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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
This commit is contained in:
kiran 2010-08-04 18:45:24 +00:00
parent bd27287fe7
commit 1a36cb9296
1 changed files with 4 additions and 1 deletions
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5
R/VariantRecalibratorReport/VariantRecalibratorReport.R
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@ -16,6 +16,9 @@ if (is.na(vcfTable)) { vcfTable = "/home/radon01/kiran/scr1/projects/DataProcess
lociFile = args[4]; lociFile = args[4];
if (is.na(lociFile)) { lociFile = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.loci"; } 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) { getAnnIndex <- function(d, ann) {
index = -1; index = -1;
for (i in c(1:length(names(d)))) { for (i in c(1:length(names(d)))) {
@ -225,7 +228,7 @@ for (ann1 in c[[1]]$anns) {
for (ann2 in c[[1]]$anns) { for (ann2 in c[[1]]$anns) {
if (ann1 != ann2) { 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);
} }
} }
} }