generated lineage dist plots combined. needs tweaking

scripts/plotting/lineage_basic_barplot.R

@@ -30,21 +30,27 @@ source("combining_dfs_plotting.R")
 # 9) my_df_u
 # 10) my_df_u_lig
 
-cat(paste0("Directories imported:"
-           , "\ndatadir:", datadir
-           , "\nindir:", indir
-           , "\noutdir:", outdir
-           , "\nplotdir:", plotdir))
+cat("Directories imported:"
+    , "\n===================="
+    , "\ndatadir:", datadir
+    , "\nindir:", indir
+    , "\noutdir:", outdir
+    , "\nplotdir:", plotdir)
+
+cat("Variables imported:"
+    , "\n====================="
+    , "\ndrug:", drug
+    , "\ngene:", gene
+    , "\ngene_match:", gene_match
+    , "\nAngstrom symbol:", angstroms_symbol
+    , "\nNo. of duplicated muts:", dup_muts_nu
+    , "\nNA count for ORs:", na_count
+    , "\nNA count in df2:", na_count_df2
+    , "\nNA count in df3:", na_count_df3
+    , "\ndr_muts_col:", dr_muts_col
+    , "\nother_muts_col:", other_muts_col
+    , "\ndrtype_col:", resistance_col)
 
-cat(paste0("Variables imported:"
-           , "\ndrug:", drug
-           , "\ngene:", gene
-           , "\ngene_match:", gene_match
-           , "\nAngstrom symbol:", angstroms_symbol
-           , "\nNo. of duplicated muts:", dup_muts_nu
-           , "\nNA count for ORs:", na_count
-           , "\nNA count in df2:", na_count_df2
-           , "\nNA count in df3:", na_count_df3))       
 
 #===========
 # input
@@ -67,7 +73,6 @@ plot_basic_bp_lineage  =  paste0(plotdir,"/", basic_bp_lineage)
 #================
 # REASSIGNMENT as necessary
 my_df  = merged_df2
-#my_df  = merged_df2_comp
 
 # clear excess variable
 rm(merged_df2_comp, merged_df3, merged_df3_comp)