#!/usr/bin/env Rscript  

#########################################################
# TASK: function for barplot showing no. of sites with nsSNP
# count
#########################################################
# load libraries and functions
library(ggplot2)
library(data.table)
library(dplyr)

theme_set(theme_grey())
#=================================================================
# site_snp_count_bp(): barplots for no. of sites and nsSNP count
# input args
## df containing data to plot
## df column name containing site/position numbers
## ...opt args

# TODO:
# legend params, currently it appears as title
# visually might be nicer for it to be inside the plot
#=================================================================

site_snp_count_bp <- function (plotdf
                               , df_colname = "position"
                               #, bp_plot_title = ""
                               #, leg_title = "Legend title"
                               , leg_text_size = 10#20
                               , axis_text_size = 10#25
                               , axis_label_size = 10#22
                               , subtitle_size = 10#20
                               , geom_ls = 10
                               , xaxis_title = "Number of nsSNPs"
                               , yaxis_title = "Number of Sites"
                               , title_colour = "chocolate4"
                               , subtitle_text = NULL
                               , subtitle_colour = "pink")
                               {
  
  plotdf = as.data.frame(plotdf)
  # dim of plotdf
  cat(paste0("\noriginal df dimensions:"
             , "\nNo. of rows:", nrow(plotdf)
             , "\nNo. of cols:", ncol(plotdf)
             , "\nNow adding column: frequency of mutational positions"))
  
  #-------------------------------------------
  # adding column: snpcount for each position 
  #-------------------------------------------
  #setDT(plotdf)[, pos_count_check := .N, by = .(eval(parse(text = df_colname)))] 
  
    # from dplyr
  plotdf = plotdf %>% 
    dplyr::add_count(eval(parse(text = df_colname)))
  class(plotdf)
  plotdf = as.data.frame(plotdf)
  class(plotdf)
  nc_change = which(colnames(plotdf) == "n")
  colnames(plotdf)[nc_change] <- "pos_count"
  class(plotdf)

  # if (all(plotdf$pos_count==plotdf$pos_count_check) ){
  #   cat("\nPASS: pos_count column created")
  #   plotdf = plotdf[, !colnames(plotdf)%in%c("pos_count_check")]
  # }else{
  #   stop("\nAbort: pos count numbes mismatch from dplyr and data.table")
  # }
  
  cat("\nCumulative nssnp count\n"
  , table(plotdf$pos_count))
  
  # calculating total no. of mutations
  tot_muts = sum(table(plotdf$pos_count))
  

  # sanity check
  if(tot_muts == nrow(plotdf)){
    cat("\nPASS: total number of mutations match"
        , "\nTotal no. of nsSNPs:", tot_muts)
  } else{
    cat("\nWARNING: total no. of muts = ", tot_muts
        , "\nExpected = ", nrow(plotdf))
  }
  
  # revised dimensions
  cat(paste0("\nrevised df dimensions:"
             , "\nNo. of rows:", nrow(plotdf)
             , "\nNo. of cols:", ncol(plotdf)))

  #------------------------------------------------------
  # creating df: average count of snpcount for each position 
  # created in earlier step
  #-------------------------------------------------------
  # use group by on pos_count
  snpsBYpos_df <- plotdf %>%
    dplyr::group_by(eval(parse(text = df_colname))) %>%
    dplyr::summarise(snpsBYpos = mean(pos_count)) # changed from summarize!
  
  cat("\nnssnp count per position\n"
      , table(snpsBYpos_df$snpsBYpos)
      , "\n")

  # calculating total no. of sites associated with nsSNPs
  tot_sites = sum(table(snpsBYpos_df$snpsBYpos))
  
  # sanity check
  if(tot_sites == length(unique(plotdf$position))){
    cat("\nPASS: total number of mutation sites match"
        , "\nTotal no. of sites with nsSNPs:", tot_sites)
  } else{
    cat("WARNING: total no. of sites = ", tot_sites
        , "\nExpected = ", length(unique(plotdf$position)))
  }
  
  # FIXME: should really be legend title
  # but atm being using as plot title
  #my_leg_title
  bp_plot_title = paste0("Total nsSNPs: ", tot_muts
                        , "\nTotal sites: ", tot_sites)
  
  #-------------
  # start plot 2
  #--------------
  # to make x axis display all positions
  # not sure if to use with sort or directly
  my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
  
  ggplot(snpsBYpos_df, aes(x = snpsBYpos)) +
    geom_bar(aes (alpha = 0.5)
             , show.legend = FALSE) +
    scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
    geom_label(stat = "count", aes(label = ..count..)
               , color = "black"
               , size = geom_ls) +
    theme(axis.text.x = element_text(size = axis_text_size
                                     , angle = 0)
          , axis.text.y = element_text(size = axis_text_size
                                       , angle = 0
                                       , hjust = 1)
          , axis.title.x = element_text(size = axis_label_size)
          , axis.title.y = element_text(size = axis_label_size)
          #, legend.position = c(0.73,0.8)
          #, legend.text = element_text(size = leg_text_size)
          #, legend.title = element_text(size =  axis_label_size)
          #, panel.grid.major = element_blank(),
          #, panel.grid.minor = element_blank(),
          , panel.grid = element_blank()
          , plot.title = element_text(size = leg_text_size
                                      , colour = title_colour
                                      , hjust = 0.5)
          , plot.subtitle = element_text(size = subtitle_size
                                         , hjust = 0.5
                                         , colour = subtitle_colour)) +
    # labs(title = bp_plot_title
    #      , subtitle = subtitle_text
    #      , x = xaxis_title
    #      , y = yaxis_title)
  
  labs(title = ""
       , subtitle = bp_plot_title
       , x = xaxis_title
       , y = yaxis_title)
}

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#               			end of function   			   
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