## This is a Shiny web application. You can run the application by clicking
# the 'Run App' button above.
#
# Find out more about building applications with Shiny here:
#
#    http://shiny.rstudio.com/
##
###################################
# load libraries and function
#source("Header_TT.R")
library(shiny)
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 : 


# INSERT HERE

# hardcoded vars
infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
drug = "streptomycin"
gene = "gid"

###################################
# 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
#----------------------------------------------

#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("Variables imported:"
           , "\ndrug:", drug
           , "\ngene:", gene))
#==========================================================
#================
# Data for plots
#================
# REASSIGNMENT as necessary
df  = my_df_u

# sanity checks
str(df)
#===========================================================
# Define UI for application that draws a histogram
ui <- fluidPage(

    # Application title
    titlePanel("Mtb target: gid"),

    # Sidebar with a slider input for number of bins 
    sidebarLayout(
        sidebarPanel(radioButtons("rb", "biophysical effect"
                         , choiceNames = list(
                             "mCSM"
                            , "FoldX")
                         , choiceValues = list(
                             "mCSM"
                             , "FoldX")
                         ))
        # Show a plot of the generated distribution
        , mainPanel(plotOutput("distPlot")
                  , textOutput("txt"))))

# Define server logic required to draw a histogram
my_ats = 25 # axis text size
my_als = 22 # axis label size

theme_set(theme_grey())

server <- function(input, output) {output$distPlot <- renderPlot({
        axisType = input$rb
        my_title = paste0("Barplots for biophyiscal effects ", axisType)
        if (axisType == "mCSM") {
            y_value = "duet_outcome"
            leg_name = "DUET outcome"}
        
        if (axisType == "FoldX") {
            y_value = "foldx_outcome"
            leg_name = "FoldX outcome"}
        
        ggplot(df, aes(x = eval(parse(text = y_value)))) + 
                       geom_bar(aes(fill = eval(parse(text = y_value))), show.legend = TRUE) +
            geom_label(stat = "count"
                       , aes(label = ..count..)
                       , color = "black"
                       , show.legend = FALSE
                       , size = 10) + 
            theme(axis.text.x = element_blank()
                  , axis.title.x = element_blank()
                  , axis.title.y = element_text(size=my_als)
                  , axis.text.y = element_text(size = my_ats)
                  , legend.position = c(0.73,0.8)
                  , legend.text = element_text(size=my_als-2)
                  , legend.title = element_text(size=my_als)
                  , plot.title = element_blank()) + 
            labs(title = ""
                 , y = "Number of nsSNPs"
                 #, fill="DUET Outcome"
            ) + 
            scale_fill_discrete(name = leg_name
                                , labels = c("Destabilising", "Stabilising"))
    })
    #output$txt <- renderText({
    #    paste("You chose", input$rb)})
    
}

stabiliyPlot <- function(input, output) {
}
# Run the application 
shinyApp(ui = ui, server = server)