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
-
+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) != 5)
- exit_with_error("Usage: rsem-gen-transcript-plots sample_name input_list is_gene show_uniq output_plot_file")
+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]
-is_gene <- as.numeric(args[3])
-show_uniq <- as.numeric(args[4])
-output_plot_file <- args[5]
-
-
+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)
- nrow <- dim(data)[1]
- readdepth <- list()
- for (i in 1:nrow) {
- readdepth[[data[i, 1]]] <- data[i, c(2, 3)]
+ 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
}
- readdepth
+
+ 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
}
-build_t2gmap <- function(filename) {
- data <- read.table(file = filename, sep = "\t", stringsAsFactors = FALSE)
- t2gmap <- list()
-
- nrow <- dim(data)[1]
- ncol <- dim(data)[2]
-
- gene_id <- ""
- tids <- c()
- for (i in 1:nrow) {
- if (gene_id != data[i, ncol]) {
- if (gene_id != "") {
- t2gmap[[gene_id]] <- tids
- }
- gene_id <- data[i, ncol]
- tids <- c()
+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 = "")
}
- tids <- c(tids, data[i, 1])
+ heights <- rbind(wiggle_uniq, wiggle - wiggle_uniq)
+ barplot(heights, space = 0, border = NA, names.arg = 1:len, col = c("black", "red"))
}
- if (gene_id != "") t2gmap[[gene_id]] <- tids
-
- t2gmap
+ title(main = id)
}
-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)
+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_gene) par(oma = c(0, 0, 3, 0))
-
- for (i in 1:n) {
- vec <- readdepth[[tids[i]]]
- if (is.null(vec)) exit_with_error(paste("Unknown transcript detected,", tids[i], "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[[tids[i]]]
- 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), len == sum(wiggle >= wiggle_uniq))
- heights <- rbind(wiggle_uniq, wiggle - wiggle_uniq)
- barplot(heights, space = 0, border = NA, names.arg = 1:len, col = c("black", "red"))
- }
- title(main = tids[i]) #, xlab = "Position in transcript", ylab = "Read depth")
- }
+ if (is_composite) par(oma = c(0, 0, 3, 0))
+ sapply(ids, make_a_plot)
+ if (is_composite) mtext(title, outer = TRUE, line = 1)
+}
- if (is_gene) mtext(gene_id, 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 = ""))
cat("Loading files is done!\n")
-if (is_gene) {
- t2gmap <- build_t2gmap(paste(sample_name, ".isoforms.results", sep = ""))
+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_gene) {
+if (!is_composite) {
n <- length(ids)
ub <- (n - 1) %/% num_plots_per_page + 1
- for (i in 1:ub) {
- fr <- (i - 1) * num_plots_per_page + 1
- to <- min(i * num_plots_per_page, n)
- generate_a_page(ids[fr:to])
- }
+ dumbvar <- sapply(1:ub, plot_individual)
} else {
- for (gene_id in ids) {
- 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)
- }
+ dumbvar <- sapply(ids, plot_composite)
}
-cat("Plots are generated!\n)
+cat("Plots are generated!\n")
dev.off.output <- dev.off()
projects / rsem.git / blobdiff