diff --git a/R/constants.R b/R/constants.R
index 3733e07..2fdfb47 100644
--- a/R/constants.R
+++ b/R/constants.R
@@ -36,7 +36,6 @@ NAMESPACE_STATMODEL = list(
   visualization_fold_change_checkbox = "visualization_fold_change_checkbox",
   visualization_fold_change_input = "visualization_fold_change_input", 
   visualization_which_comparison = "visualization_which_comparison",
-  visualization_volcano_display_protein_name = "visualization_volcano_display_protein_name",
   visualization_volcano_significance_cutoff = "visualization_volcano_significance_cutoff", 
   visualization_heatmap_number_proteins = "visualization_heatmap_number_proteins",
   visualization_heatmap_cluster_option = "visualization_heatmap_cluster_option", 
diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index 5b06cee..bac7a12 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -130,6 +130,21 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
       output[[NAMESPACE_STATMODEL$modeling_section_header]] <- renderUI({
         get_modeling_section_header(input[[NAMESPACE_STATMODEL$comparison_mode]], app_template())
       })
+
+      # Auto-generate unique default name for non-pairwise comparisons
+      observe({
+        req(input[[NAMESPACE_STATMODEL$comparison_mode]] ==
+              CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise)
+        existing_names <- if (!is.null(contrast$matrix)) rownames(contrast$matrix) else character(0)
+        # Find the next available "custom comparison N"
+        n <- 1
+        while (paste0("custom comparison ", n) %in% existing_names) {
+          n <- n + 1
+        }
+        updateTextInput(session,
+                        NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name,
+                        value = paste0("custom comparison ", n))
+      })
       
       # Reset on configuration change
       observeEvent(c(input[[NAMESPACE_STATMODEL$comparison_mode]], loadpage_input()$proceed1), {
diff --git a/R/statmodel-server-visualization.R b/R/statmodel-server-visualization.R
index 618efb3..a2aefbc 100644
--- a/R/statmodel-server-visualization.R
+++ b/R/statmodel-server-visualization.R
@@ -6,9 +6,36 @@ render_group_comparison_plot_inputs = function(output, session, rownames, get_da
   ns = session$ns
   
   output[[NAMESPACE_STATMODEL$visualization_which_comparison]] = renderUI({
+    comparison_names <- rownames()
+    req(length(comparison_names) > 0)
     selectInput(ns(NAMESPACE_STATMODEL$visualization_which_comparison),
                 label = h5("Select comparison to plot"), 
-                c("all", rownames()), selected = "all")
+                comparison_names, selected = comparison_names[1])
+  })
+
+  # Dynamically filter plot type choices based on number of comparisons.
+  # Skips response curve mode (handled separately in module-statmodel-server.R).
+  observe({
+    req(input[[NAMESPACE_STATMODEL$comparison_mode]])
+    mode <- input[[NAMESPACE_STATMODEL$comparison_mode]]
+    if (mode == CONSTANTS_STATMODEL$comparison_mode_response_curve) return()
+
+    comparison_names <- rownames()
+    n_comparisons <- length(comparison_names)
+
+    choices <- c(
+      "Volcano Plot" = CONSTANTS_STATMODEL$plot_type_volcano_plot,
+      "Comparison Plot" = CONSTANTS_STATMODEL$plot_type_comparison_plot
+    )
+    if (n_comparisons >= 2) {
+      choices <- c(
+        "Volcano Plot" = CONSTANTS_STATMODEL$plot_type_volcano_plot,
+        "Heatmap" = CONSTANTS_STATMODEL$plot_type_heatmap,
+        "Comparison Plot" = CONSTANTS_STATMODEL$plot_type_comparison_plot
+      )
+    }
+    updateSelectInput(session, NAMESPACE_STATMODEL$visualization_plot_type,
+                      choices = choices)
   })
   
   output[[NAMESPACE_STATMODEL$visualization_which_protein]] = renderUI({
@@ -21,9 +48,7 @@ render_group_comparison_plot_inputs = function(output, session, rownames, get_da
     plot_type = input[[NAMESPACE_STATMODEL$visualization_plot_type]]
     
     if (plot_type == CONSTANTS_STATMODEL$plot_type_volcano_plot) {
-      show_protein_name = !is.null(loadpage_input()$DDA_DIA) &&
-        loadpage_input()$DDA_DIA != "TMT"
-      create_volcano_plot_options(ns, show_protein_name)
+      create_volcano_plot_options(ns)
     } else if (plot_type == CONSTANTS_STATMODEL$plot_type_comparison_plot) {
       create_comparison_plot_options(ns)
     } else if (plot_type == CONSTANTS_STATMODEL$plot_type_heatmap) {
@@ -78,10 +103,6 @@ create_group_comparison_plot = function(input, loadpage_input, data_comparison)
   fold_change_cutoff = ifelse(!is.null(input[[NAMESPACE_STATMODEL$visualization_fold_change_input]]), input[[NAMESPACE_STATMODEL$visualization_fold_change_input]], FALSE)
   
   tryCatch({
-    if (input[[NAMESPACE_STATMODEL$visualization_plot_type]] == CONSTANTS_STATMODEL$plot_type_volcano_plot && input[[NAMESPACE_STATMODEL$visualization_which_comparison]] == "all") {
-      remove_modal_spinner()
-      stop('** Cannot generate multiple plots in a screen. Please refine selection or save to a pdf. **')
-    }
     if (loadpage_input$BIO == "PTM") {
       result = groupComparisonPlotsPTM(
         data_comparison,
@@ -90,7 +111,9 @@ create_group_comparison_plot = function(input, loadpage_input, data_comparison)
         FCcutoff = fold_change_cutoff,
         logBase.pvalue = as.integer(input[[NAMESPACE_STATMODEL$visualization_logp_base]]),
         ProteinName = TRUE,
-        which.Comparison = input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
+        which.Comparison = if (input[[NAMESPACE_STATMODEL$visualization_plot_type]] == 
+                               CONSTANTS_STATMODEL$plot_type_heatmap) "all" 
+                           else input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
         address = FALSE,
         isPlotly = TRUE
       )
@@ -108,7 +131,9 @@ create_group_comparison_plot = function(input, loadpage_input, data_comparison)
         ProteinName = TRUE,
         numProtein = input[[NAMESPACE_STATMODEL$visualization_heatmap_number_proteins]],
         clustering = input[[NAMESPACE_STATMODEL$visualization_heatmap_cluster_option]],
-        which.Comparison = input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
+        which.Comparison = if (input[[NAMESPACE_STATMODEL$visualization_plot_type]] == 
+                               CONSTANTS_STATMODEL$plot_type_heatmap) "all" 
+                           else input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
         which.Protein = input[[NAMESPACE_STATMODEL$visualization_which_protein]],
         height = input[[NAMESPACE_STATMODEL$visualization_plot_height_slider]],
         address = "Ex_",
@@ -121,10 +146,12 @@ create_group_comparison_plot = function(input, loadpage_input, data_comparison)
         sig = input[[NAMESPACE_STATMODEL$visualization_volcano_significance_cutoff]],
         FCcutoff = fold_change_cutoff,
         logBase.pvalue = as.numeric(input[[NAMESPACE_STATMODEL$visualization_logp_base]]),
-        ProteinName = input[[NAMESPACE_STATMODEL$visualization_volcano_display_protein_name]],
+        ProteinName = TRUE,
         numProtein = input[[NAMESPACE_STATMODEL$visualization_heatmap_number_proteins]],
         clustering = input[[NAMESPACE_STATMODEL$visualization_heatmap_cluster_option]],
-        which.Comparison = input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
+        which.Comparison = if (input[[NAMESPACE_STATMODEL$visualization_plot_type]] == 
+                               CONSTANTS_STATMODEL$plot_type_heatmap) "all" 
+                           else input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
         which.Protein = input[[NAMESPACE_STATMODEL$visualization_which_protein]],
         height = input[[NAMESPACE_STATMODEL$visualization_plot_height_slider]],
         address = "Ex_",
@@ -272,8 +299,10 @@ create_download_plot_handler <- function(output, input, contrast, preprocess_dat
                 sig = input[[NAMESPACE_STATMODEL$visualization_volcano_significance_cutoff]],
                 FCcutoff = fold_change_cutoff,
                 logBase.pvalue = as.integer(input[[NAMESPACE_STATMODEL$visualization_logp_base]]),
-                ProteinName = input[[NAMESPACE_STATMODEL$visualization_volcano_display_protein_name]],
-                which.Comparison = input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
+                ProteinName = TRUE,
+                which.Comparison = if (plot_type == 
+                                       CONSTANTS_STATMODEL$plot_type_heatmap) "all"
+                                   else input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
                 address = address_prefix
               )
             } else {
@@ -283,10 +312,12 @@ create_download_plot_handler <- function(output, input, contrast, preprocess_dat
                 sig = input[[NAMESPACE_STATMODEL$visualization_volcano_significance_cutoff]],
                 FCcutoff = fold_change_cutoff,
                 logBase.pvalue = as.numeric(input[[NAMESPACE_STATMODEL$visualization_logp_base]]),
-                ProteinName = input[[NAMESPACE_STATMODEL$visualization_volcano_display_protein_name]],
+                ProteinName = TRUE,
                 numProtein = input[[NAMESPACE_STATMODEL$visualization_heatmap_number_proteins]],
                 clustering = input[[NAMESPACE_STATMODEL$visualization_heatmap_cluster_option]],
-                which.Comparison = input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
+                which.Comparison = if (plot_type == 
+                                       CONSTANTS_STATMODEL$plot_type_heatmap) "all"
+                                   else input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
                 which.Protein = input[[NAMESPACE_STATMODEL$visualization_which_protein]],
                 height = input[[NAMESPACE_STATMODEL$visualization_plot_height_slider]],
                 address = address_prefix,
diff --git a/R/statmodel-ui-options-visualization.R b/R/statmodel-ui-options-visualization.R
index 24cb684..3d8cdc4 100644
--- a/R/statmodel-ui-options-visualization.R
+++ b/R/statmodel-ui-options-visualization.R
@@ -32,12 +32,9 @@ create_plot_type_selector <- function(ns) {
 }
 #' Create volcano plot specific options
 #' @noRd
-create_volcano_plot_options <- function(ns, show_protein_name = TRUE) {
+create_volcano_plot_options <- function(ns) {
   tagList(
     uiOutput(ns(NAMESPACE_STATMODEL$visualization_which_comparison)),
-    if (show_protein_name) {
-      checkboxInput(ns(NAMESPACE_STATMODEL$visualization_volcano_display_protein_name), label = p("display protein name"))
-    },
     selectInput(
       ns(NAMESPACE_STATMODEL$visualization_logp_base), 
       label = h5("Log transformation of adjusted p-value"),
@@ -71,7 +68,7 @@ create_heatmap_options <- function(ns) {
   tagList(
     h4("Note: Only one page will be shown in browser. To view all proteins please view this plot as a pdf. Heatmaps require at least two comparisons."),
     selectInput(
-      ns(NAMESPACE_STATMODEL$visualization_logp_base), 
+      ns(NAMESPACE_STATMODEL$visualization_logp_base),
       label = h5("Log transformation of adjusted p-value"),
       c("base 2" = "2", "base 10" = "10"), 
       selected = "10"
diff --git a/tests/testthat/test-statmodel-ui-options-visualization.R b/tests/testthat/test-statmodel-ui-options-visualization.R
index 3133bdc..b5b3955 100644
--- a/tests/testthat/test-statmodel-ui-options-visualization.R
+++ b/tests/testthat/test-statmodel-ui-options-visualization.R
@@ -39,13 +39,10 @@ test_that("Correct elements are present in create_volcano_plot_options", {
   ui_html <- htmltools::renderTags(result)$html
   expect_true(grepl(NAMESPACE_STATMODEL$visualization_which_comparison, ui_html),
               info = "Which comparison namespace should be present")
-  expect_true(grepl(NAMESPACE_STATMODEL$visualization_volcano_display_protein_name, ui_html),
-              info = "Display protein name checkbox namespace should be present")
   expect_true(grepl(NAMESPACE_STATMODEL$visualization_logp_base, ui_html),
               info = "Log p-value base namespace should be present")
   expect_true(grepl(NAMESPACE_STATMODEL$visualization_volcano_significance_cutoff, ui_html),
               info = "Significance cutoff namespace should be present")
-  
 })
 
 test_that("All possible options in create_plot_type_selector", {
diff --git a/tests/testthat/test-utils-statmodel-server.R b/tests/testthat/test-utils-statmodel-server.R
index f069bc4..aa42ee1 100644
--- a/tests/testthat/test-utils-statmodel-server.R
+++ b/tests/testthat/test-utils-statmodel-server.R
@@ -288,6 +288,8 @@ test_that("extract_significant_proteins filters PTM data correctly", {
   
   result <- extract_significant_proteins(data_comp, loadpage_input, 0.05)
   expect_equal(nrow(result$ADJUSTED.Model), 1)
+  expect_equal(nrow(result$PTM.Model), 2)
+  expect_equal(nrow(result$PROTEIN.Model), 1)
 })
 
 test_that("extract_significant_proteins filters TMT data correctly", {