3 nrow_per_page <- 3 # if input_list is composed of transcript ids
4 ncol_per_page <- 2 # if input_list is composed of transcript ids
5 num_plots_per_page <- nrow_per_page * ncol_per_page # if input_list is composed of transcript/allele ids
7 exit_with_error <- function(errmsg) {
8 cat(errmsg, "\n", sep = "", file = stderr())
9 quit(save = "no", status = 1)
12 args <- commandArgs(TRUE)
13 if (length(args) != 6)
14 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")
16 sample_name <- args[1]
18 alleleS <- as.numeric(args[3])
19 id_type <- as.numeric(args[4])
20 show_uniq <- as.numeric(args[5])
21 output_plot_file <- args[6]
23 is_composite <- (!alleleS && (id_type == 2)) || (alleleS && (id_type > 0))
25 load_readdepth_file <- function(filename) {
26 data <- read.table(file = filename, sep = "\t", stringsAsFactors = FALSE)
27 readdepth <- split(data[, 2:3], data[, 1])
30 build_map <- function(filename) {
32 if (!alleleS || (alleleS && id_type == 1)) {
38 data <- read.delim(file = filename, sep = "\t", stringsAsFactors = FALSE)
39 tmp <- aggregate(data[value_pos], data[key_pos], function(x) x)
46 make_a_plot <- function(id) {
47 vec <- readdepth[[id]]
48 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))
49 if (is.na(vec[[2]])) wiggle <- rep(0, vec[[1]]) else wiggle <- as.numeric(unlist(strsplit(vec[[2]], split = " ")))
52 plot(wiggle, type = "h")
54 vec <- readdepth_uniq[[id]]
55 stopifnot(!is.null(vec))
56 if (is.na(vec[[2]])) wiggle_uniq <- rep(0, vec[[1]]) else wiggle_uniq <- as.numeric(unlist(strsplit(vec[[2]], split = " ")))
57 stopifnot(len == length(wiggle_uniq))
58 if (len != sum(wiggle >= wiggle_uniq)) {
59 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 = "")
61 heights <- rbind(wiggle_uniq, wiggle - wiggle_uniq)
62 barplot(heights, space = 0, border = NA, names.arg = 1:len, col = c("black", "red"))
67 generate_a_page <- function(ids, title = NULL) {
69 ncol <- ifelse(is_composite, floor(sqrt(n)), ncol_per_page)
70 nrow <- ifelse(is_composite, ceiling(n / ncol), nrow_per_page)
72 par(mfrow = c(nrow, ncol), mar = c(2, 2, 2, 2))
73 if (is_composite) par(oma = c(0, 0, 3, 0))
74 sapply(ids, make_a_plot)
75 if (is_composite) mtext(title, outer = TRUE, line = 1)
78 plot_individual <- function(i) {
79 fr <- (i - 1) * num_plots_per_page + 1
80 to <- min(i * num_plots_per_page, n)
81 generate_a_page(ids[fr:to])
84 # cid, composite id, can be either a gene id or transcript id (for allele-specific expression only)
85 plot_composite <- function(cid) {
86 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))
87 generate_a_page(map[[cid]], cid)
90 readdepth <- load_readdepth_file(paste(sample_name, ".transcript.readdepth", sep = ""))
93 readdepth_uniq <- load_readdepth_file(paste(sample_name, ".uniq.transcript.readdepth", sep = ""))
96 ids <- scan(file = input_list, what = "", sep = "\n")
98 cat("Loading files is done!\n")
101 file_name <- sprintf("%s.%s.results", sample_name, ifelse(alleleS, "alleles", "isoforms"))
102 map <- build_map(file_name)
103 cat("Building transcript to gene map is done!\n")
106 pdf(output_plot_file)
110 ub <- (n - 1) %/% num_plots_per_page + 1
111 dumbvar <- sapply(1:ub, plot_individual)
113 dumbvar <- sapply(ids, plot_composite)
116 cat("Plots are generated!\n")
118 dev.off.output <- dev.off()