Fixed bug in which adding a new label to an existing annotation column would...

Fixed bug in which adding a new label to an existing annotation column would automatically assign it to current selection.

R/annotate.R

@@ -86,14 +86,14 @@ annotate_server <- function(input, output,session, rv, session_parent) {
       rv$annotationCol <- input$newCol
     } else if(!is.null(input$annotationCol) && input$annotationCol != "") {
       labels <- unique(rv$data[,input$annotationCol])
-      rv$annotationLabels <- labels[!is.na(labels)]
+      rv$annotationLabels <- unique(c(rv$annotationLabels, labels[!is.na(labels)]))
       rv$annotationCol <- input$annotationCol
     }
     if(length(input$labelsList)>0) {
       new.labels <- unlist(strsplit(input$labelsList, "\\s*,\\s*"))
       new.labels <- new.labels[!is.na(new.labels)]
       if(length(new.labels)>0) {
-        rv$annotationLabels <- c(rv$annotationLabels, new.labels)
+        rv$annotationLabels <- unique(c(rv$annotationLabels, new.labels))
       }
     }
     if(is.null(rv$annotationLabels) || length(rv$annotationLabels) == 0) {

R/explore_image.R

@@ -73,16 +73,6 @@ explore_image_server <-function(input, output, session, rv){
     }
   })
   
-  observe({
-    if(!is.null(input$pixelPosition)) {
-      rv$pixelPosition <- matrix(input$pixelPosition, ncol = 2, byrow = TRUE)
-      # Reset event to avoid triggering updates when switching workspaces
-      runjs("Shiny.setInputValue('explore_module-image-pixelPosition', null);")
-    } else {
-      rv$pixelPosition <- NULL
-    }
-  })
-  
   ## Get table row(s) associated with clicked pixel(s)
   ## Use nearest neighbour
   observe({
@@ -93,6 +83,7 @@ explore_image_server <-function(input, output, session, rv){
       ## Depends only on input$pixelPosition (input$roiX and input$roiY are not expected to change here).
       ## This prevents being run upon clearing row selection.
       isolate({
+        rv$pixelPosition <- matrix(input$pixelPosition, ncol = 2, byrow = TRUE)
         if(!is.null(rv$selectedFrame)) {
           for(i in 1:nrow(rv$pixelPosition)) {
             if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
@@ -119,6 +110,8 @@ explore_image_server <-function(input, output, session, rv){
             nn.rows.idx <- c(nn.rows.idx, as.numeric(rownames(roiData[nn$nn.idx,]))[1])
           }
           selectRows(rv$proxy, nn.rows.idx) # Set selected points in table
+          rv$selectedRows <-  nn.rows.idx
+          runjs("Shiny.setInputValue('explore_module-image-pixelPosition', null);")
         }
       }) # End isolate
     } # End if

R/explore_plot.R

@@ -103,6 +103,7 @@ plot_server <- function(input, output, session, rv) {
       brush <- event_data("plotly_selected", priority = "event", source = "A")
       if(!is.null(brush)) {
         selectRows(rv$proxy, as.numeric(unique(unlist(brush$key))))
+        rv$selectedRows <- as.numeric(unique(unlist(brush$key)))
         # Reset event to avoid triggering updates when switching workspaces
         runjs("Shiny.setInputValue('plotly_selected-A', null);")
       }

R/explore_table.R

@@ -118,19 +118,23 @@ explore_table_server <- function(input, output, session, rv, react) {
   #####################################
   ## Section to deal with annotation ##
   #####################################
-
+  
+  # Use a flag to monitor opening/closing of modal window
+  modalWindowOpened <- reactiveVal(0) 
+  
   actionFunctionselect <- function(){
     shinyjs::disable("annotateSelected")
     if(is.null(rv$annotationCol)) {
       showNotification("Annotation column not defined. Use the Annotate tab first.", type = "error")
-    } else {
+    } else if(modalWindowOpened()==0){
+      modalWindowOpened(1)
       # Show modal window with annotation options
       showModal(modalDialog(
         title = "Assign label to selected points",
         selectizeInput(inputId = ns("selectedLabel"),
                        label = "Select label",
                        multiple = FALSE,
-                       selected = ,
+                       selected = NULL,
                        choices = c("", rv$annotationLabels),
                        options = list(maxItems = 1)),
         easyClose = FALSE, # Only dismissed by clicking on a button
@@ -147,14 +151,17 @@ explore_table_server <- function(input, output, session, rv, react) {
   onclick("annotateSelected", actionFunctionselect())
   
   observeEvent(input$annotationDone, {
-    ## Add chosen label to selected rows
-    if(!is.null(rv$annotationCol)) {
-      rv$data[rv$selectedRows, rv$annotationCol] <- rep(input$selectedLabel, length(rv$selectedRows))
-    } else {
-      showNotification("Annotation column not defined.", type = "error")
-    }
-    reset("annotationDone")
-    removeModal()
+    removeModal() # causes input$annotationDone to be reset when showModal() is called again
+    isolate({
+      if(modalWindowOpened() == 1) { # modal window has been opened
+        if(!is.null(rv$annotationCol)) { # Add chosen label to selected rows
+          rv$data[rv$selectedRows, rv$annotationCol] <- rep(input$selectedLabel, length(rv$selectedRows))
+        } else {
+          showNotification("Annotation column not defined.", type = "error")
+        }
+      }
+    })
+    modalWindowOpened(0)
   })
   
   actionFunction <- function(){