#!/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("~/git/LSHTM_analysis/scripts/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_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"

if (!exists("infile_params") && exists("gene")){
#if (!is.character(infile_params) && 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_params = paste0(outdir, "/", in_filename_params)
  cat("\nInput file not specified, assuming filename: ", infile_params, "\n")
}

# Get the DFs out of plotting_data()
pd_df = plotting_data(infile_params)
#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
           , "\ngene match:" , gene_match
           , "\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()
#===============================================================