Merge 94536be into cd1d9d9

insightsengineering · Jul 29, 2022 · b2c9d9e · b2c9d9e
2 parents cd1d9d9 + 94536be
commit b2c9d9e
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Showing 16 changed files with 378 additions and 757 deletions.
diff --git a/R/geneSpec.R b/R/geneSpec.R
@@ -46,6 +46,7 @@ geneSpecInput <- function(inputId,
 
   ns <- NS(inputId)
   tagList(
+    include_css_files(pattern = "*"),
     div(
       class = "row",
       div(
@@ -94,8 +95,7 @@ geneSpecInput <- function(inputId,
             icon_off = icon("fas fa-lock-open"),
             animation = "pulse"
           )
-        ),
-        include_css_files(pattern = "*")
+        )
       )
     ),
     div(
@@ -109,8 +109,8 @@ geneSpecInput <- function(inputId,
         options = list(
           render = I("{
           option: function(item, escape) {
-              return '<div> <div style = \"font-size: inherit; display: inline\">' + item.label + '</div>' +
-                ' <div style=\"color: #808080; font-size: xx-small; display: inline\" >' + item.value + '</div> </div>'
+              return '<div> <span style=\"font-size: inherit;\">' + item.label + '</div>' +
+                ' <span style=\"color: #808080; font-size: xx-small;\" >' + item.value + '</div> </div>'
             }
           }"),
           searchField = c("value", "label"),

diff --git a/R/pca.R b/R/pca.R
@@ -67,82 +67,87 @@ ui_g_pca <- function(id,
   mae <- datasets$get_data(mae_name, filtered = FALSE)
   experiment_name_choices <- names(mae)
 
-  teal.widgets::standard_layout(
-    encoding = div(
-      ### Reporter
-      teal.reporter::simple_reporter_ui(ns("simple_reporter")),
-      ###
-      tags$label("Encodings", class = "text-primary"),
-      helpText("Analysis of MAE:", tags$code(mae_name)),
-      experimentSpecInput(ns("experiment"), datasets, mae_name),
-      assaySpecInput(ns("assay")),
-      conditionalPanel(
-        condition = "input.tab_selected == 'PCA'",
-        ns = ns,
-        sampleVarSpecInput(ns("color"), "Optional color variable"),
-        selectizeInput(ns("x_var"), "Select X-axis PC", choices = ""),
-        selectizeInput(ns("y_var"), "Select Y-axis PC", choices = "")
+  tagList(
+    teal.widgets::standard_layout(
+      include_css_files(pattern = "*"),
+      encoding = div(
+        ### Reporter
+        teal.reporter::simple_reporter_ui(ns("simple_reporter")),
+        ###
+        tags$label("Encodings", class = "text-primary"),
+        helpText("Analysis of MAE:", tags$code(mae_name)),
+        experimentSpecInput(ns("experiment"), datasets, mae_name),
+        assaySpecInput(ns("assay")),
+        conditionalPanel(
+          condition = "input.tab_selected == 'PCA'",
+          ns = ns,
+          sampleVarSpecInput(ns("color"), "Optional color variable"),
+          selectizeInput(ns("x_var"), "Select X-axis PC", choices = ""),
+          selectizeInput(ns("y_var"), "Select Y-axis PC", choices = "")
+        ),
+        teal.widgets::panel_group(
+          teal.widgets::panel_item(
+            input_id = "settings_item",
+            collapsed = TRUE,
+            title = "Additional Settings",
+            tags$label("Use only Top Variance Genes"),
+            shinyWidgets::switchInput(ns("filter_top"), value = FALSE, size = "mini"),
+            conditionalPanel(
+              condition = "input.filter_top",
+              ns = ns,
+              sliderInput(ns("n_top"), label = "Number of Top Genes", min = 10, max = 5000, value = 500)
+            ),
+            conditionalPanel(
+              condition = "input.tab_selected == 'PCA'",
+              ns = ns,
+              tags$label("Show Variance %"),
+              shinyWidgets::switchInput(ns("var_pct"), value = TRUE, size = "mini"),
+              tags$label("Show Label"),
+              shinyWidgets::switchInput(ns("label"), value = TRUE, size = "mini")
+            ),
+            conditionalPanel(
+              condition = "input.tab_selected == 'PC and Sample Correlation'",
+              ns = ns,
+              tags$label("Cluster columns"),
+              shinyWidgets::switchInput(ns("cluster_columns"), value = FALSE, size = "mini")
+            ),
+            tags$label("View Matrix"),
+            shinyWidgets::switchInput(ns("show_matrix"), value = TRUE, size = "mini")
+          )
+        )
       ),
-      teal.widgets::panel_group(
-        teal.widgets::panel_item(
-          input_id = "settings_item",
-          collapsed = TRUE,
-          title = "Additional Settings",
-          tags$label("Use only Top Variance Genes"),
-          shinyWidgets::switchInput(ns("filter_top"), value = FALSE, size = "mini"),
-          conditionalPanel(
-            condition = "input.filter_top",
-            ns = ns,
-            sliderInput(ns("n_top"), label = "Number of Top Genes", min = 10, max = 5000, value = 500)
-          ),
-          conditionalPanel(
-            condition = "input.tab_selected == 'PCA'",
-            ns = ns,
-            tags$label("Show Variance %"),
-            shinyWidgets::switchInput(ns("var_pct"), value = TRUE, size = "mini"),
-            tags$label("Show Label"),
-            shinyWidgets::switchInput(ns("label"), value = TRUE, size = "mini")
+      output = div(
+        style = "display:flow-root",
+        tabsetPanel(
+          id = ns("tab_selected"),
+          type = "tabs",
+          tabPanel(
+            "PCA",
+            column(
+              width = 12,
+              div(
+                class = "my-5",
+                plotOutput(ns("plot_pca"))
+              ),
+              DT::DTOutput(ns("table_pca"))
+            )
           ),
-          conditionalPanel(
-            condition = "input.tab_selected == 'PC and Sample Correlation'",
-            ns = ns,
-            tags$label("Cluster columns"),
-            shinyWidgets::switchInput(ns("cluster_columns"), value = FALSE, size = "mini")
-          ),
-          tags$label("View Matrix"),
-          shinyWidgets::switchInput(ns("show_matrix"), value = TRUE, size = "mini")
-        )
-      )
-    ),
-    output = div(
-      style = "display:flow-root",
-      tabsetPanel(
-        id = ns("tab_selected"),
-        type = "tabs",
-        tabPanel(
-          "PCA",
-          column(
-            width = 12,
-            div(style = "height:20px;"),
-            plotOutput(ns("plot_pca")),
-            br(), br(), br(),
-            DT::DTOutput(ns("table_pca"))
-          )
-        ),
-        tabPanel(
-          "PC and Sample Correlation",
-          column(
-            width = 12,
-            div(style = "height:20px;"),
-            plotOutput(ns("plot_cor")),
-            br(), br(), br(),
-            DT::DTOutput(ns("table_cor"))
+          tabPanel(
+            "PC and Sample Correlation",
+            column(
+              width = 12,
+              div(
+                class = "my-5",
+                plotOutput(ns("plot_cor"))
+              ),
+              DT::DTOutput(ns("table_cor"))
+            )
           )
         )
-      )
-    ),
-    pre_output = pre_output,
-    post_output = post_output
+      ),
+      pre_output = pre_output,
+      post_output = post_output
+    )
   )
 }
 

diff --git a/R/sampleVarSpec.R b/R/sampleVarSpec.R
@@ -23,6 +23,7 @@ sampleVarSpecInput <- function(inputId,
 
   ns <- NS(inputId)
   tagList(
+    include_css_files(pattern = "*"),
     div(
       class = "row",
       div(
@@ -39,8 +40,7 @@ sampleVarSpecInput <- function(inputId,
           span(icon("fas fa-table")),
           title = label_levels_button,
           class = "pull-right list-genes"
-        ),
-        include_css_files(pattern = "*")
+        )
       )
     ),
     div(
@@ -402,8 +402,8 @@ sampleVarSpecServer <- function(id,
 
           old_values <- names(assign_lists[[experiment_name]][[sample_var]])
           if (!is.null(old_values) &&
-              length(old_values) == length(sample_var_levels) &&
-              all(sort(old_values) == sort(sample_var_levels))) {
+            length(old_values) == length(sample_var_levels) &&
+            all(sort(old_values) == sort(sample_var_levels))) {
             selected_groups <- assign_lists[[experiment_name]][[sample_var]]
           }
 

diff --git a/R/utils.R b/R/utils.R
@@ -56,10 +56,9 @@ include_css_files <- function(pattern = "*") { # nolint
     system.file("css", package = "teal.modules.hermes", mustWork = TRUE),
     pattern = pattern, full.names = TRUE
   )
-  return(singleton(lapply(css_files, includeCSS)))
+  return(shiny::singleton(shiny::tags$head(lapply(css_files, includeCSS))))
 }
 
-
 #' Include `JS` files from `/inst/js/` package directory to application header
 #'
 #' `system.file` should not be used to access files in other packages, it does

diff --git a/design/design_combine_levels.Rmd b/design/design_combine_levels.Rmd
@@ -213,42 +213,44 @@ ui_g_levels <- function(id,
   mae <- datasets$get_data(mae_name, filtered = FALSE)
   experiment_name_choices <- names(mae)
 
-  teal.widgets::standard_layout(
-    encoding = div(
-      selectInput(ns("experiment_name"), "Select experiment", experiment_name_choices),
-      div(
-        class = "row",
+  tagList(
+    include_css_files(pattern = "*"),
+    teal.widgets::standard_layout(
+      encoding = div(
+        selectInput(ns("experiment_name"), "Select experiment", experiment_name_choices),
         div(
-          class = "col-sm-8",
-          tags$label(
-            class = "control-label",
-            "Select faceting variable"
+          class = "row",
+          div(
+            class = "col-sm-8",
+            tags$label(
+              class = "control-label",
+              "Select faceting variable"
+            )
+          ),
+          div(
+            class = "col-sm-4",
+            actionButton(
+              ns("open_levels_input"),
+              span(icon("font fa-object-ungroup")),
+              title = "Combine factor levels",
+              class = "pull-right list-genes"
+            )
           )
         ),
         div(
-          class = "col-sm-4",
-          actionButton(
-            ns("open_levels_input"),
-            span(icon("font fa-object-ungroup")),
-            title = "Combine factor levels",
-            class = "pull-right list-genes"
-          ),
-          include_css_files(pattern = "*")
+          class = "custom-select-input",
+          teal.widgets::optionalSelectInput(
+            ns("facet_var"),
+            label = NULL,
+            choices = "",
+            multiple = FALSE
+          )
         )
       ),
-      div(
-        class = "custom-select-input",
-        teal.widgets::optionalSelectInput(
-          ns("facet_var"),
-          label = NULL,
-          choices = "",
-          multiple = FALSE
-        )
-      )
-    ),
-    output = plotOutput(ns("plot")),
-    pre_output = pre_output,
-    post_output = post_output
+      output = plotOutput(ns("plot")),
+      pre_output = pre_output,
+      post_output = post_output
+    )
   )
 }
 ```