Address reviewer comments

Author: llrs-roche

R/tm_g_association.R

@@ -504,7 +504,7 @@ srv_tm_g_association <- function(id,
             expr = {
               plot_top <- plot_calls[[1]]
               plot_bottom <- plot_calls[[1]]
-              plot <- tern::stack_grobs(grobs = lapply(list(plot_top, plot_bottom), ggplotGrob))
+              plot <- tern::stack_grobs(grobs = lapply(list(plot_top, plot_bottom), ggplot2::ggplotGrob))
             },
             env = list(
               plot_calls = do.call(

R/tm_g_scatterplotmatrix.R

@@ -329,8 +329,8 @@ srv_g_scatterplotmatrix <- function(id,
 
     anl_merged_q <- reactive({
       req(anl_merged_input())
-      data() %>%
-        teal.code::eval_code(as.expression(anl_merged_input()$expr))
+      qenv <- teal.code::eval_code(data(), 'library("dplyr");library("lattice")') # nolint quotes
+      teal.code::eval_code(qenv, as.expression(anl_merged_input()$expr))
     })
 
     merged <- list(
@@ -366,6 +366,7 @@ srv_g_scatterplotmatrix <- function(id,
 
       # check character columns. If any, then those are converted to factors
       check_char <- vapply(ANL[, cols_names], is.character, logical(1))
+      qenv <- teal.code::eval_code(qenv, 'library("dplyr");library("lattice")') # nolint quotes
       if (any(check_char)) {
         qenv <- teal.code::eval_code(
           qenv,

R/tm_missing_data.R

@@ -533,7 +533,7 @@ srv_missing_data <- function(id,
       group_var <- input$group_by_var
       anl <- data_r()
       qenv <- teal.code::eval_code(data(), {
-        'library("dplyr");library("ggplot2");library("tidyr");library("forcats");library("glue")'
+        'library("dplyr");library("ggplot2");library("tidyr");library("gridExtra")' # nolint quotes
       })
 
       qenv <- if (!is.null(selected_vars()) && length(selected_vars()) != ncol(anl)) {
@@ -927,14 +927,14 @@ srv_missing_data <- function(id,
 
       if (isTRUE(input$if_patients_plot)) {
         within(qenv, {
-          g1 <- ggplotGrob(summary_plot_top)
-          g2 <- ggplotGrob(summary_plot_bottom)
+          g1 <- ggplot2::ggplotGrob(summary_plot_top)
+          g2 <- ggplot2::ggplotGrob(summary_plot_bottom)
           summary_plot <- gridExtra::gtable_cbind(g1, g2, size = "first")
           summary_plot$heights <- grid::unit.pmax(g1$heights, g2$heights)
         })
       } else {
         within(qenv, {
-          g1 <- ggplotGrob(summary_plot_top)
+          g1 <- ggplot2::ggplotGrob(summary_plot_top)
           summary_plot <- g1
         })
       }
@@ -1067,8 +1067,8 @@ srv_missing_data <- function(id,
       )
 
       within(qenv, {
-        g1 <- ggplotGrob(combination_plot_top)
-        g2 <- ggplotGrob(combination_plot_bottom)
+        g1 <- ggplot2::ggplotGrob(combination_plot_top)
+        g2 <- ggplot2::ggplotGrob(combination_plot_bottom)
 
         combination_plot <- gridExtra::gtable_rbind(g1, g2, size = "last")
         combination_plot$heights[7] <- grid::unit(0.2, "null") # rescale to get the bar chart smaller
@@ -1112,8 +1112,11 @@ srv_missing_data <- function(id,
       }
 
       qenv <- if (!is.null(group_var)) {
+        common_code_libraries_q <- teal.code::eval_code(common_code_q(),
+                             'library("forcats");library("glue");library("rlistings")' # nolint quotes
+        )
         teal.code::eval_code(
-          common_code_q(),
+          common_code_libraries_q,
           substitute(
             expr = {
               summary_data <- ANL %>%

R/tm_outliers.R

@@ -439,7 +439,10 @@ srv_outliers <- function(id, data, reporter, filter_panel_api, outlier_var,
 
     anl_merged_q <- reactive({
       req(anl_merged_input())
-      data() %>%
+      teal.code::eval_code(data(),
+                           paste0(
+                             'library("dplyr");library("tidyr");', # nolint quotes
+                             'library("tibble");library("ggplot2");library("rlistings")')) %>% # nolint quotes
         teal.code::eval_code(as.expression(anl_merged_input()$expr))
     })
 

R/tm_variable_browser.R

@@ -818,7 +818,7 @@ plot_var_summary <- function(var,
           theme = do.call("theme", all_ggplot2_args$theme)
         )
     }
-    plot_main <- ggplotGrob(plot_main)
+    plot_main <- ggplot2::ggplotGrob(plot_main)
   }
 
   grid::grid.draw(plot_main)

R/utils.R

@@ -90,10 +90,10 @@ add_facet_labels <- function(p, xfacet_label = NULL, yfacet_label = NULL) {
   checkmate::assert_character(xfacet_label, null.ok = TRUE, min.len = 1)
   checkmate::assert_character(yfacet_label, null.ok = TRUE, min.len = 1)
   if (is.null(xfacet_label) && is.null(yfacet_label)) {
-    return(ggplotGrob(p))
+    return(ggplot2::ggplotGrob(p))
   }
   grid::grid.grabExpr({
-    g <- ggplotGrob(p)
+    g <- ggplot2::ggplotGrob(p)
 
     # we are going to replace these, so we make sure they have nothing in them
     checkmate::assert_class(g$grobs[[grep("xlab-t", g$layout$name, fixed = TRUE)]], "zeroGrob")