Merge branch 'main' into fix-pipelines@main

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 # All available hooks: https://pre-commit.com/hooks.html
 # R specific hooks: https://github.com/lorenzwalthert/precommit
-default_stages: [commit]
+default_stages: [pre-commit]
 default_language_version:
   python: python3
 repos:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.goshawk
 Title: Longitudinal Visualization `teal` Modules
-Version: 0.2.0.9008
-Date: 2024-10-03
+Version: 0.2.0.9011
+Date: 2024-10-07
 Authors@R: c(
     person("Nick", "Paszty", , "[email protected]", role = c("aut", "cre")),
     person("Dawid", "Kaledkowski", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,4 @@
-# teal.goshawk 0.2.0.9008
+# teal.goshawk 0.2.0.9011
 
 # teal.goshawk 0.2.0
 

R/tm_g_gh_boxplot.R

@@ -206,8 +206,6 @@ tm_g_gh_boxplot <- function(label,
     server_args = list(
       dataname = dataname,
       param_var = param_var,
-      trt_group = trt_group,
-      facet_var = facet_var,
       color_manual = color_manual,
       shape_manual = shape_manual,
       plot_height = plot_height,
@@ -248,21 +246,7 @@ ui_g_boxplot <- function(id, ...) {
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
       templ_ui_dataname(a$dataname),
-      teal.widgets::optionalSelectInput(
-        ns("trt_group"),
-        label = "Select Treatment Variable",
-        choices = get_choices(a$trt_group$choices),
-        selected = a$trt_group$selected,
-        multiple = FALSE
-      ),
       uiOutput(ns("axis_selections")),
-      teal.widgets::optionalSelectInput(
-        ns("facet_var"),
-        label = "Facet by",
-        choices = get_choices(a$facet_var$choices),
-        selected = a$facet_var$selected,
-        multiple = FALSE
-      ),
       templ_ui_constraint(ns, label = "Data Constraint"), # required by constr_anl_q
       if (length(a$hline_vars) > 0) {
         teal.widgets::optionalSelectInput(
@@ -312,7 +296,6 @@ srv_g_boxplot <- function(id,
                           dataname,
                           param_var,
                           trt_group,
-                          facet_var,
                           color_manual,
                           shape_manual,
                           plot_height,
@@ -331,6 +314,9 @@ srv_g_boxplot <- function(id,
       resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
       resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
+      resolved_facet_var <- teal.transform::resolve_delayed(module_args$facet_var, env)
+      resolved_trt <- teal.transform::resolve_delayed(module_args$trt_group, env)
+
       templ_ui_params_vars(
         session$ns,
         xparam_choices = resolved_param$choices,
@@ -339,7 +325,11 @@ srv_g_boxplot <- function(id,
         xchoices = resolved_x$choices,
         xselected = resolved_x$selected,
         ychoices = resolved_y$choices,
-        yselected = resolved_y$selected
+        yselected = resolved_y$selected,
+        facet_choices = resolved_facet_var$choices,
+        facet_selected = resolved_facet_var$selected,
+        trt_choices = resolved_trt$choices,
+        trt_selected = resolved_trt$selected
       )
     })
     # reused in all modules
@@ -395,7 +385,7 @@ srv_g_boxplot <- function(id,
       iv
     })
 
-    create_plot <- reactive({
+    create_plot <- debounce(reactive({
       teal::validate_inputs(iv_r())
 
       req(anl_q())
@@ -468,15 +458,16 @@ srv_g_boxplot <- function(id,
           )
         })
       )
-    })
+    }), 800)
 
-    create_table <- reactive({
+    create_table <- debounce(reactive({
       req(iv_r()$is_valid())
       req(anl_q())
       param <- input$xaxis_param
       xaxis_var <- input$yaxis_var # nolint
       font_size <- input$font_size
       trt_group <- input$trt_group
+      facet_var <- input$facet_var
 
       anl_q()$qenv %>% teal.code::eval_code(
         code = bquote({
@@ -486,11 +477,11 @@ srv_g_boxplot <- function(id,
             param_var = .(param_var),
             param = .(param),
             xaxis_var = .(xaxis_var),
-            facet_var = .(input$facet_var)
+            facet_var = .(facet_var)
           )
         })
       )
-    })
+    }), 800)
 
     plot_r <- reactive({
       create_plot()[["p"]]
@@ -511,8 +502,7 @@ srv_g_boxplot <- function(id,
       numeric_cols <- setdiff(names(dplyr::select_if(tbl, is.numeric)), "n")
 
       DT::datatable(tbl,
-        rownames = FALSE, options = list(scrollX = TRUE),
-        callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';")
+        rownames = FALSE, options = list(scrollX = TRUE)
       ) %>%
         DT::formatRound(numeric_cols, 4)
     })
@@ -557,7 +547,7 @@ srv_g_boxplot <- function(id,
     ###
 
     # highlight plot area
-    output$brush_data <- DT::renderDataTable({
+    reactive_df <- debounce(reactive({
       boxplot_brush <- boxplot_data$brush()
 
       ANL <- isolate(anl_q()$ANL) %>% droplevels() # nolint
@@ -570,19 +560,20 @@ srv_g_boxplot <- function(id,
 
       req(all(c(xvar, yvar, facetv, trt_group) %in% names(ANL)))
 
-      df <- teal.widgets::clean_brushedPoints(
+      teal.widgets::clean_brushedPoints(
         dplyr::select(
           ANL, "USUBJID", dplyr::all_of(c(trt_group, facetv)),
           "AVISITCD", "PARAMCD", dplyr::all_of(c(xvar, yvar)), "LOQFL"
         ),
         boxplot_brush
       )
+    }), 800)
 
-      numeric_cols <- names(dplyr::select_if(df, is.numeric))
+    output$brush_data <- DT::renderDataTable({
+      numeric_cols <- names(dplyr::select_if(reactive_df(), is.numeric))
 
-      DT::datatable(df,
-        rownames = FALSE, options = list(scrollX = TRUE),
-        callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';")
+      DT::datatable(reactive_df(),
+        rownames = FALSE, options = list(scrollX = TRUE)
       ) %>%
         DT::formatRound(numeric_cols, 4)
     })

R/tm_g_gh_correlationplot.R

@@ -255,7 +255,6 @@ tm_g_gh_correlationplot <- function(label,
     server_args = list(
       dataname = dataname,
       param_var = param_var,
-      trt_group = trt_group,
       trt_facet = trt_facet,
       color_manual = color_manual,
       shape_manual = shape_manual,
@@ -283,13 +282,6 @@ ui_g_correlationplot <- function(id, ...) {
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
       templ_ui_dataname(a$dataname),
-      teal.widgets::optionalSelectInput(
-        ns("trt_group"),
-        label = "Select Treatment Variable",
-        choices = get_choices(a$trt_group$choices),
-        selected = a$trt_group$selected,
-        multiple = FALSE
-      ),
       uiOutput(ns("axis_selections")),
       templ_ui_constraint(ns, "X-Axis Data Constraint"), # required by constr_anl_q
       if (length(a$hline_vars) > 0) {
@@ -388,6 +380,7 @@ srv_g_correlationplot <- function(id,
       resolved_x_var <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_y_param <- teal.transform::resolve_delayed(module_args$yaxis_param, env)
       resolved_y_var <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
+      resolved_trt <- teal.transform::resolve_delayed(module_args$trt_group, env)
       templ_ui_params_vars(
         session$ns,
         xparam_choices = resolved_x_param$choices,
@@ -397,7 +390,9 @@ srv_g_correlationplot <- function(id,
         yparam_choices = resolved_y_param$choices,
         yparam_selected = resolved_y_param$selected,
         ychoices = resolved_y_var$choices,
-        yselected = resolved_y_var$selected
+        yselected = resolved_y_var$selected,
+        trt_choices = resolved_trt$choices,
+        trt_selected = resolved_trt$selected
       )
     })
 
@@ -722,7 +717,7 @@ srv_g_correlationplot <- function(id,
     vertical_line <- srv_arbitrary_lines("vline_arb")
 
     # plot
-    plot_q <- reactive({
+    plot_q <- debounce(reactive({
       req(plot_data_transpose())
       # nolint start
       xaxis_param <- input$xaxis_param
@@ -814,7 +809,7 @@ srv_g_correlationplot <- function(id,
           print(p)
         })
       )
-    })
+    }), 800)
 
     plot_r <- reactive(plot_q()[["p"]])
 
@@ -862,8 +857,7 @@ srv_g_correlationplot <- function(id,
     }
     ###
 
-    # highlight plot area
-    output$brush_data <- DT::renderDataTable({
+    reactive_df <- debounce(reactive({
       req(iv_r()$is_valid())
       plot_brush <- plot_data$brush()
 
@@ -876,12 +870,14 @@ srv_g_correlationplot <- function(id,
         ),
         plot_brush
       )
+    }), 800)
 
-      numeric_cols <- names(dplyr::select_if(df, is.numeric))
+    # highlight plot area
+    output$brush_data <- DT::renderDataTable({
+      numeric_cols <- names(dplyr::select_if(reactive_df(), is.numeric))
 
-      DT::datatable(df,
-        rownames = FALSE, options = list(scrollX = TRUE),
-        callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';")
+      DT::datatable(reactive_df(),
+        rownames = FALSE, options = list(scrollX = TRUE)
       ) %>%
         DT::formatRound(numeric_cols, 4)
     })

R/tm_g_gh_density_distribution_plot.R

@@ -163,7 +163,6 @@ tm_g_gh_density_distribution_plot <- function(label, # nolint
       dataname = dataname,
       param_var = param_var,
       param = param,
-      trt_group = trt_group,
       color_manual = color_manual,
       color_comb = color_comb,
       plot_height = plot_height,
@@ -196,13 +195,6 @@ ui_g_density_distribution_plot <- function(id, ...) {
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
       templ_ui_dataname(a$dataname),
-      teal.widgets::optionalSelectInput(
-        ns("trt_group"),
-        label = "Select Treatment Variable",
-        choices = get_choices(a$trt_group$choices),
-        selected = a$trt_group$selected,
-        multiple = FALSE
-      ),
       uiOutput(ns("axis_selections")),
       templ_ui_constraint(ns, label = "Data Constraint"),
       ui_arbitrary_lines(id = ns("hline_arb"), a$hline_arb, a$hline_arb_label, a$hline_arb_color),
@@ -272,13 +264,17 @@ srv_g_density_distribution_plot <- function(id, # nolint
       env <- shiny::isolate(as.list(data()@env))
       resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
+      resolved_trt <- teal.transform::resolve_delayed(module_args$trt_group, env)
+
       templ_ui_params_vars(
         session$ns,
         xparam_choices = resolved_param$choices,
         xparam_selected = resolved_param$selected,
         xparam_label = "Select a Biomarker",
         xchoices = resolved_x$choices,
-        xselected = resolved_x$selected
+        xselected = resolved_x$selected,
+        trt_choices = resolved_trt$choices,
+        trt_selected = resolved_trt$selected
       )
     })
 
@@ -322,7 +318,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
     })
 
 
-    create_plot <- reactive({
+    create_plot <- debounce(reactive({
       teal::validate_inputs(iv_r())
       req(anl_q())
 
@@ -369,9 +365,9 @@ srv_g_density_distribution_plot <- function(id, # nolint
           )
         })
       )
-    })
+    }), 800)
 
-    create_table <- reactive({
+    create_table <- debounce(reactive({
       req(iv_r()$is_valid())
       req(anl_q())
       param <- input$xaxis_param
@@ -392,7 +388,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
           )
         )
       )
-    })
+    }), 800)
 
     plot_r <- reactive({
       create_plot()[["p"]]
@@ -411,8 +407,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
       numeric_cols <- names(dplyr::select_if(tbl, is.numeric))
 
       DT::datatable(tbl,
-        rownames = FALSE, options = list(scrollX = TRUE),
-        callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';")
+        rownames = FALSE, options = list(scrollX = TRUE)
       ) %>%
         DT::formatRound(numeric_cols, 2)
     })