From 1a36cb929639a5b6f3ec8ee064c0f30df3587d59 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 Aug 2010 18:45:24 +0000
Subject: [PATCH] Can now set the maximum number of variants to see in a
 cluster plot (useful when you don't need to see a billion points to get an
 idea of what's going on.  Limit applies to known and novel variants
 separately.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3937 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/VariantRecalibratorReport/VariantRecalibratorReport.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/VariantRecalibratorReport/VariantRecalibratorReport.R b/R/VariantRecalibratorReport/VariantRecalibratorReport.R
index 187808872..78b360844 100644
--- a/R/VariantRecalibratorReport/VariantRecalibratorReport.R
+++ b/R/VariantRecalibratorReport/VariantRecalibratorReport.R
@@ -16,6 +16,9 @@ if (is.na(vcfTable)) { vcfTable = "/home/radon01/kiran/scr1/projects/DataProcess
 lociFile = args[4];
 if (is.na(lociFile)) { lociFile = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.loci"; }
 
+maxVariants = args[5];
+if (is.na(maxVariants)) { maxVariants = -1; }
+
 getAnnIndex <- function(d, ann) {
     index = -1;
     for (i in c(1:length(names(d)))) {
@@ -225,7 +228,7 @@ for (ann1 in c[[1]]$anns) {
 
     for (ann2 in c[[1]]$anns) {
         if (ann1 != ann2) {
-            plotClusters(d.known, d.novel, d.loci, c, ann1, ann2, paste(plotRoot, ".cluster.", ann1, "_vs_", ann2, ".pdf", sep=""), maxVariants=1000);
+            plotClusters(d.known, d.novel, d.loci, c, ann1, ann2, paste(plotRoot, ".cluster.", ann1, "_vs_", ann2, ".pdf", sep=""), maxVariants=maxVariants);
         }
     }
 }