unify tags.

R/adtteSpec.R

@@ -162,7 +162,7 @@ adtteSpecInput <- function(inputId, # nolint
 #'   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 #'   moduleServer(id, function(input, output, session) {
 #'     output$encoding_ui <- renderUI({
-#'       div(
+#'       tags$div(
 #'         experimentSpecInput(session$ns("experiment"), data, mae_name = "MAE"),
 #'         assaySpecInput(session$ns("assay")),
 #'         geneSpecInput(session$ns("genes"), funs = list(Mean = colMeans)),

R/assaySpec.R

@@ -55,7 +55,7 @@ assaySpecInput <- function(inputId, # nolint
 #' server <- function(id, data, filter_panel_api) {
 #'   moduleServer(id, module = function(input, output, session) {
 #'     output$encoding_ui <- renderUI({
-#'       div(
+#'       tags$div(
 #'         experimentSpecInput(session$ns("experiment"), data, "MAE"),
 #'         assaySpecInput(
 #'           session$ns("assay"),

R/barplot.R

@@ -72,7 +72,7 @@ ui_g_barplot <- function(id,
                          post_output) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/boxplot.R

@@ -73,7 +73,7 @@ ui_g_boxplot <- function(id,
                          post_output) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/experimentSpec.R

@@ -132,7 +132,7 @@ h_gene_data <- function(object, name_annotation) {
 #'   ns <- NS(id)
 #'   teal.widgets::standard_layout(
 #'     encoding = uiOutput(ns("encoding_ui")),
-#'     output = div(
+#'     output = tags$div(
 #'       verbatimTextOutput(ns("summary")),
 #'       verbatimTextOutput(ns("head"))
 #'     )
@@ -145,7 +145,7 @@ h_gene_data <- function(object, name_annotation) {
 #'                    mae_name) {
 #'   moduleServer(id, function(input, output, session) {
 #'     output$encoding_ui <- renderUI({
-#'       div(
+#'       tags$div(
 #'         experimentSpecInput(
 #'           session$ns("my_experiment"),
 #'           data,

R/forestplot.R

@@ -99,7 +99,7 @@ ui_g_forest_tte <- function(id,
                             post_output) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/geneSpec.R

@@ -47,39 +47,39 @@ geneSpecInput <- function(inputId, # nolint
   ns <- NS(inputId)
   tagList(
     include_css_files(pattern = "*"),
-    div(
+    tags$div(
       class = "row",
-      div(
+      tags$div(
         class = "col-sm-8",
         tags$label(
           class = "control-label",
           label_genes
         )
       ),
-      div(
+      tags$div(
         class = "col-sm-2",
         actionButton(
           ns("select_none_button"),
-          span(icon("remove-circle", lib = "glyphicon")),
+          tags$span(icon("remove-circle", lib = "glyphicon")),
           title = label_select_none_button,
           class = "pull-right list-genes"
         ),
         actionButton(
           ns("select_all_button"),
-          span(icon("ok-circle", lib = "glyphicon")),
+          tags$span(icon("ok-circle", lib = "glyphicon")),
           title = label_select_all_button,
           class = "pull-right list-genes"
         )
       ),
-      div(
+      tags$div(
         class = "col-sm-2",
         actionButton(
           ns("text_button"),
-          span(icon("fas fa-font")),
+          tags$span(icon("fas fa-font")),
           title = label_text_button,
           class = "pull-right list-genes"
         ),
-        div(
+        tags$div(
           class = "pull-right",
           title = label_lock_button,
           shinyWidgets::prettyToggle(
@@ -98,7 +98,7 @@ geneSpecInput <- function(inputId, # nolint
         )
       )
     ),
-    div(
+    tags$div(
       class = "custom-select-input",
       selectizeInput(
         ns("genes"),
@@ -222,7 +222,7 @@ h_parse_genes <- function(words, choices) {
 #' ui <- function(id, funs) {
 #'   ns <- NS(id)
 #'   teal.widgets::standard_layout(
-#'     encoding = div(
+#'     encoding = tags$div(
 #'       geneSpecInput(
 #'         ns("my_genes"),
 #'         funs = funs,

R/km.R

@@ -100,7 +100,7 @@ ui_g_km <- function(id,
                     post_output) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/pca.R

@@ -65,7 +65,7 @@ ui_g_pca <- function(id,
   tagList(
     teal.widgets::standard_layout(
       include_css_files(pattern = "*"),
-      encoding = div(
+      encoding = tags$div(
         ### Reporter
         teal.reporter::simple_reporter_ui(ns("simple_reporter")),
         ###
@@ -111,7 +111,7 @@ ui_g_pca <- function(id,
           )
         )
       ),
-      output = div(
+      output = tags$div(
         style = "display:flow-root",
         tabsetPanel(
           id = ns("tab_selected"),
@@ -120,7 +120,7 @@ ui_g_pca <- function(id,
             "PCA",
             column(
               width = 12,
-              div(
+              tags$div(
                 class = "my-5",
                 teal.widgets::plot_with_settings_ui(ns("plot_pca"))
               ),
@@ -131,7 +131,7 @@ ui_g_pca <- function(id,
             "PC and Sample Correlation",
             column(
               width = 12,
-              div(
+              tags$div(
                 class = "my-5",
                 teal.widgets::plot_with_settings_ui(ns("plot_cor"))
               ),

R/quality.R

@@ -116,7 +116,7 @@ ui_g_quality <- function(id,
                          post_output) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/sampleVarSpec.R

@@ -24,26 +24,26 @@ sampleVarSpecInput <- function(inputId, # nolint
   ns <- NS(inputId)
   tagList(
     include_css_files(pattern = "*"),
-    div(
+    tags$div(
       class = "row",
-      div(
+      tags$div(
         class = "col-sm-8",
         tags$label(
           class = "control-label",
           label_vars
         )
       ),
-      div(
+      tags$div(
         class = "col-sm-4",
         actionButton(
           ns("levels_button"),
-          span(icon("fas fa-table")),
+          tags$span(icon("fas fa-table")),
           title = label_levels_button,
           class = "pull-right list-genes"
         )
       )
     ),
-    div(
+    tags$div(
       class = "custom-select-input",
       teal.widgets::optionalSelectInput(
         ns("sample_var"),
@@ -218,7 +218,7 @@ validate_n_levels <- function(x, name, n_levels) {
 #'     output$encoding_ui <- renderUI({
 #'       mae <- data()[["MAE"]]
 #'       experiment_name_choices <- names(mae)
-#'       div(
+#'       tags$div(
 #'         selectInput(session$ns("experiment_name"), "Select experiment", experiment_name_choices),
 #'         sampleVarSpecInput(session$ns("facet_var"), "Select faceting variable")
 #'       )
@@ -390,7 +390,7 @@ sampleVarSpecServer <- function(id, # nolint
           choices = seq_len(n_max_groups),
           selected = selected_groups
         ),
-        span(label_modal_title),
+        tags$span(label_modal_title),
         footer = tagList(
           modalButton("Cancel"),
           actionButton(session$ns("ok"), "OK")

R/scatterplot.R

@@ -79,7 +79,7 @@ ui_g_scatterplot <- function(id,
   )
 
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/volcanoplot.R

@@ -64,13 +64,13 @@ ui_g_volcanoplot <- function(id,
   ns <- NS(id)
 
   teal.widgets::standard_layout(
-    output = div(
+    output = tags$div(
       teal.widgets::plot_with_settings_ui(ns("plot")),
       DT::DTOutput(ns("table"))
     ),
     pre_output = pre_output,
     post_output = post_output,
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

design/design_barplot.Rmd

@@ -139,7 +139,7 @@ ui_barplot <- function(id, datasets, dataname) {
   mae <- datasets$get_data(dataname, filtered = TRUE)
   teal.widgets::standard_layout(
     output = plotOutput(ns("plot")),
-    encoding = div(
+    encoding = tags$div(
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis Data:", tags$code(dataname)),
       selectInput(ns("experiment"), "experiment", names(mae)),

design/design_boxplot.Rmd

@@ -126,7 +126,7 @@ ui_boxplot <- function(id, datasets, dataname) {
   mae <- datasets$get_data(dataname, filtered = TRUE)
   teal.widgets::standard_layout(
     output = plotOutput(ns("plot")),
-    encoding = div(
+    encoding = tags$div(
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis Data:", tags$code(dataname)),
       selectInput(ns("experiment"), "experiment", names(mae)),

design/design_combine_levels.Rmd

@@ -216,28 +216,28 @@ ui_g_levels <- function(id,
   tagList(
     include_css_files(pattern = "*"),
     teal.widgets::standard_layout(
-      encoding = div(
+      encoding = tags$div(
         selectInput(ns("experiment_name"), "Select experiment", experiment_name_choices),
-        div(
+        tags$div(
           class = "row",
-          div(
+          tags$div(
             class = "col-sm-8",
             tags$label(
               class = "control-label",
               "Select faceting variable"
             )
           ),
-          div(
+          tags$div(
             class = "col-sm-4",
             actionButton(
               ns("open_levels_input"),
-              span(icon("font fa-object-ungroup")),
+              tags$span(icon("font fa-object-ungroup")),
               title = "Combine factor levels",
               class = "pull-right list-genes"
             )
           )
         ),
-        div(
+        tags$div(
           class = "custom-select-input",
           teal.widgets::optionalSelectInput(
             ns("facet_var"),
@@ -351,7 +351,7 @@ srv_g_levels <- function(input,
         choices = seq_len(n_max_groups),
         selected = selected_groups
       ),
-      span(
+      tags$span(
         "Please click to group the original factor levels"
       ),
       footer = tagList(
@@ -491,7 +491,7 @@ ui_example <- function(id,
   mae <- datasets$get_data(mae_name, filtered = FALSE)
   experiment_name_choices <- names(mae)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       selectInput(ns("experiment_name"), "Select experiment", experiment_name_choices),
       sampleVarSpecInput(ns("facet_var"), "Select faceting variable")
     ),

design/design_differetial_expression_module.Rmd

@@ -49,7 +49,7 @@ ui_volcanoplot <- function(id, datasets, dataname) {
 
   teal.widgets::standard_layout(
     output = plotOutput(ns("plot")),
-    encoding = div(
+    encoding = tags$div(
       selectInput(ns("experiment_name"), "Select experiment", names(mae)),
       selectInput(ns("facetvar"), "Facet by", choices = c("SEX" = "SEX", "AGE18" = "AGE18")),
       sliderInput(ns("log2_fc_thresh"), "Log2 folder change threshold", value = 2.5, min = 0.1, max = 10),

design/design_gene_names.R

@@ -4,7 +4,7 @@ ui <- function(id,
                datasets) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       teal.widgets::optionalSelectInput(
         ns("genes"),
         label = NULL,

design/design_km.Rmd

@@ -44,7 +44,7 @@ ui_made_up_merge_pr <- function(id, ...) {
         tabPanel(title = "ADSL", verbatimTextOutput(outputId = ns("adsl_data_table")))
       )
     ),
-    encoding = div(
+    encoding = tags$div(
       teal.widgets::optionalSelectInput(
         inputId = ns("select_experiment"),
         label = "Select experiment",
@@ -78,7 +78,7 @@ ui_made_up_merge_pr <- function(id, ...) {
         choices = c("12", "24", "36", "48", "60", "72", "84", "96")
       )
     ),
-    forms = div(
+    forms = tags$div(
       actionButton(ns("show_rcode"), "Show R Code", width = "100%")
     )
   )

design/design_scatterplot.Rmd

@@ -113,7 +113,7 @@ ui_scatterplot <- function(id, datasets, dataname) {
   mae <- datasets$get_data(dataname, filtered = TRUE)
   teal.widgets::standard_layout(
     output = plotOutput(ns("plot")),
-    encoding = div(
+    encoding = tags$div(
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis Data:", tags$code(dataname)),
       selectInput(ns("experiment"), "experiment", names(mae)),