repurposed basic_barplots_foldx.R

scripts/plotting/basic_barplots_PS.R

@@ -53,9 +53,29 @@ if(is.null(drug)|is.null(gene)) {
 }
 #########################################################
 # call functions with relevant args
-#drug = "streptomycin"
-#gene = "gid"
+
+#------------------------------------------
+# import_dirs()
+  # should return the follwoing variables:
+  # datadir
+  # indir
+  # outdir
+  # plotdir
+  # dr_muts_col
+  # other_muts_col
+  # resistance_col
+#--------------------------------------------
 import_dirs(drug, gene)
+#---------------------------------------------
+# plotting_data()
+  # should return the following dfs:
+  # my_df
+  # my_df_u
+  # my_df_u_lig
+  # dup_muts
+#----------------------------------------------
+#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile = ""
 
 #if (!exists("infile") && exists("gene")){
 if (!is.character(infile) && exists("gene")){
@@ -65,9 +85,6 @@ if (!is.character(infile) && exists("gene")){
   cat("\nInput file not specified, assuming filename: ", infile, "\n")
 }
 
-#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
-#infile = ""
-
 # Get the DFs out of plotting_data()
 pd_df = plotting_data(infile)
 my_df       = pd_df[[1]]
@@ -76,12 +93,6 @@ my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
 
 #########################################################
-# This script: should return the following dfs, directories and variables
-# my_df
-# my_df_u
-# my_df_u_lig
-# dup_muts
-
 cat(paste0("Directories imported:"
            , "\ndatadir:", datadir
            , "\nindir:", indir
@@ -94,7 +105,7 @@ cat(paste0("Directories imported:"
            #, "\ngene_match:", gene_match
            #, "\nLength of upos:", length(upos)
            #, "\nAngstrom symbol:", angstroms_symbol))       
-           #=======================================================================
+#=======================================================================
 #=======
 # output
 #=======
@@ -117,7 +128,7 @@ df  = my_df_u
 str(df)
 #=======================================================================
 #****************
-# Plot 1:Count of stabilising and destabilsing muts
+# Plot 1: Count of stabilising and destabilsing muts
 #****************
 
 svg(plot_basic_bp_duet)