moved plotting_func to functions and replaced 3 basic_barplots scripts with 1

scripts/plotting/basic_barplots_foldx.R

@@ -54,26 +54,23 @@ if(is.null(drug)|is.null(gene)) {
 }
 #########################################################
 # call functions with relevant args
-
 #------------------------------------------
-# import_dirs()
-# should return the follwoing variables:
-# datadir
-# indir
-# outdir
-# plotdir
-# dr_muts_col
-# other_muts_col
-# resistance_col
+# import_dirs(); returns
+    # 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
+# plotting_data(): returns
+    # 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 = ""
@@ -107,32 +104,20 @@ cat(paste0("Directories imported:"
            #, "\ngene_match:", gene_match
            #, "\nLength of upos:", length(upos)
            #, "\nAngstrom symbol:", angstroms_symbol))       
-#======================================================================
+
 #=======
-# output
+# output filenames
 #=======
-# plot 1
+
 basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
 plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
-#=======================================================================
-#================
-# Data for plots
-#================
-# REASSIGNMENT as necessary
-df  = my_df_u
 
-# sanity checks
-str(df)
-#=======================================================================
 #****************
 # Plot 1: Count of stabilising and destabilsing muts
 #****************
 svg(plot_basic_bp_foldx)
 print(paste0("plot1 filename:", plot_basic_bp_foldx))
 
-#--------------
-# start plot 1: call function
-#--------------
 stability_count_bp(plotdf = my_df_u
                    , df_colname = "foldx_outcome"
                    , leg_title = "FoldX outcome")