plot_chip.R

#!/bin/env Rscript

#'
#'  fixed global variables
#'  

# select the input file
chipfile <- "../test_data/CTCF.bedgraph"

# set the output file
outfile <- "CTCF.png"

# specify a region to plot
region <- NULL

dpi <- 600

width <- 6

height <- 2

minimum_signal <- NULL

# load the libraries
library_path <- "."

#
source(file.path(library_path, "chip_body.R"))
verbose <- FALSE

require(getopt, quietly = TRUE)

# set the commandline option specifications
specification <- matrix(c(
	"bedfile", "b", 1, "character",
	"outfile", "o", 2, "character",
	"chromosome", "c", 2, "character",
	"start", "s", 2, "integer",
	"end", "e", 2, "integer",
	"dpi", "d", 2, "integer",
	"minimum-signal", "s", 2, "double",
	"width", "w", 2, "integer",
	"height", "h", 2, "integer",
	"library", "l", 1, "character", 
	"verbose", "v", 0, "logical",
	"help", "", 0, "logical"
), byrow = TRUE, ncol = 4)


# parse the commandline options
commandline_options <- getopt(specification)

# print the usage if help was asked
if(!is.null(commandline_options[["help"]])) {
	cat(getopt(specification, usage = TRUE))
	q(status = 1)
}

if(!is.null(commandline_options[["verbose"]])) {
	verbose <- TRUE	
}

# set the required variables
chipfile <- commandline_options[["bedfile"]]

#
if(!is.null(commandline_options[["chromosome"]]) && !is.null(commandline_options[["start"]]) && !is.null(commandline_options[["end"]])){
	region <- list(
		"chr" = commandline_options[["chromosome"]],
		"start" = commandline_options[["start"]],
		"end" = commandline_options[["end"]])
}

if(!is.null(commandline_options[["outfile"]])){
	outfile <- commandline_options[["outfile"]]
}

if(!is.null(commandline_options[["minimum-signal"]])){
	minimum_signal <- commandline_options[["minimum-signal"]]
}

if(!is.null(commandline_options[["dpi"]])){
	dpi <- commandline_options[["dpi"]]
}

if(!is.null(commandline_options[["width"]])){
	width <- commandline_options[["width"]]
}

if(!is.null(commandline_options[["heigth"]])){
	height <- commandline_options[["heigth"]]
}

if(!is.null(commandline_options[["library"]])){
	library_path <- commandline_options[["library"]]
}

if(verbose){
	message(paste("BED file", infile))
	message(paste("Output", outfile))
	message(paste("Region", paste(region, collapse = " ")))
	message(paste("Minimum signal", minimum_signal))
	message(paste("DPI", dpi))
	message(paste("Width", width))
	message(paste("Height", height))
	message(paste("Library path", library_path))
}


# perform the analysis
source(file.path(library_path, "chip_body.R"))