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Fix to handle situation where there are no filtered variants. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4424 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-10-04 18:34:01 +00:00
parent aa00801108
commit 24cf6f9e36
1 changed files with 33 additions and 8 deletions
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41
R/VariantReport/VariantReport.R
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@ -137,12 +137,20 @@ plot.callsetConcordanceByAC <- function(eval, normalize=TRUE, novelty_name="all"
if (length(intersection$AC) > 0 && length(aonly$AC) == 0) {
aonly = intersection;
aonly$n = 0;
aonly.filtered$n = 0;
}
if (length(intersection$AC) > 0 && length(bonly$AC) == 0) {
bonly = intersection;
bonly$n = 0;
}
if (length(intersection$AC) > 0 && length(aonly.filtered$AC) == 0) {
aonly.filtered = intersection;
aonly.filtered$n = 0;
}
if (length(intersection$AC) > 0 && length(bonly.filtered$AC) == 0) {
bonly.filtered = intersection;
bonly.filtered$n = 0;
}
@ -191,24 +199,33 @@ plot.alleleCountSpectrum <- function(eval, novelty_name="all", col=c("#FF6342",
if (length(intersection$AC) > 0 && length(aonly$AC) == 0) {
aonly = intersection;
aonly$n = 0;
aonly.filtered$n = 0;
}
if (length(intersection$AC) > 0 && length(bonly$AC) == 0) {
bonly = intersection;
bonly$n = 0;
}
if (length(intersection$AC) > 0 && length(aonly.filtered$AC) == 0) {
aonly.filtered = intersection;
aonly.filtered$n = 0;
}
if (length(intersection$AC) > 0 && length(bonly.filtered$AC) == 0) {
bonly.filtered = intersection;
bonly.filtered$n = 0;
}
suppressWarnings(plot(0, 0, type="n", xlim=c(1, length(intersection$AC)), ylim=c(1, max(aonly$n + aonly.filtered$n + intersection$n, bonly$n + bonly.filtered$n + intersection$n)), xlab="Allele count", ylab="Number of variants", main=title, log="xy", bty="n", cex=1.3, cex.lab=1.3, cex.axis=1.3));
loci = (unique(eval$CountVariants$nProcessedLoci))[1];
ymax = 10*max((1/1000)*loci*(1/c(1:max(intersection$AC))));
suppressWarnings(plot(0, 0, type="n", xlim=c(1, length(intersection$AC)), ylim=c(1, ymax), xlab="Allele count", ylab="Number of variants", main=title, log="xy", bty="n", cex=1.3, cex.lab=1.3, cex.axis=1.3));
suppressWarnings(points(intersection$AC, aonly$n + aonly.filtered$n + intersection$n, type="l", lwd=2, col=col[1]));
suppressWarnings(points(intersection$AC, aonly$n + intersection$n, type="l", lwd=2, lty=2, col=col[1]));
suppressWarnings(points(intersection$AC, intersection$n, type="l", lwd=2, col=col[3]));
suppressWarnings(points(intersection$AC, bonly$n + intersection$n, type="l", lwd=2, lty=2, col=col[4]));
suppressWarnings(points(intersection$AC, bonly$n + bonly.filtered$n + intersection$n, type="l", lwd=2, col=col[5]));
loci = (unique(eval$CountVariants$nProcessedLoci))[1];
points(c(1:max(intersection$AC)), 0.9*(1/1000)*loci*(1/c(1:max(intersection$AC))), type="l", lwd=2, lty=2, col="black");
legend(
@ -246,9 +263,6 @@ plot.titvSpectrum <- function(eval, novelty_name="all", col=c("#FF6342", "#FF967
aonly$n = 0;
aonly$nTi = 0;
aonly$nTv = 0;
aonly.filtered$n = 0;
aonly.filtered$nTi = 0;
aonly.filtered$nTv = 0;
}
if (length(intersection$AC) > 0 && length(bonly$AC) == 0) {
@ -256,6 +270,17 @@ plot.titvSpectrum <- function(eval, novelty_name="all", col=c("#FF6342", "#FF967
bonly$n = 0;
bonly$nTi = 0;
bonly$nTv = 0;
}
if (length(intersection$AC) > 0 && length(aonly.filtered$AC) == 0) {
aonly.filtered = intersection;
aonly.filtered$n = 0;
aonly.filtered$nTi = 0;
aonly.filtered$nTv = 0;
}
if (length(intersection$AC) > 0 && length(bonly.filtered$AC) == 0) {
bonly.filtered = intersection;
bonly.filtered$n = 0;
bonly.filtered$nTi = 0;
bonly.filtered$nTv = 0;