moved old bp scripts to redundant

scripts/plotting/basic_barplots_foldx.R

@@ -1,129 +0,0 @@
-#!/usr/bin/env Rscript  
-#########################################################
-# TASK: producing barplots
-# basic barplots with count of mutations
-# basic barplots with frequency of count of mutations
-
-# Depends on
-## plotting_globals.R (previously dir.R)
-## plotting_data.R 
-#########################################################
-# working dir 
-getwd()
-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("plotting_globals.R")
-source("plotting_data.R")
-source("functions/stability_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"))
-           #, "\ngene_match:", gene_match
-           #, "\nLength of upos:", length(upos)
-           #, "\nAngstrom symbol:", angstroms_symbol))       
-
-#=======
-# output filenames
-#=======
-
-basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
-plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
-
-#****************
-# Plot 1: Count of stabilising and destabilsing muts
-#****************
-svg(plot_basic_bp_foldx)
-print(paste0("plot1 filename:", plot_basic_bp_foldx))
-
-stability_count_bp(plotdf = my_df_u
-                   , df_colname = "foldx_outcome"
-                   , leg_title = "FoldX outcome")
-dev.off()
-
-table(my_df_u$foldx_outcome)
-########################################################################
-#               			end of foldx barplot         			   
-########################################################################

scripts/plotting/running_plotting_scripts.txt

@@ -1,23 +1,38 @@
-#========
+#########################################################################
-# basic_barplot.R: 
+#===================
-#========
+# basic_barplot.R
-./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv 
+#===================
+ It replaces
+ basic_barplot_PS.R
+ basic_barplot_LIG.R
+ basic_barplot_foldx.R
+ These have been moved to redundant/
 
 sources:
  ## plotting_globals.R (previously dir.R)
  ## plotting_data.R 
  ## position_count_bp.R
  ## stability_count_bp.R
+ 
+ outputs:
+ ##5 svgs in the plotdir
+ 
+ note: 
+ -f flag has default if not supplied 
+#-----------------------------------------------------------------------
+./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv
+#-----------------------------------------------------------------------
 
-outputs:
-    #5 svgs in the plotdir
 
+
+
+
+########################################################################
 # TODO
 Delete: dirs.R
 after grepping
 barplots_subcolours_aa_combined.R:source("dirs.R")
 basic_barplots_PS.R:source("dirs.R")
 resolving_ambiguous_muts.R:source("dirs.R")
-
+########################################################################
-#=======================================================================