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Handle interactive and non-interactive modes more elegantly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4009 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-08-11 02:38:53 +00:00
parent a7409df1a6
commit 6037443e55
1 changed files with 12 additions and 10 deletions
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22
R/VariantReport/VariantReport.R
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@ -1,13 +1,15 @@
source(paste(Sys.getenv("STING_DIR"), "/R/gsacommons.R", sep=""));
args = commandArgs(TRUE);
if (interactive()) {
if (!exists("plotRoot")) {
plotRoot = "test.plot";
}
} else {
args = commandArgs(TRUE);
evalRoot = args[1];
#if (is.na(evalRoot)) { evalRoot = "/home/radon01/kiran/scr1/projects/ESPGabrielDownsampling/results/v1/merged.vcf.eval120/eval"; }
if (is.na(evalRoot)) { evalRoot = "/home/radon01/kiran/scr1/projects/ESPGabrielDownsampling/results/v1/merged.vcf.eval.v2/eval"; }
plotRoot = args[2];
if (is.na(plotRoot)) { plotRoot = "plot"; }
evalRoot = args[1];
plotRoot = args[2];
}
eval = read.eval(evalRoot);
@ -56,6 +58,6 @@ 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);
#plot.begin(plotRoot, "variants_per_sample", width=12, height=8);
#plot.variantsPerSample(eval);
#plot.end(plotRoot);