#!/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")
#########################################################
# 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()
# should return the follwoing variables:
# 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
#----------------------------------------------
#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
#=======
# plot 1
basic_bp_ligand =  paste0(tolower(gene), "_basic_barplot_LIG.svg")
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
#****************
#svg("basic_barplots_LIG.svg")
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")
dev.off()

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

# 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         			   
########################################################################