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AnalyzeAnnotations now breaks out its TiTv plots into novel SNPs, dbSNP sites, and combined. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2659 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-22 19:00:23 +00:00
parent e00cb688ac
commit a11503819a
2 changed files with 134 additions and 13 deletions
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26
R/plot_Annotations_BinnedTiTv.R
View File

@ -15,7 +15,13 @@ c <- read.table(input, header=T)
# Plot TiTv ratio as a function of the annotation
#
gt = c[c$numVariants>minBinCutoff,]
gt = c[c$numVariants>minBinCutoff & c$category==0,]
novel = c[c$numVariants>minBinCutoff & c$category==1,]
dbsnp = c[c$numVariants>minBinCutoff & c$category==2,]
d = c[c$numVariants>minBinCutoff,]
cmin = min(d$titv)
cmax = max(d$titv)
outfile = paste(outputDir, "binnedTiTv.", annotationName, ".pdf", sep="")
pdf(outfile, height=7, width=7)
@ -31,6 +37,24 @@ abline(v=m75,lty=2)
abline(v=m25,lty=2)
dev.off()
outfile = paste(outputDir, "binnedTiTv_novel.", annotationName, ".pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(gt$value,gt$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20,yim=c(cmin,cmax));
m = weighted.mean(gt$value,gt$numVariants/sum(gt$numVariants))
ma = gt[gt$value > m,]
mb = gt[gt$value < m,]
m75 = weighted.mean(ma$value,ma$numVariants/sum(ma$numVariants))
m25 = weighted.mean(mb$value,mb$numVariants/sum(mb$numVariants))
abline(v=m,lty=2)
abline(v=m75,lty=2)
abline(v=m25,lty=2)
points(novel$value,novel$titv,col="green",pch=20)
points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
legend("topleft", c("overall","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
dev.off()
outfile = paste(outputDir, "binnedTiTv_quartiles.", annotationName, ".pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)

121
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
View File

@ -41,10 +41,16 @@ import java.io.FileNotFoundException;
public class AnnotationDataManager {
public final HashMap<String, TreeSet<AnnotationDatum>> data;
public final HashMap<String, TreeSet<AnnotationDatum>> dataFull;
public final HashMap<String, TreeSet<AnnotationDatum>> dataNovel;
public final HashMap<String, TreeSet<AnnotationDatum>> dataDBsnp;
public final HashMap<String, TreeSet<AnnotationDatum>> dataTruthSet;
public AnnotationDataManager() {
data = new HashMap<String, TreeSet<AnnotationDatum>>();
dataFull = new HashMap<String, TreeSet<AnnotationDatum>>();
dataNovel = new HashMap<String, TreeSet<AnnotationDatum>>();
dataDBsnp = new HashMap<String, TreeSet<AnnotationDatum>>();
dataTruthSet = new HashMap<String, TreeSet<AnnotationDatum>>();
}
public void addAnnotations( RodVCF variant ) {
@ -57,10 +63,51 @@ public class AnnotationDataManager {
}
final float value = Float.parseFloat( infoField.get( annotationKey ) );
TreeSet<AnnotationDatum> treeSet = data.get( annotationKey );
if( variant.getID().equals(".") ) { // This is a novel variant
TreeSet<AnnotationDatum> treeSet = dataNovel.get( annotationKey );
if( treeSet == null ) { // This annotation hasn't been seen before
treeSet = new TreeSet<AnnotationDatum>( new AnnotationDatum() ); // AnnotationDatum is a Comparator that orders variants by the value of the Annotation
dataNovel.put( annotationKey, treeSet );
}
AnnotationDatum datum = new AnnotationDatum( value );
if( treeSet.contains(datum) ) {
datum = treeSet.tailSet(datum).first();
} else {
treeSet.add(datum);
}
// Decide if it was a Ti or a Tv
if( BaseUtils.isTransition(variant.getReferenceForSNP(), variant.getAlternativeBaseForSNP()) ) {
datum.incrementTi();
} else {
datum.incrementTv();
}
} else { // This is a DBsnp variant
TreeSet<AnnotationDatum> treeSet = dataDBsnp.get( annotationKey );
if( treeSet == null ) { // This annotation hasn't been seen before
treeSet = new TreeSet<AnnotationDatum>( new AnnotationDatum() ); // AnnotationDatum is a Comparator that orders variants by the value of the Annotation
dataDBsnp.put( annotationKey, treeSet );
}
AnnotationDatum datum = new AnnotationDatum( value );
if( treeSet.contains(datum) ) {
datum = treeSet.tailSet(datum).first();
} else {
treeSet.add(datum);
}
// Decide if it was a Ti or a Tv
if( BaseUtils.isTransition(variant.getReferenceForSNP(), variant.getAlternativeBaseForSNP()) ) {
datum.incrementTi();
} else {
datum.incrementTv();
}
}
// the overall set, containing both novel and DBsnp variants
TreeSet<AnnotationDatum> treeSet = dataFull.get( annotationKey );
if( treeSet == null ) { // This annotation hasn't been seen before
treeSet = new TreeSet<AnnotationDatum>( new AnnotationDatum() ); // AnnotationDatum is a Comparator that orders variants by the value of the Annotation
data.put( annotationKey, treeSet );
dataFull.put( annotationKey, treeSet );
}
AnnotationDatum datum = new AnnotationDatum( value );
if( treeSet.contains(datum) ) {
@ -81,7 +128,7 @@ public class AnnotationDataManager {
public void plotCumulativeTables( final String PATH_TO_RSCRIPT, final String PATH_TO_RESOURCES, final String OUTPUT_DIR,
final int MIN_VARIANTS_PER_BIN, final int MAX_VARIANTS_PER_BIN ) {
for( String annotationKey: data.keySet() ) {
for( String annotationKey: dataFull.keySet() ) {
/*
PrintStream output;
@ -130,13 +177,13 @@ public class AnnotationDataManager {
}
// Output a header line
output.println("value\ttitv\tnumVariants\t");
output.println("value\ttitv\tnumVariants\tcategory");
// Bin SNPs and calculate truth metrics for each bin, right now this is just TiTv
int numTi = 0;
int numTv = 0;
AnnotationDatum lastDatum = null;
for( AnnotationDatum datum : data.get( annotationKey ) ) {
for( AnnotationDatum datum : dataFull.get( annotationKey ) ) {
numTi += datum.numTransitions;
numTv += datum.numTransversions;
lastDatum = datum;
@ -144,7 +191,7 @@ public class AnnotationDataManager {
float titv;
if( numTv == 0) { titv = 0.0f; }
else { titv = ((float) numTi) / ((float) numTv); }
output.println(datum.value + "\t" + titv + "\t" + (numTi+numTv));
output.println(datum.value + "\t" + titv + "\t" + (numTi+numTv) + "\t0");
numTi = 0;
numTv = 0;
}
@ -154,9 +201,59 @@ public class AnnotationDataManager {
float titv;
if( numTv == 0) { titv = 0.0f; }
else { titv = ((float) numTi) / ((float) numTv); }
output.println(lastDatum.value + "\t" + titv + "\t" + (numTi+numTv));
output.println(lastDatum.value + "\t" + titv + "\t" + (numTi+numTv)+ "\t0");
}
numTi = 0;
numTv = 0;
lastDatum = null;
for( AnnotationDatum datum : dataNovel.get( annotationKey ) ) {
numTi += datum.numTransitions;
numTv += datum.numTransversions;
lastDatum = datum;
if( numTi + numTv >= MAX_VARIANTS_PER_BIN/3 ) { // This annotation bin is full
float titv;
if( numTv == 0) { titv = 0.0f; }
else { titv = ((float) numTi) / ((float) numTv); }
output.println(datum.value + "\t" + titv + "\t" + (numTi+numTv) + "\t1");
numTi = 0;
numTv = 0;
}
// else, continue accumulating variants because this bin isn't full yet
}
if( numTi != 0 || numTv != 0 ) { // one final bin that may not have been dumped out
float titv;
if( numTv == 0) { titv = 0.0f; }
else { titv = ((float) numTi) / ((float) numTv); }
output.println(lastDatum.value + "\t" + titv + "\t" + (numTi+numTv)+ "\t1");
}
numTi = 0;
numTv = 0;
lastDatum = null;
for( AnnotationDatum datum : dataDBsnp.get( annotationKey ) ) {
numTi += datum.numTransitions;
numTv += datum.numTransversions;
lastDatum = datum;
if( numTi + numTv >= MAX_VARIANTS_PER_BIN ) { // This annotation bin is full
float titv;
if( numTv == 0) { titv = 0.0f; }
else { titv = ((float) numTi) / ((float) numTv); }
output.println(datum.value + "\t" + titv + "\t" + (numTi+numTv) + "\t2");
numTi = 0;
numTv = 0;
}
// else, continue accumulating variants because this bin isn't full yet
}
if( numTi != 0 || numTv != 0 ) { // one final bin that may not have been dumped out
float titv;
if( numTv == 0) { titv = 0.0f; }
else { titv = ((float) numTi) / ((float) numTv); }
output.println(lastDatum.value + "\t" + titv + "\t" + (numTi+numTv)+ "\t2");
}
/*
System.out.println(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_CumulativeTiTv.R" + " " +
OUTPUT_DIR + annotationKey + ".cumulative.dat" + " " + OUTPUT_DIR + " " + annotationKey);
@ -169,9 +266,9 @@ public class AnnotationDataManager {
}
*/
//System.out.println(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTiTv.R" + " " +
// OUTPUT_DIR + annotationKey + ".binned.dat" + " " + OUTPUT_DIR + " " + annotationKey +
// " " + MIN_VARIANTS_PER_BIN);
System.out.println(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTiTv.R" + " " +
OUTPUT_DIR + annotationKey + ".binned.dat" + " " + OUTPUT_DIR + " " + annotationKey +
" " + MIN_VARIANTS_PER_BIN);
// Execute the RScript command to plot the table of TiTv values
try {