getwd()
setwd("~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/plotting")
getwd()

########################################################################
# 				Installing and loading required packages 			   #
########################################################################

source("../Header_TT.R")

########################################################################
#		 Read file: call script for combining df for lig		   	   #
########################################################################

source("../combining_two_df_lig.R") 

#---------------------- PAY ATTENTION
# the above changes the working dir
#[1] "git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts"
#---------------------- PAY ATTENTION

#==========================
# This will return:

# df with NA:
# merged_df2
# merged_df3

# df without NA:
# merged_df2_comp
# merged_df3_comp
#===========================

###########################
# Data for Lig plots
# you need merged_df3
# or
# merged_df3_comp
# since these have unique SNPs
# I prefer to use the merged_df3
# because using the _comp dataset means
# we lose some muts and at this level, we should use
# as much info as available
###########################

# uncomment as necessary
#%%%%%%%%%%%%%%%%%%%%%%%%
# REASSIGNMENT
my_df  = merged_df3
#my_df = merged_df3_comp
#%%%%%%%%%%%%%%%%%%%%%%%%

# delete variables not required
rm(merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)

# quick checks
colnames(my_df)
str(my_df)

#############################
# Extra sanity check:
# for mcsm_lig ONLY
# Dis_lig_Ang should be <10
#############################

if (max(my_df$Dis_lig_Ang) < 10){
  print ("Sanity check passed: lig data is <10Ang")
}else{
  print ("Error: data should be filtered to be within 10Ang")
}
########################################################################
#               end of data extraction and cleaning for plots          #
########################################################################

#==========================
# Plot: Barplot with scores (unordered)
# corresponds to Lig_outcome
# Stacked Barplot with colours: Lig_outcome @ position coloured by 
# Lig_outcome. This is a barplot where each bar corresponds 
# to a SNP and is coloured by its corresponding Lig_outcome.
#============================

#===================
# Data for plots
#===================

#%%%%%%%%%%%%%%%%%%%%%%%%
# REASSIGNMENT
df  = my_df 
#%%%%%%%%%%%%%%%%%%%%%%%%

rm(my_df)

# sanity checks
upos = unique(my_df$Position)

# should be a factor
is.factor(df$Lig_outcome)
#TRUE

table(df$Lig_outcome)

# should be -1 and 1: may not be in this case because you have filtered the data
# FIXME: normalisation before or after filtering?
min(df$ratioPredAff) #
max(df$ratioPredAff) #

# sanity checks
tapply(df$ratioPredAff, df$Lig_outcome, min)
tapply(df$ratioPredAff, df$Lig_outcome, max)

#******************
# generate plot
#******************

# set output dir for plots
getwd()
setwd("~/git/Data/pyrazinamide/output/plots")
getwd()

my_title = "Ligand affinity"

# axis label size
my_xaxls = 13
my_yaxls = 15

# axes text size
my_xaxts = 15
my_yaxts = 15

# no ordering of x-axis
g = ggplot(df, aes(factor(Position, ordered = T)))
g + 
  geom_bar(aes(fill = Lig_outcome), colour = "grey") +
  theme( axis.text.x = element_text(size = my_xaxls
                                    , angle = 90
                                    , hjust = 1
                                    , vjust = 0.4)
         , axis.text.y = element_text(size = my_yaxls 
                                      , angle = 0
                                      , hjust = 1
                                      , vjust = 0)
         , axis.title.x = element_text(size = my_xaxts)
         , axis.title.y = element_text(size = my_yaxts ) ) +
  labs(title = my_title
       , x = "Position"
       , y = "Frequency")

# for sanity and good practice
rm(df)
#======================= end of plot
# axis colours labels
# https://stackoverflow.com/questions/38862303/customize-ggplot2-axis-labels-with-different-colors
# https://stackoverflow.com/questions/56543485/plot-coloured-boxes-around-axis-label