`
`1147`	`1134`	`})`
`1148`	`1135`	`}`
Original file line number	Diff line number	Diff line change
`@@ -289,9 +289,6 @@ ui_tm_g_association <- function(id, ...) {`
`289`	`289`	`)`
`290`	`290`	`)`
`291`	`291`	`),`
`292`		`- forms = tagList(`
`293`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`294`		`- ),`
`295`	`292`	`pre_output = args$pre_output,`
`296`	`293`	`post_output = args$post_output`
`297`	`294`	`)`
`@@ -545,18 +542,8 @@ srv_tm_g_association <- function(id,`
`545`	`542`	`width = plot_width`
`546`	`543`	`)`
`547`	`544`
`548`		`- decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_grob_q)`
`549`		`-`
`550`	`545`	`output$title <- renderText(output_q()[["title"]])`
`551`	`546`
`552`		`- # Render R code.`
`553`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))`
`554`		`-`
`555`		`- teal.widgets::verbatim_popup_srv(`
`556`		`- id = "rcode",`
`557`		`- verbatim_content = source_code_r,`
`558`		`- title = "Association Plot"`
`559`		`- )`
`560`		`- decorated_output_dims_q`
	`547`	`+ set_chunk_dims(pws, decorated_output_grob_q)`
`561`	`548`	`})`
`562`	`549`	`}`
Original file line number	Diff line number	Diff line change
`@@ -466,9 +466,6 @@ ui_g_bivariate <- function(id, ...) {`
`466`	`466`	`)`
`467`	`467`	`)`
`468`	`468`	`),`
`469`		`- forms = tagList(`
`470`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`471`		`- ),`
`472`	`469`	`pre_output = args$pre_output,`
`473`	`470`	`post_output = args$post_output`
`474`	`471`	`)`
`@@ -737,18 +734,7 @@ srv_g_bivariate <- function(id,`
`737`	`734`	`width = plot_width`
`738`	`735`	`)`
`739`	`736`
`740`		`- decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q_facets)`
`741`		`-`
`742`		`- # Render R code.`
`743`		`-`
`744`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))`
`745`		`-`
`746`		`- teal.widgets::verbatim_popup_srv(`
`747`		`- id = "rcode",`
`748`		`- verbatim_content = source_code_r,`
`749`		`- title = "Bivariate Plot"`
`750`		`- )`
`751`		`- decorated_output_dims_q`
	`737`	`+ set_chunk_dims(pws, decorated_output_q_facets)`
`752`	`738`	`})`
`753`	`739`	`}`
`754`	`740`
Original file line number	Diff line number	Diff line change
`@@ -377,9 +377,6 @@ ui_distribution <- function(id, ...) {`
`377`	`377`	`)`
`378`	`378`	`)`
`379`	`379`	`),`
`380`		`- forms = tagList(`
`381`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`382`		`- ),`
`383`	`380`	`pre_output = args$pre_output,`
`384`	`381`	`post_output = args$post_output`
`385`	`382`	`)`
`@@ -1402,14 +1399,6 @@ srv_distribution <- function(id,`
`1402`	`1399`
`1403`	`1400`	`output$t_stats <- DT::renderDataTable(tests_r())`
`1404`	`1401`
`1405`		`- # Render R code.`
`1406`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))`
`1407`		`-`
`1408`		`- teal.widgets::verbatim_popup_srv(`
`1409`		`- id = "rcode",`
`1410`		`- verbatim_content = source_code_r,`
`1411`		`- title = "R Code for distribution"`
`1412`		`- )`
`1413`	`1402`	`decorated_output_q`
`1414`	`1403`	`})`
`1415`	`1404`	`}`
Original file line number	Diff line number	Diff line change
`@@ -320,9 +320,6 @@ ui_g_response <- function(id, ...) {`
`320`	`320`	`)`
`321`	`321`	`)`
`322`	`322`	`),`
`323`		`- forms = tagList(`
`324`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`325`		`- ),`
`326`	`323`	`pre_output = args$pre_output,`
`327`	`324`	`post_output = args$post_output`
`328`	`325`	`)`
`@@ -594,16 +591,6 @@ srv_g_response <- function(id,`
`594`	`591`	`width = plot_width`
`595`	`592`	`)`
`596`	`593`
`597`		`- decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_plot_q)`
`598`		`-`
`599`		`- # Render R code.`
`600`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))`
`601`		`-`
`602`		`- teal.widgets::verbatim_popup_srv(`
`603`		`- id = "rcode",`
`604`		`- verbatim_content = source_code_r,`
`605`		`- title = "Show R Code for Response"`
`606`		`- )`
`607`		`- decorated_output_dims_q`
	`594`	`+ set_chunk_dims(pws, decorated_output_plot_q)`
`608`	`595`	`})`
`609`	`596`	`}`
Original file line number	Diff line number	Diff line change
`@@ -495,9 +495,6 @@ ui_g_scatterplot <- function(id, ...) {`
`495`	`495`	`)`
`496`	`496`	`)`
`497`	`497`	`),`
`498`		`- forms = tagList(`
`499`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`500`		`- ),`
`501`	`498`	`pre_output = args$pre_output,`
`502`	`499`	`post_output = args$post_output`
`503`	`500`	`)`
`@@ -1037,8 +1034,6 @@ srv_g_scatterplot <- function(id,`
`1037`	`1034`	`brushing = TRUE`
`1038`	`1035`	`)`
`1039`	`1036`
`1040`		`- decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_plot_q)`
`1041`		`-`
`1042`	`1037`	`output$data_table <- DT::renderDataTable({`
`1043`	`1038`	`plot_brush <- pws$brush()`
`1044`	`1039`
`@@ -1067,14 +1062,6 @@ srv_g_scatterplot <- function(id,`
`1067`	`1062`	`}`
`1068`	`1063`	`})`
`1069`	`1064`
`1070`		`- # Render R code.`
`1071`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))`
`1072`		`-`
`1073`		`- teal.widgets::verbatim_popup_srv(`
`1074`		`- id = "rcode",`
`1075`		`- verbatim_content = source_code_r,`
`1076`		`- title = "R Code for scatterplot"`
`1077`		`- )`
`1078`		`- decorated_output_dims_q`
	`1065`	`+ set_chunk_dims(pws, decorated_output_plot_q)`
`1079`	`1066`	`})`
`1080`	`1067`	`}`
Original file line number	Diff line number	Diff line change
`@@ -288,9 +288,6 @@ ui_g_scatterplotmatrix <- function(id, ...) {`
`288`	`288`	`)`
`289`	`289`	`)`
`290`	`290`	`),`
`291`		`- forms = tagList(`
`292`		`- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")`
`293`		`- ),`
`294`	`291`	`pre_output = args$pre_output,`
`295`	`292`	`post_output = args$post_output`
`296`	`293`	`)`
`@@ -479,8 +476,6 @@ srv_g_scatterplotmatrix <- function(id,`
`479`	`476`	`width = plot_width`
`480`	`477`	`)`
`481`	`478`
`482`		`- decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)`
`483`		`-`
`484`	`479`	`# show a message if conversion to factors took place`
`485`	`480`	`output$message <- renderText({`
`486`	`481`	`req(iv_r()$is_valid())`
`@@ -503,15 +498,7 @@ srv_g_scatterplotmatrix <- function(id,`
`503`	`498`	`}`
`504`	`499`	`})`
`505`	`500`
`506`		`- # Render R code.`
`507`		`- source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))`
`508`		`-`
`509`		`- teal.widgets::verbatim_popup_srv(`
`510`		`- id = "rcode",`
`511`		`- verbatim_content = source_code_r,`
`512`		`- title = "Show R Code for Scatterplotmatrix"`
`513`		`- )`
`514`		`- decorated_output_dims_q`
	`501`	`+ set_chunk_dims(pws, decorated_output_q)`
`515`	`502`	`})`
`516`	`503`	`}`
`517`	`504`