799 qenv prints plots to the device when running shiny app

R/tm_a_gee.R

@@ -525,7 +525,7 @@ srv_gee <- function(id,
     })
 
     table_r <- shiny::reactive({
-      table_q()[["result_table"]]
+      teal.code::get_var(table_q(), "result_table")
     })
 
     teal.widgets::table_with_settings_srv(

R/tm_a_mmrm.R

@@ -1396,8 +1396,8 @@ srv_mmrm <- function(id,
 
     plot_r <- shiny::reactive({
       switch(input$output_function,
-        g_mmrm_lsmeans = plot_q()[["lsmeans_plot"]],
-        g_mmrm_diagnostic = plot_q()[["diagnostic_plot"]]
+        g_mmrm_lsmeans = teal.code::get_var(plot_q(), "lsmeans_plot"),
+        g_mmrm_diagnostic = teal.code::get_var(plot_q(), "diagnostic_plot")
       )
     })
 

R/tm_g_barchart_simple.R

@@ -487,11 +487,11 @@ srv_g_barchart_simple <- function(id,
       teal.code::eval_code(qenv3, code = quote(print(plot)))
     })
 
-    plot_r <- shiny::reactive(all_q()[["plot"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "plot"))
 
     output$table <- shiny::renderTable({
       shiny::req(iv_r()$is_valid())
-      all_q()[["counts"]]
+      teal.code::get_var(all_q(), "counts")
     })
 
     # get grouping variables

R/tm_g_ci.R

@@ -412,15 +412,17 @@ srv_g_ci <- function(id, # nolint
 
     all_q <- shiny::reactive({
       teal::validate_inputs(iv_r())
-      teal::validate_has_data(anl_q()[["ANL"]], min_nrow = 2)
+      teal::validate_has_data(teal.code::get_var(anl_q(), "ANL"),
+        min_nrow = 2
+      )
 
       x <- anl_inputs()$columns_source$x_var
       y <- anl_inputs()$columns_source$y_var
       color <- anl_inputs()$columns_source$color
 
       shiny::validate(
         shiny::need(
-          !all(is.na(anl_q()[["ANL"]][[y]])),
+          !all(is.na(teal.code::get_var(anl_q(), "ANL")[[y]])),
           "No valid data. Please check the filtering option for analysis value (y axis)"
         )
       )
@@ -459,7 +461,7 @@ srv_g_ci <- function(id, # nolint
       teal.code::eval_code(anl_q(), list_calls)
     })
 
-    plot_r <- shiny::reactive(all_q()[["gg"]])
+    plot_r <- shiny::reactive(teal.code::get_var(anl_q(), "gg"))
 
     teal.widgets::verbatim_popup_srv(
       id = "warning",

R/tm_g_forest_rsp.R

@@ -537,7 +537,7 @@ srv_g_forest_rsp <- function(id,
       ),
       handlerExpr = {
         shiny::req(anl_q())
-        anl <- anl_q()[["ANL"]]
+        anl <- teal.code::get_var(anl_q(), "ANL")
         aval_var <- anl_inputs()$columns_source$aval_var
         paramcd_level <- unlist(anl_inputs()$filter_info$paramcd[[1]]$selected)
         if (length(paramcd_level) == 0) {
@@ -694,7 +694,7 @@ srv_g_forest_rsp <- function(id,
       teal.code::eval_code(qenv, as.expression(my_calls))
     })
 
-    plot_r <- shiny::reactive(all_q()[["p"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "p"))
 
     pws <- teal.widgets::plot_with_settings_srv(
       id = "myplot",

R/tm_g_forest_tte.R

@@ -628,7 +628,7 @@ srv_g_forest_tte <- function(id,
     })
 
     # Outputs to render.
-    plot_r <- shiny::reactive(all_q()[["p"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "p"))
 
     pws <- teal.widgets::plot_with_settings_srv(
       id = "myplot",

R/tm_g_ipp.R

@@ -586,7 +586,7 @@ srv_g_ipp <- function(id,
     })
 
     # Outputs to render.
-    plot_r <- shiny::reactive(all_q()[["plot"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "plot"))
 
     # Insert the plot into a plot with settings module from teal.widgets
     pws <- teal.widgets::plot_with_settings_srv(

R/tm_g_km.R

@@ -742,7 +742,7 @@ srv_g_km <- function(id,
       teal.code::eval_code(qenv, as.expression(my_calls))
     })
 
-    plot_r <- shiny::reactive(all_q()[["plot"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "plot"))
 
     # Insert the plot into a plot with settings module from teal.widgets
     pws <- teal.widgets::plot_with_settings_srv(

R/tm_g_lineplot.R

@@ -623,7 +623,7 @@ srv_g_lineplot <- function(id,
       teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
     })
 
-    plot_r <- shiny::reactive(all_q()[["plot"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "plot"))
 
     # Insert the plot into a plot with settings module from teal.widgets
     pws <- teal.widgets::plot_with_settings_srv(

R/tm_g_pp_adverse_events.R

@@ -527,13 +527,13 @@ srv_g_adverse_events <- function(id,
       teal.code::eval_code(qenv2, as.expression(calls))
     })
     output$table <- DT::renderDataTable(
-      expr = all_q()[["table"]],
+      expr = teal.code::get_var(all_q(), "table"),
       options = list(pageLength = input$table_rows)
     )
 
     plot_r <- shiny::reactive({
       shiny::req(iv_r()$is_valid())
-      all_q()[["plot"]]
+      teal.code::get_var(all_q(), "plot")
     })
 
     pws <- teal.widgets::plot_with_settings_srv(

R/tm_g_pp_patient_timeline.R

@@ -793,7 +793,7 @@ srv_g_patient_timeline <- function(id,
       ae_chart_vars_null <- any(vapply(list(aeterm, aetime_start, aetime_end), is.null, FUN.VALUE = logical(1)))
       ds_chart_vars_null <- any(vapply(list(cmdecod, dstime_start, dstime_end), is.null, FUN.VALUE = logical(1)))
 
-      p_timeline_data <- anl_q()[["ANL"]]
+      p_timeline_data <- teal.code::get_var(anl_q(), "ANL")
       # time variables can not be NA
       p_time_data_pat <- p_timeline_data[p_timeline_data[[patient_col]] == patient_id(), ]
 
@@ -873,7 +873,7 @@ srv_g_patient_timeline <- function(id,
         teal.code::eval_code(as.expression(patient_timeline_calls))
     })
 
-    plot_r <- shiny::reactive(all_q()[["patient_timeline_plot"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "patient_timeline_plot"))
 
     pws <- teal.widgets::plot_with_settings_srv(
       id = "patient_timeline_plot",

R/tm_g_pp_therapy.R

@@ -650,14 +650,14 @@ srv_g_therapy <- function(id,
 
     output$therapy_table <- DT::renderDataTable(
       expr = {
-        all_q()[["therapy_table"]]
+        teal.code::get_var(all_q(), "therapy_table")
       },
       options = list(pageLength = input$therapy_table_rows)
     )
 
     plot_r <- shiny::reactive({
       shiny::req(iv_r()$is_valid())
-      all_q()[["therapy_plot"]]
+      teal.code::get_var(all_q(), "therapy_plot")
     })
 
     pws <- teal.widgets::plot_with_settings_srv(

R/tm_g_pp_vitals.R

@@ -504,7 +504,7 @@ srv_g_vitals <- function(id,
         teal.code::eval_code(as.expression(my_calls))
     })
 
-    plot_r <- shiny::reactive(all_q()[["result_plot"]])
+    plot_r <- shiny::reactive(teal.code::get_var(all_q(), "result_plot"))
 
     pws <- teal.widgets::plot_with_settings_srv(
       id = "vitals_plot",