// Keywords: live plotting

initialize() {
	initializeMutationRate(1e-7);
	initializeMutationType("m1", 0.5, "f", 0.0);
	initializeGenomicElementType("g1", m1, 1.0);
	initializeGenomicElement(g1, 0, 99999);
	initializeRecombinationRate(1e-8);
}
1 {
	sim.addSubpop("p1", 5000);
	sim.setValue("fixed", NULL);
	
	defineConstant("pdfPath", writeTempFile("plot_", ".pdf", ""));
	
	// If we're running in SLiMgui, open a plot window
	if (exists("slimgui"))
	{
		slimgui.openDocument(pdfPath);
		sim.setValue("pdfPid", 0);
	}
	else
		sim.setValue("pdfPid", -1);
}
1: {
	if (sim.generation % 10 == 0)
	{
		count = sim.substitutions.size();
		sim.setValue("fixed", c(sim.getValue("fixed"), count));
	}
	
	if (sim.generation % 1000 != 0)
		return;
	
	y = sim.getValue("fixed");
	
	rstr = paste(c('{',
		'x <- (1:' + size(y) + ') * 10',
		'y <- c(' + paste(y, sep=", ") + ')',
		'pdf(file="' + pdfPath + '", width=4, height=4)',
		'par(mar=c(4.0, 4.0, 1.5, 1.5))',
		'plot(x=x, y=y, xlim=c(0, 50000), ylim=c(0, 500), type="l",',
			'xlab="Generation", ylab="Fixed mutations", cex.axis=0.95,',
			'cex.lab=1.2, mgp=c(2.5, 0.7, 0), col="red", lwd=2,',
			'xaxp=c(0, 50000, 2))',
		'box()',
		'dev.off()',
		'}'), sep="\n");
	
	scriptPath = writeTempFile("plot_", ".R", rstr);
	system("/usr/local/bin/Rscript", args=scriptPath);
	deleteFile(scriptPath);

	if (!exists("slimgui"))
	{
		if (sim.getValue("pdfPid") < 0)
		{
			system("mupdf " + pdfPath, wait=F);
			pid = system("pgrep -a mupdf|grep " + pdfPath + " | cut -f1 -d' '");
			sim.setValue("pdfPid", pid);
		}
		else
			system("kill -HUP " + sim.getValue("pdfPid"));
	}
}
50000 late() { sim.outputFixedMutations(); }