rsem-gen-transcript-plots

#!/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/allele ids

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

args <- commandArgs(TRUE)
if (length(args) != 6) 
  exit_with_error("Usage: rsem-gen-transcript-plots sample_name input_list is_allele_specific id_type<0,allele;1,isoform;2,gene> show_uniq output_plot_file")

sample_name <- args[1]
input_list <- args[2]
alleleS <- as.numeric(args[3])
id_type <- as.numeric(args[4])
show_uniq <- as.numeric(args[5])
output_plot_file <- args[6]

is_composite <- (!alleleS && (id_type == 2)) || (alleleS && (id_type > 0))
 
load_readdepth_file <- function(filename) {
  data <- read.table(file = filename, sep = "\t", stringsAsFactors = FALSE)
  readdepth <- split(data[, 2:3], data[, 1])
}

build_map <- function(filename) {
  value_pos <- 1
  if (!alleleS || (alleleS && id_type == 1)) {
    key_pos <- 2
  } else {
    key_pos <- 3
  }

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

  map
}

make_a_plot <- function(id) {
  vec <- readdepth[[id]]	
  if (is.null(vec)) exit_with_error(sprintf("Unknown %s detected, %s is not included in RSEM's indices.", ifelse(alleleS, "allele-specific transcript", "transcript"), id))
  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[[id]]
    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: ", ifelse(alleleS, "allele-specific transcript", "transcript"), " ", id, " 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 = id)
}

generate_a_page <- function(ids, title = NULL) {
  n <- length(ids)
  ncol <- ifelse(is_composite, floor(sqrt(n)), ncol_per_page)
  nrow <- ifelse(is_composite, ceiling(n / ncol), nrow_per_page)

  par(mfrow = c(nrow, ncol), mar = c(2, 2, 2, 2))
  if (is_composite) par(oma = c(0, 0, 3, 0)) 
  sapply(ids, make_a_plot)
  if (is_composite) mtext(title, outer = TRUE, line = 1)
}

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

# cid, composite id, can be either a gene id or transcript id (for allele-specific expression only)
plot_composite <- function(cid) {
  if (is.null(map[[cid]])) exit_with_error(sprintf("Unknown %s detected, %s is not included in RSEM's indices.", ifelse(alleleS && id_type == 1, "transcript", "gene"), cid))
  generate_a_page(map[[cid]], cid)
}

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_composite) {
  file_name <- sprintf("%s.%s.results", sample_name, ifelse(alleleS, "alleles", "isoforms"))
  map <- build_map(file_name)
  cat("Building transcript to gene map is done!\n")
}

pdf(output_plot_file)

if (!is_composite) {	
  n <- length(ids)
  ub <- (n - 1) %/% num_plots_per_page + 1
  dumbvar <- sapply(1:ub, plot_individual)
} else {
  dumbvar <- sapply(ids, plot_composite)
}

cat("Plots are generated!\n")

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