diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
index 2e14c5df..af25da6e 100644
--- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
+++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
@@ -370,16 +370,33 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
     config <- plot_configs[[i]]
     df <- config$df
 
+    # Initialize tooltip_text
+    tooltip_text <- NULL
+
     # Define aes_mapping based on plot type
     if (config$plot_type == "scatter") {
+      # Check if y_var is provided
+      if (is.null(config$y_var)) {
+        warning(paste("Plot", i, "of type 'scatter' is missing 'y_var'. Skipping this plot."))
+        next
+      }
+
+      # Construct tooltip_text based on configuration flags
       if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
-        tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene, "<br>delta_bg:", df$delta_bg)
+        # Ensure 'delta_bg' exists
+        if (!"delta_bg" %in% names(df)) {
+          warning(paste("Plot", i, "requires 'delta_bg' column for tooltip, but it's missing."))
+          tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene)
+        } else {
+          tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene, "<br>delta_bg:", df$delta_bg)
+        }
       } else if (!is.null(config$gene_point) && config$gene_point) {
         tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene)
       } else {
         tooltip_text <- paste("x:", df[[config$x_var]], "<br>y:", df[[config$y_var]])
       }
 
+      # Define aesthetic mapping with or without color_var
       aes_mapping <- if (is.null(config$color_var)) {
         aes(x = .data[[config$x_var]], y = .data[[config$y_var]], text = tooltip_text)
       } else {
@@ -387,13 +404,34 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
             color = as.factor(.data[[config$color_var]]), text = tooltip_text)
       }
     } else {
-      # Define aes_mapping for other plot types without 'text' aesthetic
-      aes_mapping <- if (is.null(config$color_var)) {
-        aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
-      } else {
-        aes(x = .data[[config$x_var]], y = .data[[config$y_var]],
-            color = as.factor(.data[[config$color_var]]))
+      # Handle other plot types
+      # For 'box' plots, y_var is required
+      if (config$plot_type == "box") {
+        if (is.null(config$y_var)) {
+          warning(paste("Plot", i, "of type 'box' is missing 'y_var'. Skipping this plot."))
+          next
+        }
       }
+
+      # Define aes_mapping for non-scatter plots
+      aes_mapping <- if (is.null(config$color_var)) {
+        if (config$plot_type %in% c("density", "bar")) {
+          aes(x = .data[[config$x_var]])
+        } else {
+          aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
+        }
+      } else {
+        if (config$plot_type %in% c("density", "bar")) {
+          aes(x = .data[[config$x_var]],
+            color = as.factor(.data[[config$color_var]]))
+        } else {
+          aes(x = .data[[config$x_var]], y = .data[[config$y_var]],
+            color = as.factor(.data[[config$color_var]]))
+        }
+      }
+
+      # No tooltip for non-scatter plots
+      tooltip_text <- NULL
     }
 
     # Start building the plot with aes_mapping
@@ -405,7 +443,10 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
       "box" = generate_box_plot(plot_base, config),
       "density" = plot_base + geom_density(),
       "bar" = plot_base + geom_bar(),
-      plot_base  # default case if no type matches
+      {
+        warning(paste("Unknown plot_type:", config$plot_type, "- using base plot"))
+        plot_base
+      }
     )
 
     # Apply additional settings if provided
@@ -429,7 +470,6 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
       plotly_plot <- ggplotly(plot, tooltip = "text")
     } else {
       # For non-scatter plots, decide if tooltips are needed
-      # If not, you can set tooltip to NULL or specify relevant aesthetics
       plotly_plot <- ggplotly(plot, tooltip = "none")
     }