From 6f24fc1fac5f70bc5f0cd075b661bf78b4bb194d Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 8 Jun 2021 16:53:07 +0100
Subject: [PATCH] uddated how to run plotting scripts. This is a cleaner
 version to keep up-to-date

---
 scripts/plotting/running_plotting_scripts.txt | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/scripts/plotting/running_plotting_scripts.txt b/scripts/plotting/running_plotting_scripts.txt
index 8555354..ce217f0 100644
--- a/scripts/plotting/running_plotting_scripts.txt
+++ b/scripts/plotting/running_plotting_scripts.txt
@@ -1,20 +1,14 @@
 #========
 # basic_barplots_PS.R: 
 #========
-Rscript basic_barplots_PS.R
-# Calls 'plotting_data.R' --> calls 'dirs.R'
- 'Plotting_data.R':
-#drug = opt$drug
-#gene = opt$gene
+./basic_barplots_PS.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv 
 
-# hardcoding when not using cmd
-drug = "streptomycin"
-gene = "gid"
+sources:
+ ## plotting_globals.R (previously dir.R)
+ ## plotting_data.R 
 
-#TODO
-making such that cmd line agrs are passed to basic_barplots_PS.R for gene, drug and maybe input file
-and then these call functions
 
+# TODO
 Delete: dirs.R
 after grepping
 barplots_subcolours_aa_combined.R:source("dirs.R")