diff --git a/scripts/plotCustomAllelePlot.py b/scripts/plotCustomAllelePlot.py
index 0025706e..f5ec2431 100644
--- a/scripts/plotCustomAllelePlot.py
+++ b/scripts/plotCustomAllelePlot.py
@@ -28,7 +28,7 @@ def main():
     parser.add_argument("--plot_left",help="Number of bases to plot to the left of the cut site",type=int,default=20)
     parser.add_argument("--plot_right",help="Number of bases to plot to the right of the cut site",type=int,default=20)
     parser.add_argument("--plot_center",help="Center of plot. If set, plots for guide RNAs will not be generated -- only a plot centered at this position will be plotted.",type=int,default=None)
-    
+
     # CRISPRessoPro params
     parser.add_argument('--use_matplotlib', action='store_true',
                         help='Use matplotlib for plotting instead of plotly/d3 when CRISPRessoPro is installed')
@@ -132,14 +132,14 @@ def plot_alleles_tables_from_folder(crispresso_output_folder,fig_filename_root,p
             for (int_start, int_end) in refs[ref_name]['sgRNA_intervals']:
                 new_sgRNA_intervals += [(int_start - new_sel_cols_start - 1,int_end - new_sel_cols_start - 1)]
 
+
             fig_filename_root = fig_filename_root+"_"+ref_name+"_"+sgRNA_label
+            df_alleles_prep = CRISPRessoPlot.prep_alleles_table(df_alleles_around_cut, ref_seq_around_cut, MAX_N_ROWS, MIN_FREQUENCY)
             CRISPRessoPlot.plot_alleles_table(ref_seq_around_cut,
-                                              df_alleles=df_alleles_around_cut,
+                                              df_alleles_prep=df_alleles_prep,
                                               fig_filename_root=fig_filename_root,
                                               cut_point_ind=cut_point-new_sel_cols_start,
                                               custom_colors=custom_colors,
-                                              MIN_FREQUENCY=MIN_FREQUENCY,
-                                              MAX_N_ROWS=MAX_N_ROWS,
                                               SAVE_ALSO_PNG=SAVE_ALSO_PNG,
                                               plot_cut_point=plot_cut_point,
                                               sgRNA_intervals=new_sgRNA_intervals,
@@ -174,13 +174,12 @@ def plot_alleles_tables_from_folder(crispresso_output_folder,fig_filename_root,p
                     new_sgRNA_intervals += [(int_start - new_sel_cols_start - 1,int_end - new_sel_cols_start - 1)]
 
                 fig_filename_root = fig_filename_root+"_"+ref_name+"_"+sgRNA_label
+                df_alleles_prep = CRISPRessoPlot.prep_alleles_table(df_alleles_around_cut, ref_seq_around_cut, MAX_N_ROWS, MIN_FREQUENCY)
                 CRISPRessoPlot.plot_alleles_table(ref_seq_around_cut,
-                                                  df_alleles=df_alleles_around_cut,
+                                                  df_alleles_prep=df_alleles_prep,
                                                   fig_filename_root=fig_filename_root,
                                                   cut_point_ind=cut_point-new_sel_cols_start,
                                                   custom_colors=custom_colors,
-                                                  MIN_FREQUENCY=MIN_FREQUENCY,
-                                                  MAX_N_ROWS=MAX_N_ROWS,
                                                   SAVE_ALSO_PNG=SAVE_ALSO_PNG,
                                                   plot_cut_point=plot_cut_point,
                                                   sgRNA_intervals=new_sgRNA_intervals,
@@ -194,4 +193,3 @@ def plot_alleles_tables_from_folder(crispresso_output_folder,fig_filename_root,p
 if __name__ == "__main__":
     # execute only if run as a script
     main()
-