fix: R CMD check errors and adds lifecycle to dependencies

Author: averissimo

DESCRIPTION

@@ -35,6 +35,7 @@ Imports:
     DT (>= 0.13),
     forcats (>= 1.0.0),
     grid,
+    lifecycle (>= 0.2.0),
     scales,
     shinyjs,
     shinyTree (>= 0.2.8),
@@ -84,7 +85,7 @@ VignetteBuilder:
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, insightsengineering/teal,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
-    rstudio/DT, tidyverse/forcats, r-lib/scales, daattali/shinyjs,
+    rstudio/DT, tidyverse/forcats, r-lib/lifecycle, r-lib/scales, daattali/shinyjs,
     shinyTree/shinyTree, rstudio/shinyvalidate, dreamRs/shinyWidgets,
     tidyverse/stringr, insightsengineering/teal.code,
     insightsengineering/teal.data, insightsengineering/teal.logger,

R/tm_a_regression.R

@@ -225,6 +225,8 @@ tm_a_regression <- function(label = "Regression Analysis",
       .var.name = "label_segment_threshold"
     )
   }
+  decorators <- normalize_decorators(decorators)
+  assert_decorators(decorators, "plot", null.ok = TRUE)
   # End of assertions
 
   # Make UI args
@@ -319,7 +321,7 @@ ui_a_regression <- function(id, ...) {
           label = "Outlier label"
         )
       ),
-      ui_transform_teal_data(ns("decorate"), transformators = args$decorators),
+      ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(args$decorators, "plot")),
       teal.widgets::panel_group(
         teal.widgets::panel_item(
           title = "Plot settings",
@@ -582,22 +584,15 @@ srv_a_regression <- function(id,
         shinyjs::show("size")
         shinyjs::show("alpha")
         plot <- substitute(
+          expr = ggplot(fit$model[, 2:1], aes_string(regressor, response)) +
+            geom_point(size = size, alpha = alpha) +
+            stat_smooth(method = "lm", formula = y ~ x, se = FALSE),
           env = list(
             regressor = regression_var()$regressor,
             response = regression_var()$response,
             size = input$size,
             alpha = input$alpha
-          ),
-          expr = ggplot(
-            fit$model[, 2:1],
-            aes_string(regressor, response)
-          ) +
-            geom_point(size = size, alpha = alpha) +
-            stat_smooth(
-              method = "lm",
-              formula = y ~ x,
-              se = FALSE
-            )
+          )
         )
         if (input$show_outlier) {
           plot <- substitute(
@@ -979,12 +974,16 @@ srv_a_regression <- function(id,
       )
     })
 
-    decorated_output_q_no_print <- srv_transform_teal_data("decorate", data = output_q, transformators = decorators)
-    decorated_output_q <- reactive(within(decorated_output_q_no_print(), expr = print(plot)))
+    decorated_output_q <- srv_decorate_teal_data(
+      "decorator",
+      data = output_q,
+      decorators = select_decorators(decorators, "plot"),
+      expr = print(plot)
+    )
 
     fitted <- reactive({
       req(output_q())
-      decorated_output_q_no_print()[["fit"]]
+      decorated_output_q()[["fit"]]
     })
     plot_r <- reactive({
       req(output_q())

R/tm_g_association.R

@@ -178,7 +178,6 @@ tm_g_association <- function(label = "Association",
 
   decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, null.ok = TRUE, "plot")
-
   # End of assertions
 
   # Make UI args
@@ -529,7 +528,7 @@ srv_tm_g_association <- function(id,
 
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
-      verbatim_content = reactive(teal.code::get_code(req(decorated_output_q()))),
+      verbatim_content = reactive(teal.code::get_code(req(decorated_output_grob_q()))),
       title = "Association Plot"
     )
 
@@ -548,7 +547,7 @@ srv_tm_g_association <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(teal.code::get_code(req(decorated_output_q())))
+        card$append_src(teal.code::get_code(req(decorated_output_grob_q())))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

R/tm_missing_data.R

@@ -923,20 +923,19 @@ srv_missing_data <- function(id,
           )
         )
       }
-      expr <- if (isTRUE(input$if_patients_plot)) {
-        quote({
+      if (isTRUE(input$if_patients_plot)) {
+        teal.code::eval_code(qenv, {
           g1 <- ggplotGrob(summary_plot_top)
           g2 <- ggplotGrob(summary_plot_bottom)
           summary_plot <- gridExtra::gtable_cbind(g1, g2, size = "first")
           summary_plot$heights <- grid::unit.pmax(g1$heights, g2$heights)
         })
       } else {
-        quote({
+        teal.code::eval_code(qenv, {
           g1 <- ggplotGrob(summary_plot_top)
           summary_plot <- g1
         })
       }
-      teal.code::eval_code(qenv, expr)
     })
 
     combination_plot_q <- reactive({

R/tm_outliers.R

@@ -1323,7 +1323,7 @@ srv_outliers <- function(id, data, reporter, filter_panel_api, outlier_var,
         }
         card$append_text("Plot", "header3")
         if (tab_type == "Boxplot") {
-          card$append_plot(boxplot_r(), dim = box_pws$dim())
+          card$append_plot(box_plot_r(), dim = box_pws$dim())
         } else if (tab_type == "Density Plot") {
           card$append_plot(density_plot_r(), dim = density_pws$dim())
         } else if (tab_type == "Cumulative Distribution Plot") {

R/utils.R

@@ -311,9 +311,9 @@ srv_decorate_teal_data <- function(id, data, decorators, expr, expr_is_reactive
       if (missing_expr) {
         decorated_output()
       } else if (expr_is_reactive) {
-        eval_code(decorated_output(), expr())
+        teal.code::eval_code(decorated_output(), expr())
       } else {
-        eval_code(decorated_output(), expr)
+        teal.code::eval_code(decorated_output(), expr)
       }
     })
   })