tweaking baic bp to make generic

scripts/plotting/basic_barplots_PS.R

@@ -14,7 +14,49 @@ getwd()
 library(ggplot2)
 library(data.table)
 library(dplyr)
+
+# Set globals: 
+source("plotting_globals.R")
+# pretent cli
+drug = "streptomycin"
+gene = "gid"
+infile = "merged_df3_short.csv"
+
+import_dirs(drug, gene)
+
 source("plotting_data.R")
+plotting_data("merged_df3_short.csv")
+
+if (!exists("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)
+}
+
+plotting_data(infile)
+
+
+#=======================================================================
+# command line args
+spec = matrix(c(
+  "drug"   , "d", 1, "character",
+  "gene"   , "g", 1, "character"
+), byrow = TRUE, ncol = 4)
+
+opt = getopt(spec)
+
+#FIXME: detect if script running from cmd, then set these
+drug = opt$drug
+gene = opt$gene
+
+# hardcoding when not using cmd
+#drug = "streptomycin"
+#gene = "gid"
+
+if(is.null(drug)|is.null(gene)) {
+  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+}
+#=======================================================================
 
 # should return the following dfs, directories and variables
 # my_df
@@ -31,7 +73,7 @@ cat(paste0("Directories imported:"
  cat(paste0("Variables imported:"
            , "\ndrug:", drug
            , "\ngene:", gene
-           , "\ngene_match:", gene_match
+           #, "\ngene_match:", gene_match
            , "\nLength of upos:", length(upos)
            , "\nAngstrom symbol:", angstroms_symbol))