diff --git a/R/maaslin3.R b/R/maaslin3.R
index b1550d3..e33f93d 100755
--- a/R/maaslin3.R
+++ b/R/maaslin3.R
@@ -584,17 +584,17 @@ options <-
     )
 
 options <-
-  optparse::add_option(
-    options,
-    c("--summary_plot_balanced"),
-    type = "logical",
-    dest = "make_summary_plot_balanced",
-    default = args$summary_plot_balanced,
-    help = paste(
-      "If coef_plot_vars is selected this will",
-      "select balanced top features [ Default: %default ]"
+    optparse::add_option(
+        options,
+        c("--summary_plot_balanced"),
+        type = "logical",
+        dest = "make_summary_plot_balanced",
+        default = args$summary_plot_balanced,
+        help = paste(
+            "If coef_plot_vars is selected this will",
+            "select balanced top features [ Default: %default ]"
+        )
     )
-  )
 
 option_not_valid_error <- function(message, valid_options) {
     logging::logerror(paste(message, ": %s"), toString(valid_options))
@@ -2325,7 +2325,7 @@ maaslin_plot_results <- function(output,
                                 heatmap_vars = NULL,
                                 plot_associations = TRUE,
                                 max_pngs = 30,
-                                balanced=FALSE) {
+                                balanced = FALSE) {
     # create an output folder and figures folder if it does not exist
     if (!file.exists(output)) {
         logging::loginfo("Creating output folder")
@@ -2373,7 +2373,7 @@ maaslin_plot_results <- function(output,
             heatmap_vars = heatmap_vars,
             median_comparison_abundance = median_comparison_abundance,
             median_comparison_prevalence = median_comparison_prevalence,
-            balanced=balanced
+            balanced = balanced
         )
     }
     
@@ -2490,7 +2490,7 @@ maaslin_plot_results_from_output <- function(output,
             heatmap_vars = heatmap_vars,
             median_comparison_abundance = median_comparison_abundance,
             median_comparison_prevalence = median_comparison_prevalence,
-            balanced=balanced
+            balanced = balanced
         )
     }
     
@@ -2681,7 +2681,8 @@ maaslin3 <- function(input_data,
         max_pngs,
         cores,
         save_models,
-        verbosity
+        verbosity,
+        balanced
     )
     
     # Read data in
@@ -2821,7 +2822,7 @@ maaslin3 <- function(input_data,
                     heatmap_vars,
                     plot_associations,
                     max_pngs,
-                    balanced=summary_plot_balanced
+                    summary_plot_balanced
                 )
             },
             warning = function(w) {
@@ -2922,6 +2923,6 @@ if (identical(environment(), globalenv()) &&
             evaluate_only = current_args$evaluate_only,
             reference = current_args$reference,
             unscaled_abundance = current_args$unscaled_abundance,
-            summary_plot_balanced=current_args$summary_plot_balanced
+            summary_plot_balanced = current_args$summary_plot_balanced
         )
 }