diff --git a/scripts/plotting/logo_plot.R b/scripts/plotting/logo_plot.R
index 707df8a..b311d11 100755
--- a/scripts/plotting/logo_plot.R
+++ b/scripts/plotting/logo_plot.R
@@ -57,7 +57,7 @@ import_dirs(drug, gene)
 # call: plotting_data()
 #---------------------------
 #if (!exists("infile_params") && exists("gene")){
-if (!is.character(infile_params) && exists("gene")){
+if (!is.character(infile_params) && exists("gene")){ # when running as cmd
   #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
   in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
   infile_params = paste0(outdir, "/", in_filename_params)
@@ -65,22 +65,23 @@ if (!is.character(infile_params) && exists("gene")){
 }
 
 # Input 1: read <gene>_comb_afor.csv
-my_df = read.csv(infile_params, header = T)
-pd_df = plotting_data(my_df)
+cat("\nReading mcsm combined data file: ", infile_params)
+mcsm_df = read.csv(infile_params, header = T)
+pd_df = plotting_data(mcsm_df)
 my_df_u       = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
 
 #--------------------------------
 # call: combining_dfs_plotting()
 #--------------------------------
 #if (!exists("infile_metadata") && exists("gene")){
-if (!is.character(infile_params) && exists("gene")){
+if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
   in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
   infile_metadata = paste0(outdir, "/", in_filename_metadata)
   cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
 }
 
 # Input 2: read <gene>_meta data.csv
-cat("\nReading meta data file:", infile_metadata)
+cat("\nReading meta data file: ", infile_metadata)
 
 gene_metadata <- read.csv(infile_metadata
                           , stringsAsFactors = F
@@ -91,12 +92,7 @@ all_plot_dfs = combining_dfs_plotting(my_df_u
                                       , lig_dist_colname = 'ligand_distance'
                                       , lig_dist_cutoff = 10)
 
-#merged_df2        = all_plot_dfs[[1]]
-merged_df3        = all_plot_dfs[[2]]
-#merged_df2_comp   = all_plot_dfs[[3]]
-#merged_df3_comp   = all_plot_dfs[[4]]
-#merged_df2_lig    = all_plot_dfs[[5]]
-#merged_df3_lig    = all_plot_dfs[[6]]
+merged_df3 = all_plot_dfs[[2]]
 
 #===========
 # output