feat: add Spectronaut pivot report import and inline experimental design editor

- Add Spectronaut pivot report as a new data source with per-file
  preprocessing, condition setup TSV import, and wiring through
  identifier and experimental design steps
- Replace file-upload experimental design with inline rhandsontable
  editor for CSV/Excel workflows; adds column classification,
  validation helpers, and collapsible data preview panel
- Fix sidebar setup next button reactivity
- Fix .data$ pronoun usage in color-mod helper
- Add rhandsontable dependency; expose DTOutput/renderDT and p.adjust
- Add tests for Spectronaut processing and expand CSV/Excel test coverage

Author: cliandouble08

.gitignore

@@ -17,3 +17,11 @@ CLAUDE.md
 # Pak lockfiles (optional, platform-specific)
 pkg.lock
 .github/pkg.lock
+
+.worktrees/
+
+firebase-debug.log
+
+docs/
+
+.observer.lock

DESCRIPTION

@@ -56,7 +56,8 @@ Imports:
     snakecase,
     shinyjs,
     future,
-    furrr
+    furrr,
+    rhandsontable
 Depends:
     R (>= 4.0.0),
     shiny

NAMESPACE

@@ -13,14 +13,17 @@ import(janitor)
 import(khroma)
 import(limma)
 import(markdown)
+import(rhandsontable)
 import(shiny, except=c(dataTableOutput, renderDataTable, runExample))
 import(shinyBS)
 import(shinyWidgets)
 import(snakecase)
 import(stringr)
 import(tidyr)
+importFrom(DT,DTOutput)
 importFrom(DT,dataTableOutput)
 importFrom(DT,datatable)
+importFrom(DT,renderDT)
 importFrom(DT,renderDataTable)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,crossprod)
@@ -72,6 +75,7 @@ importFrom(stats,lm)
 importFrom(stats,mad)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
+importFrom(stats,p.adjust)
 importFrom(stats,prcomp)
 importFrom(stats,qnorm)
 importFrom(stats,qt)

R/app_server.R

@@ -19,6 +19,7 @@ app_server <- function(input, output, session) {
   GCTs_and_params <- sidebar_output$GCTs_and_params
   globals <- sidebar_output$globals
   GCTs_original <- sidebar_output$GCTs_original
+  column_rename_map <- sidebar_output$column_rename_map
 
 
   ## Clear all notifications functionality
@@ -37,7 +38,8 @@ app_server <- function(input, output, session) {
   all_summary_exports <- summaryTabServer(
     GCTs_and_params = GCTs_and_params,
     globals = globals,
-    GCTs_original = GCTs_original
+    GCTs_original = GCTs_original,
+    column_rename_map = column_rename_map
   )
 
   ## QC boxplots module

R/app_ui.R

@@ -58,6 +58,40 @@ app_UI <- function(request) {dashboardPage(
       });
     ")),
 
+    # Experimental design panel - shown during CSV/Excel experimental design step
+    conditionalPanel(
+      condition = "output['setupSidebar-showExpDesignPanel']",
+      div(id = "exp-design-panel", style = "padding: 10px 15px;",
+          uiOutput("setupSidebar-expDesignPanelContent")
+      )
+    ),
+
+    # Separator between experimental design and data preview
+    conditionalPanel(
+      condition = "output['setupSidebar-showDataPreview']",
+      hr(style = "margin: 4px 15px;")
+    ),
+
+    # Data preview panel - shown when a CSV/Excel file is uploaded
+    conditionalPanel(
+      condition = "output['setupSidebar-showDataPreview']",
+      div(id = "data-preview-panel", style = "padding: 10px 15px;",
+        div(style = "display:flex; align-items:center; gap:8px; margin-bottom:6px;",
+          tags$strong(shiny::icon("table"), " Data Preview (first 20 rows)"),
+          actionButton("toggleDataPreview", "Hide", class = "btn btn-xs btn-default",
+                       onclick = "$('#data-preview-content').slideToggle(); $(this).text($(this).text() === 'Hide' ? 'Show' : 'Hide');")
+        ),
+        uiOutput("setupSidebar-previewFileSelector"),
+        div(id = "data-preview-content",
+            DT::DTOutput("setupSidebar-dataPreviewTable"))
+      )
+    ),
+
+    conditionalPanel(
+      condition = "output['setupSidebar-showDataPreview']",
+      div(style = "padding-top: 20px;")
+    ),
+
     navbarPage(
       title = '',
       id = "navbar-tabs",

R/protigy-package.R

@@ -30,12 +30,13 @@
 #' @importFrom shinyjqui orderInput updateOrderInput
 #' @importFrom grDevices colorRampPalette dev.off pdf boxplot.stats
 #' @importFrom methods new
-#' @importFrom stats density mad median quantile sd aggregate coef qnorm qt setNames cor anova lm prcomp var complete.cases model.matrix
+#' @importFrom stats density mad median quantile sd aggregate coef qnorm qt setNames cor anova lm prcomp var complete.cases model.matrix p.adjust
 #' @importFrom zip zip
 #' @importFrom utils tail stack combn compareVersion packageVersion write.csv write.table head
 #' @importFrom rlang .data
 #' @importFrom ggthemes geom_tufteboxplot
-#' @importFrom DT datatable renderDataTable dataTableOutput
+#' @importFrom DT datatable renderDataTable dataTableOutput DTOutput renderDT
+#' @import rhandsontable
 #' @importFrom future plan availableCores
 #' @importFrom furrr future_map future_map2
 #' @importFrom Matrix Matrix