wrapper script basic_barplots_PS.R now takes cmd and calls functions to generate plots.Tested and verfiied.

scripts/plotting/basic_barplots_PS.R

@@ -25,16 +25,24 @@ source("plotting_globals.R")
 source("plotting_data.R")
 #########################################################
 # command line args
+#********************
+# !!!FUTURE TODO!!!
+# Can pass additional params of output/plot dir by user. 
+# Not strictly required for my workflow  since it is optimised
+# to have a streamlined input/output flow without filename worries.
+#********************
 spec = matrix(c(
-  "drug"   , "d", 1, "character",
-  "gene"   , "g", 1, "character"
+  "drug"   ,"d", 1, "character",
+  "gene"   ,"g", 1, "character",
+  "data"   ,"f", 2, "character" 
 ), byrow = TRUE, ncol = 4)
 
 opt = getopt(spec)
 
 #FIXME: detect if script running from cmd, then set these
-drug = opt$drug
-gene = opt$gene
+drug   = opt$drug
+gene   = opt$gene
+infile = opt$data
 
 # hardcoding when not using cmd
 #drug = "streptomycin"
@@ -45,14 +53,16 @@ if(is.null(drug)|is.null(gene)) {
 }
 #########################################################
 # call functions with relevant args
-drug = "streptomycin"
-gene = "gid"
+#drug = "streptomycin"
+#gene = "gid"
 import_dirs(drug, gene)
 
-if (!exists("infile") && exists("gene")){
-  #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+#if (!exists("infile") && exists("gene")){
+if (!is.character(infile) && exists("gene")){
+    #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
   in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
   infile = paste0(outdir, "/", in_filename_params)
+  cat("\nInput file not specified, assuming filename: ", infile, "\n")
 }
 
 #infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
@@ -64,6 +74,7 @@ my_df       = pd_df[[1]]
 my_df_u     = pd_df[[2]]
 my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
+
 #########################################################
 # This script: should return the following dfs, directories and variables
 # my_df
@@ -79,15 +90,11 @@ cat(paste0("Directories imported:"
            
  cat(paste0("Variables imported:"
            , "\ndrug:", drug
-           , "\ngene:", gene
+           , "\ngene:", gene))
            #, "\ngene_match:", gene_match
-           , "\nLength of upos:", length(upos)
-           , "\nAngstrom symbol:", angstroms_symbol))       
-           
-# clear excess variable
-rm(my_df, upos, dup_muts, my_df_u_lig)
-
-#=======================================================================
+           #, "\nLength of upos:", length(upos)
+           #, "\nAngstrom symbol:", angstroms_symbol))       
+           #=======================================================================
 #=======
 # output
 #=======