40 lines
955 B
R
40 lines
955 B
R
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);
|
|
|
|
plot.begin(plotRoot, "variantReport");
|
|
|
|
# Venn diagram
|
|
plot.callsetConcordance(eval);
|
|
|
|
# Venn by AC
|
|
plot.callsetConcordanceByAC(eval, novelty_name="all");
|
|
plot.callsetConcordanceByAC(eval, novelty_name="known");
|
|
plot.callsetConcordanceByAC(eval, novelty_name="novel");
|
|
|
|
# Allele count spectrum
|
|
plot.alleleCountSpectrum(eval, novelty_name="all");
|
|
plot.alleleCountSpectrum(eval, novelty_name="known");
|
|
plot.alleleCountSpectrum(eval, novelty_name="novel");
|
|
|
|
# Ti/Tv spectrum
|
|
plot.titvSpectrum(eval, novelty_name="all");
|
|
plot.titvSpectrum(eval, novelty_name="known");
|
|
plot.titvSpectrum(eval, novelty_name="novel");
|
|
|
|
# Per-sample
|
|
#plot.variantsPerSample(eval);
|
|
|
|
plot.end(plotRoot);
|