moved plotting_func to functions and replaced 3 basic_barplots scripts with 1

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()
+#===============================================================