Finish Bubbleplot GUI

- Removed bpRowUI, selected after imports now
compbiomed · Jan 3, 2024 · 91a9191 · 91a9191
1 parent 71c60d5
commit 91a9191
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Showing 3 changed files with 11 additions and 17 deletions.
diff --git a/R/runNormalization.R b/R/runNormalization.R
@@ -48,8 +48,8 @@
 #'  outAssayName = "logcounts")
 runNormalization <- function(inSCE,
                              useAssay = "counts",
-                             outAssayName = "customNormalizedAssay",
-                             normalizationMethod = NULL,
+                             outAssayName = "logcounts",
+                             normalizationMethod = "logNormCounts",
                              scale = FALSE,
                              seuratScaleFactor = 10000,
                              transformation = NULL,

diff --git a/inst/shiny/server.R b/inst/shiny/server.R
@@ -5713,22 +5713,17 @@ shinyServer(function(input, output, session) {
     req(vals$counts)
     selectInput(
       'bpCluster',
-      "Select Feature for Annotation",
+      "",
       colnames(colData(vals$counts)), multiple = FALSE, width = '550px')
   })
 
-  output$bpRowUI <- renderUI({
-    req(vals$counts)
-    selectNonNARowData <- names(apply(rowData(vals$counts), 2, anyNA)[apply(rowData(vals$counts), 2, anyNA) == FALSE])
-    selectInput(
-      "bpRow",
-      "Select Row Data Name",
-      selectNonNARowData, selected = names(rowData(vals$counts))[1], multiple = FALSE, width = '550px')
-  })
-
-  observeEvent(input$bpRow, {
-    req(vals$counts)
-    updateSelectizeInput(session, "bpFeatures", choices = rowData(vals$counts)[[input$bpRow]], server = TRUE)
+  observe({
+    req(vals$counts) 
+
+    if (!is.null(metadata(vals$counts)$featureDisplay) && metadata(vals$counts)$featureDisplay %in% names(rowData(vals$counts))) {
+      featureDisplayValue <- metadata(vals$counts)$featureDisplay
+      updateSelectizeInput(session, "bpFeatures", choices = rowData(vals$counts)[[featureDisplayValue]], server = TRUE)
+    }
   })
 
   observeEvent(input$plotBubbleplot, {

diff --git a/inst/shiny/ui_08_4_bubbleplot.R b/inst/shiny/ui_08_4_bubbleplot.R
@@ -10,7 +10,7 @@ shinyPanelBubbleplot <- fluidPage(
         column(width = 4,
                hr(),
                # Subset ####
-               h3("Select Annotation"),
+               h3("Select Cell Annotation"),
                uiOutput("bpClusterUI"),
                h3("Feature"),
                fluidRow(
@@ -24,7 +24,6 @@ shinyPanelBubbleplot <- fluidPage(
                           options = NULL)
                  )
                ),
-               uiOutput('bpRowUI'),
                selectizeInput(
                  'bpFeatures',
                  "Select Features",