#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
if (length(args) < 3){
stop("No enough input parameters!\n",
call.=FALSE)
}
library("ggplot2")
library("data.table")
library("grid")
library(stringr)
rRNA.stack <- function(file.address, file.name, rRNA.length){
length.dis <- read.table(paste(file.address
, file.name
, "_result/"
, file.name
, "_length_distribution.txt", sep = ""),
header = TRUE,
sep = "\t",
col.names = c("name", "length", "reads")
)
length.dis <- length.dis[!grepl("antisense", length.dis$name, ignore.case = TRUE), ]
len.min <- min(length.dis$length)
len.max <- max(length.dis$length)
len <- len.min : len.max
sum.clean <- sum(length.dis[which(length.dis$name == "Clean_Reads"), 3])
length.dis <- data.frame(length.dis[ ,1:2], reads = length.dis$reads * 1000000 / sum.clean)
dis.clean <- length.dis[which(length.dis$name == "Clean_Reads"), 2:3]
stack.all <- c()
dis.total.rRNA <- length.dis[grep("-rRNA|_rRNA", length.dis$name, ignore.case = TRUE), ]
dis.total.rRNA <- dis.total.rRNA[!grepl("antisense|S-rRNA|other-rRNA", dis.total.rRNA$name, ignore.case = TRUE), 2:3]
dis.other.rRNA <- data.frame(name = "other.rRNA", length.combine(dis.total.rRNA, len))
rRNA.length <- unlist(strsplit(rRNA.length, ","))
k <- 0
for(i in 1:length(rRNA.length)){
temp.length <- unlist(strsplit(rRNA.length[i], "="))
if (!grepl("RNY|other", temp.length[1])){
dis.rRNA <- length.dis[grep(paste("-", temp.length[1], sep = ""), length.dis$name), 2:3]
dis.rRNA <- data.frame(name = paste(temp.length[1], ".rRNA", sep = ""), length.combine(dis.rRNA, len))
sum.rRNA <- sum(dis.rRNA$reads)
if(sum.rRNA > 0){
k <- k+1
stack.all <- rbind(stack.all, dis.rRNA)
dis.other.rRNA <- data.frame(dis.other.rRNA[1:2], dis.other.rRNA[3] - dis.rRNA[3])
}
}
}
stack.all <- rbind(stack.all, dis.other.rRNA)
stack.all$name <- factor(stack.all$name, levels = unique(stack.all$name))
stack.sep <- ggplot(stack.all, aes(x = length, y = reads, fill = name)) +
geom_bar(stat = "identity") +
facet_grid(. ~ name) +
labs(x = "length", y = "RPM", title = "") +
theme(axis.line = element_line()
, panel.grid.minor = element_blank()
, panel.grid.major = element_blank()
, panel.background = element_rect(fill = "transparent", colour = NA)
, plot.background = element_rect(fill = "transparent", colour = NA)
, panel.border = element_rect(fill = "transparent")
)
stack.pic <- ggplot(stack.all, aes(x = length, y = reads, fill = name)) +
geom_bar(stat = "identity") +
theme(axis.line = element_line()
, panel.grid.minor = element_blank()
, panel.grid.major = element_blank()
, panel.background = element_rect(fill = "transparent", colour = NA)
, plot.background = element_rect(fill = "transparent", colour = NA)
, legend.title = element_blank()
, legend.background = element_rect(fill = "transparent", colour = NA)
, legend.box.background = element_rect(fill = "transparent", colour = NA)
, legend.position = "top"
, axis.text = element_text(size = 15, color = "black")
, axis.title = element_text(size = 15)
) +
labs(x = "length", y = "RPM", title = "")
pdf(paste(file.address, file.name, "_result/", file.name, "_rsRNA_distribution.pdf", sep=""), width = 8+0.5 * k, height = 12)
grid.newpage()
pushViewport(viewport(layout = grid.layout(4, 1, heights = unit(c(1, 4, 4, 4), "null"))))
pdf.title <- paste("rRNAs Length Distribution of ", file.name, sep = "")
vplayout <- function(x,y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.text(pdf.title, vp = vplayout(1, 1), gp = gpar(fontsize = 20))
print(stack.pic, vp = vplayout(2:3, 1))
print(stack.sep, vp = vplayout(4, 1))
invisible(dev.off())
}
length.combine <- function(distr, len){
if(is.data.frame(distr) && nrow(distr) == 0){
distr <- data.frame(length = len, reads = 0)
}
tmp <- data.table(distr)
tmp <- as.data.frame(tmp[, lapply(.SD, sum), by=list(length)])
tmp <- tmp[order(as.numeric(tmp$length)), ]
if(length(len[-c(match(distr[ ,1], len))]) != 0){
tmp <- rbind(tmp, data.frame(length = len[-c(match(distr[ ,1], len))], reads = 0))
}
distr <- tmp[order(as.numeric(tmp$length)), ]
}
rRNA.stack(file.address = args[1], file.name = args[2], rRNA.length = args[3])
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