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Transpose rows/cols in AF table to make it molten (so I can plot easily in R)

This commit is contained in:
Eric Banks 2012-02-06 16:23:32 -05:00
parent fbbd04621d
commit 91897f5fe7
1 changed files with 21 additions and 14 deletions
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35
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
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@ -91,25 +91,31 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
//@DataPoint(description = "Multi-allelic Indel Novelty Rate") //@DataPoint(description = "Multi-allelic Indel Novelty Rate")
public String indelNoveltyRate = "NA"; public String indelNoveltyRate = "NA";
@DataPoint(description="Histogram of allele frequencies for most common alternate allele") @DataPoint(description="Histogram of allele frequencies for most common SNP alternate allele")
AFHistogram AFhistogramMax = new AFHistogram(); AFHistogram AFhistogramMaxSnp = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common alternate alleles") @DataPoint(description="Histogram of allele frequencies for less common SNP alternate alleles")
AFHistogram AFhistogramMin = new AFHistogram(); AFHistogram AFhistogramMinSnp = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for most common Indel alternate allele")
AFHistogram AFhistogramMaxIndel = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common Indel alternate alleles")
AFHistogram AFhistogramMinIndel = new AFHistogram();
/* /*
* AF histogram table object * AF histogram table object
*/ */
static class AFHistogram implements TableType { static class AFHistogram implements TableType {
private Object[] colKeys, rowKeys = {"pairwise_AF"}; private Object[] rowKeys, colKeys = {"count"};
private int[] AFhistogram; private int[] AFhistogram;
private static final double AFincrement = 0.01; private static final double AFincrement = 0.01;
private static final int numBins = (int)(1.00 / AFincrement); private static final int numBins = (int)(1.00 / AFincrement);
public AFHistogram() { public AFHistogram() {
colKeys = initColKeys(); rowKeys = initRowKeys();
AFhistogram = new int[colKeys.length]; AFhistogram = new int[rowKeys.length];
} }
public Object[] getColumnKeys() { public Object[] getColumnKeys() {
@ -121,10 +127,10 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
} }
public Object getCell(int row, int col) { public Object getCell(int row, int col) {
return AFhistogram[col]; return AFhistogram[row];
} }
private static Object[] initColKeys() { private static Object[] initRowKeys() {
ArrayList<String> keyList = new ArrayList<String>(numBins + 1); ArrayList<String> keyList = new ArrayList<String>(numBins + 1);
for ( double a = 0.00; a <= 1.01; a += AFincrement ) { for ( double a = 0.00; a <= 1.01; a += AFincrement ) {
keyList.add(String.format("%.2f", a)); keyList.add(String.format("%.2f", a));
@ -164,6 +170,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
nMultiSNPs++; nMultiSNPs++;
calculatePairwiseTiTv(eval); calculatePairwiseTiTv(eval);
calculateSNPPairwiseNovelty(eval, comp); calculateSNPPairwiseNovelty(eval, comp);
updateAFhistogram(eval, AFhistogramMaxSnp, AFhistogramMinSnp);
} }
break; break;
case INDEL: case INDEL:
@ -171,13 +178,13 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
if ( !eval.isBiallelic() ) { if ( !eval.isBiallelic() ) {
nMultiIndels++; nMultiIndels++;
calculateIndelPairwiseNovelty(eval, comp); calculateIndelPairwiseNovelty(eval, comp);
updateAFhistogram(eval, AFhistogramMaxIndel, AFhistogramMinIndel);
} }
break; break;
default: default:
throw new UserException.BadInput("Unexpected variant context type: " + eval); throw new UserException.BadInput("Unexpected variant context type: " + eval);
} }
updateAFhistogram(eval);
return null; // we don't capture any interesting sites return null; // we don't capture any interesting sites
} }
@ -209,7 +216,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) { private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) {
} }
private void updateAFhistogram(VariantContext vc) { private void updateAFhistogram(VariantContext vc, AFHistogram max, AFHistogram min) {
final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null); final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
if ( obj == null || !(obj instanceof List) ) if ( obj == null || !(obj instanceof List) )
@ -222,9 +229,9 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
} }
Collections.sort(AFs); Collections.sort(AFs);
AFhistogramMax.update(AFs.get(AFs.size()-1)); max.update(AFs.get(AFs.size()-1));
for ( int i = 0; i < AFs.size() - 1; i++ ) for ( int i = 0; i < AFs.size() - 1; i++ )
AFhistogramMin.update(AFs.get(i)); min.update(AFs.get(i));
} }
private final String noveltyRate(final int all, final int known) { private final String noveltyRate(final int all, final int known) {