diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
index 025d02f0..ef756191 100644
--- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
+++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
@@ -376,14 +376,27 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
             plot <- plot + geom_smooth(method = "lm", se = FALSE)
           }
         }
-        
-        plot <- plot +
-          geom_errorbar(aes(
-            ymin = !!sym(paste0("mean_", config$y_var)) - !!sym(paste0("sd_", config$y_var)),
-            ymax = !!sym(paste0("mean_", config$y_var)) + !!sym(paste0("sd_", config$y_var))),
-            width = 0.1) +
-          geom_point(aes(y = !!sym(paste0("mean_", config$y_var))), size = 0.6)
-        
+
+        if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label) && config$plot_type != "box") {
+          plot <- plot + scale_x_continuous(
+            name = config$x_label,
+            breaks = config$x_breaks,
+            labels = config$x_labels
+          )
+        }
+
+        if (!is.null(config$ylim_vals)) {
+          plot <- plot + scale_y_continuous(limits = config$ylim_vals)
+        }
+    
+        if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
+          plot <- plot +
+            geom_errorbar(aes(
+              ymin = !!sym(paste0("mean_", config$y_var)) - !!sym(paste0("sd_", config$y_var)),
+              ymax = !!sym(paste0("mean_", config$y_var)) + !!sym(paste0("sd_", config$y_var))),
+              width = 0.1) +
+            geom_point(aes(y = !!sym(paste0("mean_", config$y_var))), size = 0.6)
+        }
         plot
       },
       
@@ -414,25 +427,19 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
         geom_abline(intercept = config$lm_line$intercept, slope = config$lm_line$slope, color = "tomato3") +
         annotate("text", x = 0, y = 0, label = config$correlation_text),
       
-      "box" = plot + geom_boxplot(),
+      "box" = {
+        plot <- plot + geom_boxplot()
+        if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label) && config$plot_type == "box") {
+          plot <- plot + scale_x_discrete(
+            name = config$x_label,
+            breaks = config$x_breaks,
+            labels = config$x_labels
+          )
+        }},
       "density" = plot + geom_density(),
       "bar" = plot + geom_bar()
     )
     
-    # Conditionally apply scale_x_continuous if x_breaks, x_labels, and x_label are present
-    if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
-      plot <- plot + scale_x_continuous(
-        name = config$x_label,
-        breaks = config$x_breaks,
-        labels = config$x_labels
-      )
-    }
-    
-    # Conditionally apply scale_y_continuous if ylim_vals is present
-    if (!is.null(config$ylim_vals)) {
-      plot <- plot + scale_y_continuous(limits = config$ylim_vals)
-    }
-    
     plot
   })