From dccdfe97425b2588f8c35a6d5977914477599f60 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 10 Jun 2021 16:09:58 +0100
Subject: [PATCH] moved plotting_func to functions and replaced 3
 basic_barplots scripts with 1

---
 scripts/plotting/basic_barplots.R             | 182 ++++++++++++++++++
 scripts/plotting/basic_barplots_LIG.R         |  95 +--------
 scripts/plotting/basic_barplots_PS.R          |  94 +--------
 scripts/plotting/basic_barplots_foldx.R       |  47 ++---
 .../plotting/{ => functions}/plotting_data.R  |   0
 .../{ => functions}/plotting_globals.R        |   0
 .../plotting/functions/position_count_bp.R    |   4 +-
 scripts/plotting/functions/test_functions.R   |  74 ++++++-
 scripts/plotting/running_plotting_scripts.txt |  28 +--
 9 files changed, 287 insertions(+), 237 deletions(-)
 create mode 100755 scripts/plotting/basic_barplots.R
 rename scripts/plotting/{ => functions}/plotting_data.R (100%)
 rename scripts/plotting/{ => functions}/plotting_globals.R (100%)

diff --git a/scripts/plotting/basic_barplots.R b/scripts/plotting/basic_barplots.R
new file mode 100755
index 0000000..16e9c42
--- /dev/null
+++ b/scripts/plotting/basic_barplots.R
@@ -0,0 +1,182 @@
+#!/usr/bin/env Rscript  
+#########################################################
+# TASK: Barplots for mCSM DUET, ligand affinity, and foldX
+# basic barplots with count of mutations
+# basic barplots with frequency of count of mutations
+#########################################################
+# working dir 
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+
+
+# load libraries
+#source("Header_TT.R")
+library(ggplot2)
+library(data.table)
+library(dplyr)
+require("getopt", quietly = TRUE) # cmd parse arguments
+
+# load functions
+source("functions/plotting_globals.R")
+source("functions/plotting_data.R")
+source("functions/stability_count_bp.R")
+source("functions/position_count_bp.R")
+#############################################################
+# command line args
+#********************
+# !!!FUTURE TODO!!!
+# Can pass additional params of output/plot dir by user. 
+# Not strictly required for my workflow  since it is optimised
+# to have a streamlined input/output flow without filename worries.
+#********************
+spec = matrix(c(
+  "drug"   ,"d", 1, "character",
+  "gene"   ,"g", 1, "character",
+  "data"   ,"f", 2, "character" 
+), byrow = TRUE, ncol = 4)
+
+opt = getopt(spec)
+
+#FIXME: detect if script running from cmd, then set these
+drug   = opt$drug
+gene   = opt$gene
+infile = opt$data
+
+# hardcoding when not using cmd
+#drug = "streptomycin"
+#gene = "gid"
+
+if(is.null(drug)|is.null(gene)) {
+  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+}
+#########################################################
+# call functions with relevant args
+#***********************************
+# import_dirs(): returns
+  # datadir
+  # indir
+  # outdir
+  # plotdir
+  # dr_muts_col
+  # other_muts_col
+  # resistance_col
+#***********************************
+import_dirs(drug, gene)
+#***********************************
+# plotting_data(): returns
+  # my_df
+  # my_df_u
+  # my_df_u_lig
+  # dup_muts
+#***********************************
+#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile = ""
+
+#if (!exists("infile") && exists("gene")){
+if (!is.character(infile) && exists("gene")){
+  #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+  in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
+  infile = paste0(outdir, "/", in_filename_params)
+  cat("\nInput file not specified, assuming filename: ", infile, "\n")
+}
+
+# Get the DFs out of plotting_data()
+pd_df = plotting_data(infile)
+my_df       = pd_df[[1]]
+my_df_u     = pd_df[[2]]
+my_df_u_lig = pd_df[[3]]
+dup_muts    = pd_df[[4]]
+
+cat(paste0("Directories imported:"
+           , "\ndatadir:", datadir
+           , "\nindir:", indir
+           , "\noutdir:", outdir
+           , "\nplotdir:", plotdir))
+
+cat(paste0("\nVariables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene
+           , "\n"))
+#=======================================================================
+#=======
+# output
+#=======
+cat("plots will output to:", plotdir)
+#=======================================================================
+# begin plots
+
+# ------------------------------
+# barplot for mscm stability
+# ------------------------------
+basic_bp_duet =  paste0(tolower(gene), "_basic_barplot_PS.svg")
+plot_basic_bp_duet  =  paste0(plotdir,"/", basic_bp_duet)
+
+svg(plot_basic_bp_duet)
+print(paste0("plot filename:", basic_bp_duet))
+
+# function only
+stability_count_bp(plotdf = my_df_u
+               , df_colname = "duet_outcome"
+               , leg_title = "DUET outcome")
+
+dev.off()
+
+# ------------------------------
+# barplot for ligand affinity
+# ------------------------------
+basic_bp_ligand =  paste0(tolower(gene), "_basic_barplot_LIG.svg")
+plot_basic_bp_ligand  =  paste0(plotdir, "/", basic_bp_ligand)
+
+svg(plot_basic_bp_ligand)
+print(paste0("plot filename:", basic_bp_ligand))
+
+# function only
+stability_count_bp(plotdf = my_df_u_lig
+               , df_colname = "ligand_outcome"
+               , leg_title = "Ligand outcome"
+               , bp_plot_title = "Sites < 10 Ang of ligand")
+
+dev.off()
+# ------------------------------
+# barplot for foldX
+# ------------------------------
+basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
+plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
+
+svg(plot_basic_bp_foldx)
+print(paste0("plot filename:", plot_basic_bp_foldx))
+
+stability_count_bp(plotdf = my_df_u
+                   , df_colname = "foldx_outcome"
+                   , leg_title = "FoldX outcome")
+dev.off()
+#===============================================================
+# ------------------------------
+# barplot for nssnp site count: all
+# ------------------------------
+pos_count_duet =  paste0(tolower(gene), "_position_count_PS.svg")
+plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
+
+svg(plot_pos_count_duet)
+print(paste0("plot filename:", plot_pos_count_duet))
+
+# function only
+site_snp_count_bp(plotdf = my_df_u
+                  , df_colname = "position")
+
+dev.off()
+# ------------------------------
+# barplot for nssnp site count: within 10 Ang
+# ------------------------------
+pos_count_ligand =  paste0(tolower(gene), "_position_count_LIG.svg")
+plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
+
+svg(plot_pos_count_ligand)
+print(paste0("plot filename:", plot_pos_count_ligand))
+
+# function only
+site_snp_count_bp(plotdf = my_df_u_lig
+                  , df_colname = "position")
+
+dev.off()
+#===============================================================
diff --git a/scripts/plotting/basic_barplots_LIG.R b/scripts/plotting/basic_barplots_LIG.R
index 5b4ae4a..8789086 100755
--- a/scripts/plotting/basic_barplots_LIG.R
+++ b/scripts/plotting/basic_barplots_LIG.R
@@ -21,8 +21,10 @@ library(dplyr)
 require("getopt", quietly = TRUE) # cmd parse arguments
 
 # load functions
-source("plotting_globals.R")
-source("plotting_data.R")
+source("functions/plotting_globals.R")
+source("functions/plotting_data.R")
+source("functions/stability_count_bp.R")
+source("functions/position_count_bp.R")
 #########################################################
 # command line args
 #********************
@@ -117,17 +119,7 @@ plot_basic_bp_ligand  =  paste0(plotdir,"/", basic_bp_ligand)
 # plot 2
 pos_count_ligand =  paste0(tolower(gene), "_position_count_LIG.svg")
 plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
-
 #=======================================================================
-#================
-# Data for plots
-#================
-# REASSIGNMENT as necessary
-df  = my_df_u_lig
-
-# sanity checks
-str(df)
-#=====================================================================
 #****************
 # Plot 1: Count of stabilising and destabilsing muts
 #****************
@@ -135,9 +127,6 @@ str(df)
 svg(plot_basic_bp_ligand)
 print(paste0("plot1 filename:", basic_bp_ligand))
 
-#--------------
-# start plot 1: call function
-#--------------
 stability_count_bp(plotdf = my_df_u_lig
                    , df_colname = "ligand_outcome"
                    , leg_title = "Ligand outcome")
@@ -148,84 +137,12 @@ table(my_df_u_lig$ligand_outcome)
 #****************
 # Plot 2: frequency of positions
 #****************
-df_ncols = ncol(df)
-df_nrows = nrow(df)
-
-cat(paste0("original df dimensions:"
-    , "\nNo. of rows:", df_nrows
-    , "\nNo. of cols:", df_ncols
-    , "\nNow adding column: frequency of mutational positions"))
-
-#setDT(df)[, .(pos_count := .N), by = .(position)] 
-setDT(df)[, pos_count := .N, by = .(position)]
-
-rm(df_nrows, df_ncols) 
-
-df_nrows = nrow(df)
-df_ncols = ncol(df)
-
-cat(paste0("revised df dimensions:"
-           , "\nNo. of rows:", df_nrows
-           , "\nNo. of cols:", df_ncols))
-
-# this is cummulative
-table(df$pos_count)
-
-# use group by on this
-snpsBYpos_df <- df %>%
-  group_by(position) %>%
-  summarize(snpsBYpos = mean(pos_count))
-
-table(snpsBYpos_df$snpsBYpos)
-
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-# FIXME, get this mutation_info, perhaLIG useful!
-foo = select(df, mutationinformation
-             , wild_pos
-             , wild_type
-             , mutant_type
-             #, mutation_info # comes from meta data, notused yet
-             , position
-             , pos_count)
-
-#write.csv(foo, "/pos_count_freq.csv")
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-#--------------
-# start plot 2
-#--------------
-#svg("position_count_LIG.svg")
 svg(plot_pos_count_ligand)
 print(paste0("plot filename:", plot_pos_count_ligand))
 
-my_ats = 25 # axis text size
-my_als = 22 # axis label size
+site_snp_count_bp(plotdf = my_df_u
+                  , df_colname = "position")
 
-# to make x axis display all positions
-# not sure if to use with sort or directly
-my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
-
-g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
-OutPlot_lig_pos_count = g + geom_bar(aes (alpha = 0.5)
-                         , show.legend = FALSE) +
-  scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
-  #scale_x_continuous(breaks = my_x) +
-  geom_label(stat = "count", aes(label = ..count..)
-             , color = "black"
-             , size = 10) +
-  theme(axis.text.x = element_text(size = my_ats
-                                   , angle = 0)
-        , axis.text.y = element_text(size = my_ats
-                                     , angle = 0
-                                     , hjust = 1)
-        , axis.title.x = element_text(size = my_als)
-        , axis.title.y = element_text(size = my_als)
-        , plot.title = element_blank()) +
-  
-  labs(x = "Number of nsSNPs"
-       , y = "Number of Sites")
-
-print(OutPlot_lig_pos_count)
 dev.off()
 ########################################################################
 #               			end of LIG barplots         			   
diff --git a/scripts/plotting/basic_barplots_PS.R b/scripts/plotting/basic_barplots_PS.R
index fd41ca4..20f8457 100755
--- a/scripts/plotting/basic_barplots_PS.R
+++ b/scripts/plotting/basic_barplots_PS.R
@@ -21,9 +21,10 @@ library(dplyr)
 require("getopt", quietly = TRUE) # cmd parse arguments
 
 # load functions
-source("plotting_globals.R")
-source("plotting_data.R")
+source("functions/plotting_globals.R")
+source("functions/plotting_data.R")
 source("functions/stability_count_bp.R")
+source("functions/position_count_bp.R")
 #########################################################
 # command line args
 #********************
@@ -118,15 +119,6 @@ plot_basic_bp_duet  =  paste0(plotdir,"/", basic_bp_duet)
 pos_count_duet =  paste0(tolower(gene), "_position_count_PS.svg")
 plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
 
-#=======================================================================
-#================
-# Data for plots
-#================
-# REASSIGNMENT as necessary
-df  = my_df_u
-
-# sanity checks
-str(df)
 #=======================================================================
 #****************
 # Plot 1: Count of stabilising and destabilsing muts
@@ -134,9 +126,7 @@ str(df)
 svg(plot_basic_bp_duet)
 print(paste0("plot1 filename:", basic_bp_duet))
 
-#--------------
-# start plot 1: call function
-#--------------
+
 stability_count_bp(plotdf = my_df_u
                    , df_colname = "duet_outcome"
                    , leg_title = "DUET outcome")
@@ -147,82 +137,12 @@ table(my_df_u$duet_outcome)
 #****************
 # Plot 2: frequency of positions
 #****************
-df_ncols = ncol(df)
-df_nrows = nrow(df)
-
-cat(paste0("original df dimensions:"
-    , "\nNo. of rows:", df_nrows
-    , "\nNo. of cols:", df_ncols
-    , "\nNow adding column: frequency of mutational positions"))
-
-#setDT(df)[, .(pos_count := .N), by = .(position)] 
-setDT(df)[, pos_count := .N, by = .(position)]
-
-rm(df_nrows, df_ncols) 
-
-df_nrows = nrow(df)
-df_ncols = ncol(df)
-
-cat(paste0("revised df dimensions:"
-           , "\nNo. of rows:", df_nrows
-           , "\nNo. of cols:", df_ncols))
-
-# this is cummulative
-table(df$pos_count)
-
-# use group by on this
-snpsBYpos_df <- df %>%
-  group_by(position) %>%
-  summarize(snpsBYpos = mean(pos_count))
-
-table(snpsBYpos_df$snpsBYpos)
-
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-# FIXME, get this mutation_info, perhaps useful!
-foo = select(df, mutationinformation
-             , wild_pos
-             , wild_type
-             , mutant_type
-             #, mutation_info # comes from meta data, notused yet
-             , position
-             , pos_count)
-
-#write.csv(foo, "/pos_count_freq.csv")
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-#--------------
-# start plot 2
-#--------------
 svg(plot_pos_count_duet)
 print(paste0("plot filename:", plot_pos_count_duet))
-my_ats = 25 # axis text size
-my_als = 22 # axis label size
 
-# to make x axis display all positions
-# not sure if to use with sort or directly
-my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
-
-g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
-OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
-                                 , show.legend = FALSE) +
-  scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
-  #scale_x_continuous(breaks = my_x) +
-  geom_label(stat = "count", aes(label = ..count..)
-             , color = "black"
-             , size = 10) +
-  theme(axis.text.x = element_text(size = my_ats
-                                   , angle = 0)
-        , axis.text.y = element_text(size = my_ats
-                                     , angle = 0
-                                     , hjust = 1)
-        , axis.title.x = element_text(size = my_als)
-        , axis.title.y = element_text(size = my_als)
-        , plot.title = element_blank()) +
-  
-  labs(x = "Number of nsSNPs"
-       , y = "Number of Sites")
-
-print(OutPlot_pos_count)
+# function only
+site_snp_count_bp(plotdf = my_df_u
+                  , df_colname = "position")
 
 dev.off()
 ########################################################################
diff --git a/scripts/plotting/basic_barplots_foldx.R b/scripts/plotting/basic_barplots_foldx.R
index e78840d..68621c6 100755
--- a/scripts/plotting/basic_barplots_foldx.R
+++ b/scripts/plotting/basic_barplots_foldx.R
@@ -54,26 +54,23 @@ if(is.null(drug)|is.null(gene)) {
 }
 #########################################################
 # call functions with relevant args
-
 #------------------------------------------
-# import_dirs()
-# should return the follwoing variables:
-# datadir
-# indir
-# outdir
-# plotdir
-# dr_muts_col
-# other_muts_col
-# resistance_col
+# import_dirs(); returns
+    # datadir
+    # indir
+    # outdir
+    # plotdir
+    # dr_muts_col
+    # other_muts_col
+    # resistance_col
 #--------------------------------------------
 import_dirs(drug, gene)
 #---------------------------------------------
-# plotting_data()
-# should return the following dfs:
-# my_df
-# my_df_u
-# my_df_u_lig
-# dup_muts
+# plotting_data(): returns
+    # my_df
+    # my_df_u
+    # my_df_u_lig
+    # dup_muts
 #----------------------------------------------
 #infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 #infile = ""
@@ -107,32 +104,20 @@ cat(paste0("Directories imported:"
            #, "\ngene_match:", gene_match
            #, "\nLength of upos:", length(upos)
            #, "\nAngstrom symbol:", angstroms_symbol))       
-#======================================================================
+
 #=======
-# output
+# output filenames
 #=======
-# plot 1
+
 basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
 plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
-#=======================================================================
-#================
-# Data for plots
-#================
-# REASSIGNMENT as necessary
-df  = my_df_u
 
-# sanity checks
-str(df)
-#=======================================================================
 #****************
 # Plot 1: Count of stabilising and destabilsing muts
 #****************
 svg(plot_basic_bp_foldx)
 print(paste0("plot1 filename:", plot_basic_bp_foldx))
 
-#--------------
-# start plot 1: call function
-#--------------
 stability_count_bp(plotdf = my_df_u
                    , df_colname = "foldx_outcome"
                    , leg_title = "FoldX outcome")
diff --git a/scripts/plotting/plotting_data.R b/scripts/plotting/functions/plotting_data.R
similarity index 100%
rename from scripts/plotting/plotting_data.R
rename to scripts/plotting/functions/plotting_data.R
diff --git a/scripts/plotting/plotting_globals.R b/scripts/plotting/functions/plotting_globals.R
similarity index 100%
rename from scripts/plotting/plotting_globals.R
rename to scripts/plotting/functions/plotting_globals.R
diff --git a/scripts/plotting/functions/position_count_bp.R b/scripts/plotting/functions/position_count_bp.R
index 071d1cc..2e1c26c 100755
--- a/scripts/plotting/functions/position_count_bp.R
+++ b/scripts/plotting/functions/position_count_bp.R
@@ -26,7 +26,7 @@ site_snp_count_bp <- function (plotdf
                                , df_colname = "position"
                                #, bp_plot_title = ""
                                #, leg_title = "Legend title"
-                               #, leg_text_size = 20
+                               , leg_text_size = 20
                                , axis_text_size = 25
                                , axis_label_size = 22
                                , xaxis_title = "Number of nsSNPs"
@@ -111,7 +111,7 @@ site_snp_count_bp <- function (plotdf
           #, legend.position = c(0.73,0.8)
           #, legend.text = element_text(size = leg_text_size)
           #, legend.title = element_text(size =  axis_label_size)
-          , plot.title = element_text(size =  axis_label_size)) + 
+          , plot.title = element_text(size =  leg_text_size)) + 
     
     labs(title = bp_plot_title
       , x = xaxis_title
diff --git a/scripts/plotting/functions/test_functions.R b/scripts/plotting/functions/test_functions.R
index 172083c..bf8621e 100644
--- a/scripts/plotting/functions/test_functions.R
+++ b/scripts/plotting/functions/test_functions.R
@@ -1,9 +1,10 @@
 setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
 getwd()
-
-# =================
-# Test function
-# ==================
+#############################################################
+#===========================================
+# load functions, data, dirs, hardocded vars
+# that will be used in testing the functions
+#===========================================
 source("../plotting_data.R")
 infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 pd_df = plotting_data(infile)
@@ -12,30 +13,91 @@ my_df_u     = pd_df[[2]]
 my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
 
+source("../plotting_globals.R")
+drug = "streptomycin"
+gene = "gid"
+
+import_dirs(drug, gene)
+
+#=====================
+# functions to test 
+#=====================
+source("stability_count_bp.R")
+source("position_count_bp.R")
+
+##################################################################
 # ------------------------------
 # barplot for mscm stability
 # ------------------------------
+basic_bp_duet =  paste0(tolower(gene), "_basic_barplot_PS.svg")
+plot_basic_bp_duet  =  paste0(plotdir,"/", basic_bp_duet)
+
+svg(plot_basic_bp_duet)
+print(paste0("plot filename:", basic_bp_duet))
+
+# function only
 stability_count_bp(plotdf = my_df_u
                , df_colname = "duet_outcome"
                , leg_title = "DUET outcome")
 
+dev.off()
+
 # ------------------------------
 # barplot for ligand affinity
 # ------------------------------
+basic_bp_ligand =  paste0(tolower(gene), "_basic_barplot_LIG.svg")
+plot_basic_bp_ligand  =  paste0(plotdir, "/", basic_bp_ligand)
+
+svg(plot_basic_bp_ligand)
+print(paste0("plot filename:", basic_bp_ligand))
+
+# function only
 stability_count_bp(plotdf = my_df_u_lig
                , df_colname = "ligand_outcome"
                , leg_title = "Ligand outcome"
-               , bp_plot_title = "Sites < 10 Ang of ligand"
-)
+               , bp_plot_title = "Sites < 10 Ang of ligand")
 
+dev.off()
+# ------------------------------
+# barplot for foldX
+# ------------------------------
+basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
+plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
+
+svg(plot_basic_bp_foldx)
+print(paste0("plot filename:", plot_basic_bp_foldx))
+
+stability_count_bp(plotdf = my_df_u
+                   , df_colname = "foldx_outcome"
+                   , leg_title = "FoldX outcome")
+dev.off()
+#===============================================================
 # ------------------------------
 # barplot for nssnp site count: all
 # ------------------------------
+pos_count_duet =  paste0(tolower(gene), "_position_count_PS.svg")
+plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
+
+svg(plot_pos_count_duet)
+print(paste0("plot filename:", plot_pos_count_duet))
+
+# function only
 site_snp_count_bp(plotdf = my_df_u
                   , df_colname = "position")
 
+dev.off()
 # ------------------------------
 # barplot for nssnp site count: within 10 Ang
 # ------------------------------
+pos_count_ligand =  paste0(tolower(gene), "_position_count_LIG.svg")
+plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
+
+svg(plot_pos_count_ligand)
+print(paste0("plot filename:", plot_pos_count_ligand))
+
+# function only
 site_snp_count_bp(plotdf = my_df_u_lig
                   , df_colname = "position")
+
+dev.off()
+#===============================================================
\ No newline at end of file
diff --git a/scripts/plotting/running_plotting_scripts.txt b/scripts/plotting/running_plotting_scripts.txt
index 949b7c6..9bae858 100644
--- a/scripts/plotting/running_plotting_scripts.txt
+++ b/scripts/plotting/running_plotting_scripts.txt
@@ -1,12 +1,16 @@
 #========
-# basic_barplots_PS.R: 
+# basic_barplot.R: 
 #========
-./basic_barplots_PS.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv 
+./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv 
 
 sources:
  ## plotting_globals.R (previously dir.R)
  ## plotting_data.R 
+ ## position_count_bp.R
+ ## stability_count_bp.R
 
+outputs:
+    #5 svgs in the plotdir
 
 # TODO
 Delete: dirs.R
@@ -17,23 +21,3 @@ resolving_ambiguous_muts.R:source("dirs.R")
 
 #=======================================================================
 
-#========
-# basic_barplots_foldx.R: 
-#========
-./basic_barplots_foldx.R -d streptomycin -g gid
-# picks default file name, or you can specify by the -f flag
-
-sources:
- ## plotting_globals.R (previously dir.R)
- ## plotting_data.R 
- 
-#========
-# basic_barplots_LIG.R: 
-#========
-./basic_barplots_LIG.R -d streptomycin -g gid
-# picks default file name, or you can specify by the -f flag
-
-sources:
- ## plotting_globals.R (previously dir.R)
- ## plotting_data.R 
-