add dirs and resolving_ambiguous_muts

scripts/plotting/dirs.R

@@ -0,0 +1,66 @@
+#!/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
+#########################################################
+# 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"
+
+cat('columns based on variables:\n'
+      , drug
+      , '\n'
+      , dr_muts_col
+      , '\n'
+      , other_muts_col
+      , "\n"
+      , resistance_col
+      , '\n===============================================================')
+
+#%%===============================================================
+
+
+