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)
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
+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[tpos], data[gpos], function(x) x)
- t2gmap <- tmp[,2]
- names(t2gmap) <- tmp[,1]
+ tmp <- aggregate(data[value_pos], data[key_pos], function(x) x)
+ map <- tmp[,2]
+ names(map) <- tmp[,1]
- t2gmap
+ map
}
-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."))
+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[[tid]]
+ 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: 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 = "")
+ 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 = tid) #, xlab = "Position in transcript", ylab = "Read depth")
+ 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))
- sapply(tids, make_a_plot)
- if (is_gene) mtext(gene_id, outer = TRUE, line = 1)
+ 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_a_transcript <- function(i) {
+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])
}
-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)
+# 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
- tmp <- sapply(1:ub, plot_a_transcript)
+ dumbvar <- sapply(1:ub, plot_individual)
} else {
- tmp <- sapply(ids, plot_a_gene)
+ dumbvar <- sapply(ids, plot_composite)
}
cat("Plots are generated!\n")
dev.off.output <- dev.off()
-
-
-
projects / rsem.git / blobdiff