feat: DE summary table & volcano protein searching and labeling

.gitignore

@@ -11,9 +11,16 @@ rsconnect/
 # Documentation images
 # inst/doc_images/workflow_diagram.png  # Commented out so image appears on GitHub
 .claude/
+.cursor/
 
 CLAUDE.md
 
 # Pak lockfiles (optional, platform-specific)
 pkg.lock
 .github/pkg.lock
+
+.worktrees/
+
+firebase-debug.log
+
+docs/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Protigy
 Title: Proteomics Toolset for Integrative Data Analysis
-Version: 2.3.2
+Version: 2.4.0
 Authors@R: c(
     person("Stephanie", "Vartany", , "svartany@broadinstitute.org", role = "aut"),
     person("D R", "Mani", , "manidr@broadinstitute.org", role = "aut"),
@@ -13,13 +13,15 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Imports:
+    AnnotationDbi,
     circlize,
     cmapR,
     colourpicker,
     ComplexHeatmap,
     dplyr,
     DT,
     ggplot2,
+    ggrepel,
     khroma,
     plotly (>= 4.10.1),
     RColorBrewer,
@@ -42,6 +44,8 @@ Imports:
     preprocessCore,
     mixtools,
     mclust,
+    org.Hs.eg.db,
+    org.Mm.eg.db,
     markdown,
     utils,
     rlang,

NAMESPACE

@@ -8,6 +8,7 @@ import(cmapR)
 import(dplyr)
 import(ggfortify)
 import(ggplot2)
+import(ggrepel)
 import(glue)
 import(janitor)
 import(khroma)
@@ -45,7 +46,11 @@ importFrom(mclust,mclustBIC)
 importFrom(methods,existsFunction)
 importFrom(methods,new)
 importFrom(mixtools,normalmixEM)
+importFrom(plotly,add_annotations)
+importFrom(plotly,event_data)
+importFrom(plotly,event_register)
 importFrom(plotly,ggplotly)
+importFrom(plotly,layout)
 importFrom(plotly,plotlyOutput)
 importFrom(plotly,renderPlotly)
 importFrom(plotly,style)

R/app_ui.R

@@ -32,8 +32,20 @@ app_UI <- function(request) {dashboardPage(
     # JavaScript to manage Clear All Notifications button visibility
     tags$script(HTML("
       $(document).ready(function() {
+        var MAX_NOTIFICATIONS = 10;
+
+        // Shiny appends new notifications; earliest in DOM are oldest - drop excess first.
+        function trimNotificationsToMax() {
+          var notifications = $('.shiny-notification');
+          var extra = notifications.length - MAX_NOTIFICATIONS;
+          if (extra > 0) {
+            notifications.slice(0, extra).remove();
+          }
+        }
+
         // Function to update button visibility based on notification presence
         function updateClearButton() {
+          trimNotificationsToMax();
           var notifications = $('.shiny-notification');
           if (notifications.length > 0) {
             $('#clear_all_notifications_header').show();

R/protigy-package.R

@@ -5,6 +5,7 @@
 #' @export
 #' @rawNamespace import(shiny, except=c(dataTableOutput, renderDataTable, runExample))
 #' @import ggplot2
+#' @import ggrepel
 #' @import dplyr
 #' @import tidyr
 #' @import ComplexHeatmap
@@ -20,7 +21,7 @@
 #' @importFrom shinydashboard dashboardBody dashboardSidebar
 #' @importFrom shinydashboardPlus dashboardPage dashboardHeader box boxSidebar boxDropdown
 #' @importFrom grid gpar
-#' @importFrom plotly ggplotly plotlyOutput renderPlotly style
+#' @importFrom plotly ggplotly plotlyOutput renderPlotly style add_annotations event_register event_data layout
 #' @importFrom circlize colorRamp2
 #' @importFrom colourpicker colourInput updateColourInput
 #' @importFrom shinyBS tipify