adpated combining_dfs.py and plotting.R for gid and attempting to make it generic

scripts/plotting/dirs.R

@@ -1,56 +1,24 @@
 #!/usr/bin/env Rscript             
 #########################################################
-# TASK: formatting data that will be used for various plots
-
-# useful links
-#https://stackoverflow.com/questions/38851592/r-append-column-in-a-dataframe-with-frequency-count-based-on-two-columns
+# TASK: importing dir str 
+# create a function that takes 'drug' and 'gene' as args, 
+# This script is sourced by plotting.R to import dir str
+# for various plots, etc.
 #########################################################
-# working dir and loading libraries
-getwd()
-setwd("~/git/LSHTM_analysis/scripts/plotting")
-getwd()
-
-#source("Header_TT.R")
-library(ggplot2)
-library(data.table)
-library(dplyr)
-
-require("getopt", quietly = TRUE) #cmd parse arguments
-#========================================================
-# command line args
-#spec = matrix(c(
-#  "drug"   , "d", 1, "character",
-#  "gene"   , "g", 1, "character"
-#), byrow = TRUE, ncol = 4)
-
-#opt = getopt(spec)
-
-#drug = opt$druggene = opt$gene
-
-#if(is.null(drug)|is.null(gene)) {
-#  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
-#}
-#========================================================
-# FIXME: change to cmd
-#%% variable assignment: input and output paths & filenames
-drug = "pyrazinamide"
-gene = "pncA"
-gene_match = paste0(gene,"_p.")
-cat(gene_match)
-
-#=============
-# directories and variables
-#=============
-datadir = paste0("~/git/Data")
-indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0("~/git/Data", "/", drug, "/output")
-plotdir = paste0("~/git/Data", "/", drug, "/output/plots")
-
-dr_muts_col = paste0('dr_mutations_', drug)
-other_muts_col  = paste0('other_mutations_', drug)
-resistance_col = "drtype"
-
-#%%===============================================================
-
-
-
+import_dirs <- function(drug, gene) {
+  gene_match = paste0(gene,"_p.")
+  cat(gene_match)
+  
+  #=============
+  # directories and variables
+  #=============
+  datadir        <<- paste0("~/git/Data")
+  indir          <<- paste0(datadir, "/", drug, "/input")
+  outdir         <<- paste0("~/git/Data", "/", drug, "/output")
+  plotdir        <<- paste0("~/git/Data", "/", drug, "/output/plots")
+  
+  dr_muts_col    <<- paste0('dr_mutations_', drug)
+  other_muts_col <<- paste0('other_mutations_', drug)
+  resistance_col <<- "drtype"
+  
+}