`resolved ambiguous muts and generated clean output. Also seaprated dir.R

scripts/plotting/plotting_data.R

@@ -15,7 +15,10 @@ library(ggplot2)
 library(data.table)
 library(dplyr)
 
+source("dirs.R")
+
 require("getopt", quietly = TRUE) #cmd parse arguments
+
 #========================================================
 # command line args
 #spec = matrix(c(
@@ -31,19 +34,6 @@ require("getopt", quietly = TRUE) #cmd parse arguments
 #  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
 #}
 #========================================================
-#%% variable assignment: input and output paths & filenames
-drug = "pyrazinamide"
-gene = "pncA"
-gene_match = paste0(gene,"_p.")
-cat(gene_match)
-
-#=============
-# directories
-#=============
-datadir = paste0("~/git/Data")
-indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0("~/git/Data", "/", drug, "/output")
-plotdir = paste0("~/git/Data", "/", drug, "/output/plots")
 #======
 # input
 #======
@@ -53,15 +43,14 @@ infile_params = paste0(outdir, "/", in_filename_params)
 cat(paste0("Input file 1:", infile_params) )
 
 
-dr_muts_col = paste0('dr_mutations_', drug)
-dr_muts_col  = paste0('other_mutations_', drug)
-
-cat('Extracting columns based on variables:\n'
+cat('columns based on variables:\n'
       , drug
       , '\n'
       , dr_muts_col
       , '\n'
       , other_muts_col
+      , "\n"
+      , resistance_col
       , '\n===============================================================')
 
 #%%===============================================================
@@ -74,9 +63,6 @@ my_df = read.csv(infile_params, header = T)
 
 cat("\nInput dimensions:", dim(my_df)) 
 
-# quick checks
-#colnames(my_df)
-#str(my_df)
 
 ###########################
 # extract unique mutation entries