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

#########################################################
# TASK: output barplot by position with each bar coloured by 
# its stability value and NO coloured positions indicated
#########################################################
#=======================================================================

############################################################
# 1: Installing and loading required packages and functions
#############################################################

#source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2)
library(data.table)
source("barplot_colour_function.R")
source("plotting_data.R")

# should return the following dfs, directories and variables
# mut_pos_cols
# my_df
# my_df_u
# my_df_u_lig
# dup_muts

cat(paste0("Directories imported:"
           , "\ndatadir:", datadir
           , "\nindir:", indir
           , "\noutdir:", outdir
           , "\nplotdir:", plotdir))

cat(paste0("Variables imported:"
           , "\ndrug:", drug
           , "\ngene:", gene
           , "\ngene_match:", gene_match
           , "\nLength of upos:", length(upos)
           , "\nAngstrom symbol:", angstroms_symbol))

# clear excess variable
rm(my_df, upos, dup_muts, my_df_u_lig)
########################################################

#=======
# output
#=======
print(paste0("plot will be in:", plotdir))
bp_subcols_duet = "barplot_coloured_PS.svg"
plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)

#===================
# Data for plots
#===================
# REASSIGNMENT as necessary
df  = my_df_u

# sanity checks
str(df)
upos = unique(df$position)

# should be a factor
if (is.factor(df$duet_outcome)){
  print("duet_outcome is factor")
}else{
  print("convert duet_outcome to factor")
  df$duet_outcome = as.factor(df$duet_outcome)
}

is.factor(df$duet_outcome)

table(df$duet_outcome)

# should be -1 and 1
min(df$duet_scaled)
max(df$duet_scaled)

tapply(df$duet_scaled, df$duet_outcome, min)
tapply(df$duet_scaled, df$duet_outcome, max)

#******************
# generate plot
#******************
#==========================
# Barplot with scores (unordered)
# corresponds to duet_outcome
# Stacked Barplot with colours: duet_outcome @ position coloured by 
# stability scores. This is a barplot where each bar corresponds 
# to a SNP and is coloured by its corresponding DUET stability value.
# Normalised values (range between -1 and 1 ) to aid visualisation
# NOTE: since barplot plots discrete values, colour = score, so number of
# colours will be equal to the no. of unique normalised scores 
# rather than a continuous scale
# will require generating the colour scale separately.
#============================

# My colour FUNCTION: based on group and subgroup
# in my case;
# df = df
# group = duet_outcome
# subgroup = normalised score i.e duet_scaled

# check unique values in normalised data
u = unique(df$duet_scaled) 

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Run this section if rounding is to be used
n = 3 
df$duet_scaledR = round(df$duet_scaled, n)
ur = unique(df$duet_scaledR)

# create an extra column called group which contains the "gp name and score" 
# so colours can be generated for each unique values in this column

#my_grp = df$duet_scaledR # rounding
my_grp = df$duet_scaled # no rounding
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

df$group <- paste0(df$duet_outcome, "_", my_grp, sep = "")

# Call the function to create the palette based on the group defined above
colours <- ColourPalleteMulti(df, "duet_outcome", "my_grp")
print(paste0("Colour palette generated for: ", length(colours), " colours"))
my_title = "Protein stability (DUET)"

# axis label size
my_xaxls = 13
my_yaxls = 15

# axes text size
my_xaxts = 15
my_yaxts = 15

#******************
# generate plot: NO axis colours
#******************
print(paste0("plot name:", plot_bp_subcols_duet))

svg(plot_bp_subcols_duet, width = 26, height = 4)

g = ggplot(df, aes(factor(position, ordered = T)))
outPlot = g + 
  geom_bar(aes(fill = group), colour = "grey") +
  scale_fill_manual( values = colours
                     , guide = "none") +
  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 = ""
       #title = my_title
       , x = "position"
       , y = "Frequency")
       
print(outPlot)
dev.off()
# 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