updated running_plotting_scripts.R

scripts/plotting/lineage_basic_barplots_combined.R

@@ -3,9 +3,10 @@ getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting/")
 getwd()
 #########################################################
-# TASK: Basic lineage barplot showing numbers
+# TASK: Basic lineage barplots showing numbers
 
 # Output: Basic barplot with lineage samples and mut count
+# + SNP diversity
 
 ##########################################################
 # 				Installing and loading required packages 			 
@@ -16,6 +17,27 @@ source("../functions/bp_lineage.R")
 #===========
 # input
 #===========
+#drug = 'streptomycin'
+#gene = 'gid'
+
+spec = matrix(c(
+    "drug"       , "d",  1, "character",
+    "gene"       , "g",  1, "character",
+    "data_file1" , "fa", 2, "character",
+    "data_file2" , "fb", 2, "character" 
+), byrow = TRUE, ncol = 4)
+
+opt = getopt(spec)
+
+drug            = opt$drug
+gene            = opt$gene
+infile_params   = opt$data_file1
+infile_metadata = opt$data_file2
+
+if(is.null(drug)|is.null(gene)) {
+    stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+}
+
 source ('get_plotting_dfs.R')
 
 cat("Directories imported:"