#!/usr/bin/env Rscript

nrow_per_page <- 3 # if input_list is composed of transcript ids
ncol_per_page <- 2 # if input_list is composed of transcript ids
num_plots_per_page <- nrow_per_page * ncol_per_page # if input_list is composed of transcript ids


exit_with_error <- function(errmsg) {
  cat(errmsg, "\n", sep = "", file = stderr())
  quit(save = "no", status = 1)
}


args <- commandArgs(TRUE)
if (length(args) != 5) 
  exit_with_error("Usage: rsem-gen-transcript-plots sample_name input_list is_gene show_uniq output_plot_file")

sample_name <- args[1]
input_list <- args[2]
is_gene <- as.numeric(args[3])
show_uniq <- as.numeric(args[4])
output_plot_file <- args[5]

load_readdepth_file <- function(filename) {
  data <- read.table(file = filename, sep = "\t", stringsAsFactors = FALSE)
  readdepth <- split(data[, 2:3], data[, 1])
}

build_t2gmap <- function(filename) {
  tpos <- 1   # the position of transcript_id
  gpos <- 2   # the position of gene_id

  data <- read.delim(file = filename, sep = "\t", stringsAsFactors = FALSE)
  tmp <- aggregate(data[tpos], data[gpos], function(x) x)
  t2gmap <- tmp[,2]
  names(t2gmap) <- tmp[,1]

  t2gmap
}

make_a_plot <- function(tid) {
  vec <- readdepth[[tid]]	
  if (is.null(vec)) exit_with_error(paste("Unknown transcript detected,", tid, "is not included in RSEM's indices."))
  if (is.na(vec[[2]])) wiggle <- rep(0, vec[[1]]) else wiggle <- as.numeric(unlist(strsplit(vec[[2]], split = " ")))
  len <- length(wiggle)
  if (!show_uniq) {
    plot(wiggle, type = "h")
  } else {
    vec <- readdepth_uniq[[tid]]
    stopifnot(!is.null(vec))
    if (is.na(vec[[2]])) wiggle_uniq <- rep(0, vec[[1]]) else wiggle_uniq <- as.numeric(unlist(strsplit(vec[[2]], split = " ")))
    stopifnot(len == length(wiggle_uniq))
    if (len != sum(wiggle >= wiggle_uniq)) {
      cat("Warning: transcript ", tid, " has position(s) that read covarege with multireads is smaller than read covarge without multireads.\n", "         The 1-based position(s) is(are) : ", which(wiggle < wiggle_uniq), ".\n", "         This may be due to floating point arithmetics.\n", sep = "") 
    }
    heights <- rbind(wiggle_uniq, wiggle - wiggle_uniq)	
    barplot(heights, space = 0, border = NA, names.arg = 1:len, col = c("black", "red")) 
  }
  title(main = tid) #, xlab = "Position in transcript", ylab = "Read depth")
}

generate_a_page <- function(tids, gene_id = NULL) {
  n <- length(tids)
  ncol <- ifelse(is_gene, floor(sqrt(n)), ncol_per_page)
  nrow <- ifelse(is_gene, ceiling(n / ncol), nrow_per_page)

  par(mfrow = c(nrow, ncol), mar = c(2, 2, 2, 2))
  if (is_gene) par(oma = c(0, 0, 3, 0)) 
  sapply(tids, make_a_plot)
  if (is_gene) mtext(gene_id, outer = TRUE, line = 1)
}

plot_a_transcript <- function(i) {
  fr <- (i - 1) * num_plots_per_page + 1
  to <- min(i * num_plots_per_page, n)
  generate_a_page(ids[fr:to])
}

plot_a_gene <- function(gene_id) {
  if (is.null(t2gmap[[gene_id]])) exit_with_error(paste("Unknown gene detected,", gene_id, "is not included in RSEM's in indices."))
  generate_a_page(t2gmap[[gene_id]], gene_id)
}

readdepth <- load_readdepth_file(paste(sample_name, ".transcript.readdepth", sep = ""))

if (show_uniq) {
  readdepth_uniq <- load_readdepth_file(paste(sample_name, ".uniq.transcript.readdepth", sep = ""))
}

ids <- scan(file = input_list, what = "", sep = "\n")

cat("Loading files is done!\n")

if (is_gene) {
  t2gmap <- build_t2gmap(paste(sample_name, ".isoforms.results", sep = ""))
  cat("Building transcript to gene map is done!\n")
}

pdf(output_plot_file)

if (!is_gene) {	
  n <- length(ids)
  ub <- (n - 1) %/% num_plots_per_page + 1
  tmp <- sapply(1:ub, plot_a_transcript)
} else {
  tmp <- sapply(ids, plot_a_gene)
}

cat("Plots are generated!\n")

dev.off.output <- dev.off()