#!/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()