diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R
index ca73f6dc..6c1de05c 100644
--- a/workflow/apps/r/calculate_interaction_zscores5.R
+++ b/workflow/apps/r/calculate_interaction_zscores5.R
@@ -158,7 +158,10 @@ update_gene_names <- function(df, sgd_gene_list) {
 
 generate_plot <- function(df, x_var, y_var = NULL, plot_type, color_var = "conc_num", title, x_label = NULL, y_label = NULL) {
   # Base ggplot object with conditional y mapping
-  if (!is.null(y_var)) {
+  if (plot_type == "box") {
+    # Ensure x_var is treated as a factor for box plots
+    plot <- ggplot(df, aes(x = as.factor(!!sym(x_var)), y = !!sym(y_var), color = !!sym(color_var)))
+  } else if (!is.null(y_var)) {
     plot <- ggplot(df, aes(x = !!sym(x_var), y = !!sym(y_var), color = !!sym(color_var)))
   } else {
     plot <- ggplot(df, aes(x = !!sym(x_var), color = !!sym(color_var)))
@@ -166,7 +169,7 @@ generate_plot <- function(df, x_var, y_var = NULL, plot_type, color_var = "conc_
   
   # Handle different plot types
   if (plot_type == "scatter") {
-    plot <- plot + 
+    plot <- plot +
       geom_point(shape = 3, size = 0.2, position = "jitter") +
       stat_summary(fun.data = mean_sdl, geom = "errorbar") +
       stat_summary(fun = mean, geom = "point", size = 0.6)
@@ -188,17 +191,15 @@ generate_plot <- function(df, x_var, y_var = NULL, plot_type, color_var = "conc_
   return(plot)
 }
 
-
-
 generate_and_save_plots <- function(df, output_dir, prefix, variables, include_qc = FALSE) {
   plots <- list()
   
   for (var in variables) {
     scatter_plot <-
-      generate_plot(df, x_var = scan, y_var = !!sym(var), plot_type = "scatter",
+      generate_plot(df, x_var = "scan", y_var = var, plot_type = "scatter",
       title = paste(prefix, "Scatter Plot for", var))
     boxplot <-
-      generate_plot(df, x_var = as.factor(scan), y_var = !!sym(var), plot_type = "box",
+      generate_plot(df, x_var = "scan", y_var = var, plot_type = "box",
       title = paste(prefix, "Box Plot for", var))
     
     plots[[paste0(var, "_scatter")]] <- scatter_plot
@@ -207,13 +208,13 @@ generate_and_save_plots <- function(df, output_dir, prefix, variables, include_q
   
   if (include_qc) {
     plots[["Raw_L_vs_K"]] <-
-      generate_plot(df, x_var = L, y_var = K, plot_type = "scatter",
+      generate_plot(df, x_var = "L", y_var = "K", plot_type = "scatter",
       title = "Raw L vs K before QC")
     plots[["Delta_bg_Density"]] <-
-      generate_plot(df, x_var = delta_bg, plot_type = "density", color_var = "conc_num",
+      generate_plot(df, x_var = "delta_bg", plot_type = "density", color_var = "conc_num",
       title = "Density plot for Delta Background by Conc All Data")
     plots[["Delta_bg_Bar"]] <-
-      generate_plot(df, x_var = delta_bg, plot_type = "bar",
+      generate_plot(df, x_var = "delta_bg", plot_type = "bar",
       title = "Bar plot for Delta Background by Conc All Data")
   }
   
@@ -424,12 +425,13 @@ generate_rf_plots <- function(df_calculations, df_interactions, output_dir, file
 generate_summary_plots <- function(df, output_dir) {
   variables <- c("L", "K", "r", "AUC")
   plot_list <- lapply(variables, function(var) {
-    generate_plot(df, x_var = conc_num_factor, y_var = !!sym(var), plot_type = "scatter", title = paste("Summary Plot for", var))
+    generate_plot(df, x_var = "conc_num_factor", y_var = var, plot_type = "scatter", title = paste("Summary Plot for", var))
   })
 
   save_plots("Summary_Plots", plot_list, output_dir)
 }
 
+
 generate_cpp_correlation_plots <- function(df_na_rm, lm_list, output_dir) {
   lm_summaries <- lapply(lm_list, summary)
   plot_titles <- c("Interaction L vs. Interaction K", "Interaction L vs. Interaction r", "Interaction L vs. Interaction AUC",