source(paste(Sys.getenv("STING_DIR"), "/R/gsacommons.R", sep=""));

if (interactive()) {
    if (!exists("plotRoot")) {
        plotRoot = "test.plot";
    }
} else {
    args = commandArgs(TRUE);

    evalRoot = args[1];
    plotRoot = args[2];
}

eval = read.eval(evalRoot);

# Venn diagram
plot.begin(plotRoot, "venn");
plot.callsetConcordance(eval);
plot.end(plotRoot);

# Venn by AC
plot.begin(plotRoot, "venn_by_ac.all", width=12, height=8);
plot.callsetConcordanceByAC(eval, novelty_name="all");
plot.end(plotRoot);

plot.begin(plotRoot, "venn_by_ac.known", width=12, height=8);
plot.callsetConcordanceByAC(eval, novelty_name="known");
plot.end(plotRoot);

plot.begin(plotRoot, "venn_by_ac.novel", width=12, height=8);
plot.callsetConcordanceByAC(eval, novelty_name="novel");
plot.end(plotRoot);

# Allele count spectrum
plot.begin(plotRoot, "acs.all", width=12, height=8);
plot.alleleCountSpectrum(eval, novelty_name="all");
plot.end(plotRoot);

plot.begin(plotRoot, "acs.known", width=12, height=8);
plot.alleleCountSpectrum(eval, novelty_name="known");
plot.end(plotRoot);

plot.begin(plotRoot, "acs.novel", width=12, height=8);
plot.alleleCountSpectrum(eval, novelty_name="novel");
plot.end(plotRoot);

# Ti/Tv spectrum
plot.begin(plotRoot, "titv.all", width=12, height=8);
plot.titvSpectrum(eval, novelty_name="all");
plot.end(plotRoot);

plot.begin(plotRoot, "titv.known", width=12, height=8);
plot.titvSpectrum(eval, novelty_name="known");
plot.end(plotRoot);

plot.begin(plotRoot, "titv.novel", width=12, height=8);
plot.titvSpectrum(eval, novelty_name="novel");
plot.end(plotRoot);

# Per-sample
#plot.begin(plotRoot, "variants_per_sample", width=12, height=8);
#plot.variantsPerSample(eval);
#plot.end(plotRoot);