diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
index 49d5cbf2..f8ff7b35 100644
--- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
+++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R
@@ -538,28 +538,21 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
         next  # skip plot if insufficient data is available
       }
 
-      aes_mapping <- if (config$plot_type == "bar") {
-        if (!is.null(config$color_var)) {
-          aes(x = .data[[config$x_var]], fill = .data[[config$color_var]], color = .data[[config$color_var]])
-        } else {
-          aes(x = .data[[config$x_var]])
-        }
-      } else if (config$plot_type == "density") {
-        if (!is.null(config$color_var)) {
-          aes(x = .data[[config$x_var]], color = .data[[config$color_var]])
-        } else {
-          aes(x = .data[[config$x_var]])
-        }
-      } else {
-        if (!is.null(config$y_var) && !is.null(config$color_var)) {
-          aes(x = .data[[config$x_var]], y = .data[[config$y_var]], color = .data[[config$color_var]])
-        } else if (!is.null(config$y_var)) {
-          aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
-        } else {
-          aes(x = .data[[config$x_var]])
-        }
+      # Create initial aes mappings for all plot types
+      aes_mapping <- aes(x = .data[[config$x_var]])  # required
+      if (!is.null(config$y_var)) {
+        aes_mapping <- modifyList(aes_mapping, aes(y = .data[[config$y_var]])) # optional for density/bar plots
+      }
+      if (!is.null(config$color_var)) {
+        aes_mapping <- modifyList(aes_mapping, aes(color = .data[[config$color_var]])) # dynamic color_var
+      } else if (!is.null(config$color)) {
+        aes_mapping <- modifyList(aes_mapping, aes(color = config$color)) # static color
+      }
+      if (config$plot_type == "bar" && !is.null(config$color_var)) {
+        aes_mapping <- modifyList(aes_mapping, aes(fill = .data[[config$color_var]])) # only fill bar plots
       }
 
+      # Begin plot generation
       plot <- ggplot(df, aes_mapping) + theme_publication(legend_position = config$legend_position)
 
       plot <- switch(config$plot_type,
@@ -567,7 +560,7 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
         "box" = generate_boxplot(plot, config),
         "density" = plot + geom_density(),
         "bar" = plot + geom_bar(),
-        plot  # default
+        plot # default
       )
 
       if (!is.null(config$title)) {
@@ -798,21 +791,21 @@ generate_scatter_plot <- function(plot, config) {
       )
   }
 
-  # Add rectangles if specified
-  if (!is.null(config$rectangles)) {
-    for (rect in config$rectangles) {
-      plot <- plot + annotate(
-        "rect",
-        xmin = rect$xmin,
-        xmax = rect$xmax,
-        ymin = rect$ymin,
-        ymax = rect$ymax,
-        fill = ifelse(is.null(rect$fill), NA, rect$fill),
-        color = ifelse(is.null(rect$color), "black", rect$color),
-        alpha = ifelse(is.null(rect$alpha), 0.1, rect$alpha)
-      )
-    }
-  }
+  # # Add rectangles if specified
+  # if (!is.null(config$rectangles)) {
+  #   for (rect in config$rectangles) {
+  #     plot <- plot + annotate(
+  #       "rect",
+  #       xmin = rect$xmin,
+  #       xmax = rect$xmax,
+  #       ymin = rect$ymin,
+  #       ymax = rect$ymax,
+  #       fill = ifelse(is.null(rect$fill), NA, rect$fill),
+  #       color = ifelse(is.null(rect$color), "black", rect$color),
+  #       alpha = ifelse(is.null(rect$alpha), 0.1, rect$alpha)
+  #     )
+  #   }
+  # }
 
   # Customize X-axis if specified
   if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
@@ -1201,10 +1194,6 @@ generate_correlation_plot_configs <- function(df, df_reference) {
     list(x = "r", y = "AUC")
   )
 
-  # This filtering was in the original script
-  # df_reference <- df_reference %>%
-  #   filter(!is.na(Z_lm_L))
-
   plot_configs <- list()
 
   # Iterate over the option to highlight cyan points (TRUE/FALSE)
@@ -1500,10 +1489,10 @@ main <- function() {
     )
 
     # Parallelize background and quality control plot generation
-    # furrr::future_map(plot_configs, function(config) {
-    #   generate_and_save_plots(config$out_dir, config$filename, config$plot_configs,
-    #     page_width = config$page_width, page_height = config$page_height)
-    # }, .options = furrr_options(seed = TRUE))
+    furrr::future_map(plot_configs, function(config) {
+      generate_and_save_plots(config$out_dir, config$filename, config$plot_configs,
+        page_width = config$page_width, page_height = config$page_height)
+    }, .options = furrr_options(seed = TRUE))
 
     # Loop over background strains
     # TODO currently only tested against one strain, if we want to do multiple strains we'll
@@ -1612,9 +1601,9 @@ main <- function() {
       write.csv(deletion_results$calculations, file = file.path(out_dir, "zscore_calculations.csv"), row.names = FALSE)
       write.csv(df_interactions, file = file.path(out_dir, "zscore_interactions.csv"), row.names = FALSE)
 
-      message("Generating deletion interaction plots")
-      deletion_plot_configs <- generate_interaction_plot_configs(df_reference_summary_stats, df_interactions_joined, "deletion")
-      generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, page_width = 16, page_height = 16)
+      # message("Generating deletion interaction plots")
+      # deletion_plot_configs <- generate_interaction_plot_configs(df_reference_summary_stats, df_interactions_joined, "deletion")
+      # generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, page_width = 16, page_height = 16)
 
       message("Writing enhancer/suppressor csv files")
       interaction_threshold <- 2  # TODO add to study config?