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AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2654 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-21 21:15:11 +00:00
parent 4fc926232c
commit d9df72e1b5
4 changed files with 125 additions and 12 deletions
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47
R/plot_Annotations_BinnedTiTv.R 100644
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@ -0,0 +1,47 @@
#!/broad/tools/apps/R-2.6.0/bin/Rscript
args <- commandArgs(TRUE)
verbose = TRUE
input = args[1]
outputDir = args[2]
annotationName = args[3]
minBinCutoff = as.numeric(args[4])
c <- read.table(input, header=T)
#
# Plot TiTv ratio as a function of the annotation
#
gt = c[c$numVariants>minBinCutoff,]
outfile = paste(outputDir, "binnedTiTv.", annotationName, ".pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(gt$value,gt$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20);
m = weighted.mean(gt$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)
dev.off()
outfile = paste(outputDir, "binnedTiTv_quartiles.", 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,xlim=c(0,80))
abline(v=m,lty=2)
abline(v=m75,lty=2)
abline(v=m25,lty=2)
dev.off()
outfile = paste(outputDir, "binnedTiTv_hist.", annotationName, ".pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(gt$value,gt$numVariants,xlab=annotationName,ylab="num Variants in bin",type="h");
dev.off()

9
R/plot_Annotations_CumulativeTiTv.R
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@ -4,25 +4,26 @@ args <- commandArgs(TRUE)
verbose = TRUE
input = args[1]
annotationName = args[2]
outputDir = args[2]
annotationName = args[3]
c <- read.table(input, header=T)
#
# Plot residual error as a function of the covariate
# Plot cumulative Ti/Tv ratio as a function of the annotation
#
gt = c[c$GT==1 & c$numVariants>1000,]
lt = c[c$GT==0 & c$numVariants>1000,]
outfile = paste(input, ".cumulativeTiTv_", annotationName, "_GTfilter.pdf", sep="")
outfile = paste(outputDir, "cumulativeTiTv.", annotationName, ".GTfilter.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(gt$value,gt$cumulativeTiTv,xlab=annotationName,ylab="Ti/Tv ratio",main=paste("Filter out SNPs with",annotationName,"> x",sep=" "),pch=20);
dev.off()
outfile = paste(input, ".cumulativeTiTv_", annotationName, "_LTfilter.pdf", sep="")
outfile = paste(outputDir, "cumulativeTiTv.", annotationName, ".GTfilter.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(lt$value,lt$cumulativeTiTv,xlab=annotationName,ylab="Ti/Tv ratio",main=paste("Filter out SNPs with",annotationName,"< x",sep=" "),pch=20);

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
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@ -52,6 +52,11 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
private String PATH_TO_RSCRIPT = "/broad/tools/apps/R-2.6.0/bin/Rscript";
@Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
private String PATH_TO_RESOURCES = "R/";
@Argument(fullName = "min_variants_per_bin", shortName = "minBinSize", doc = "The minimum number of variants in a bin in order to calculate truth metrics.", required = false)
private int MIN_VARIANTS_PER_BIN = 1000;
@Argument(fullName = "max_variants_per_bin", shortName = "maxBinSize", doc = "The maximum number of variants in a bin.", required = false)
private int MAX_VARIANTS_PER_BIN = 20000;
/////////////////////////////
// Private Member Variables
@ -116,6 +121,6 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
public void onTraversalDone( Integer sum ) {
// For each annotation, decide how to cut up the data, output intermediate cumulative p(true) tables, and call RScript to plot the tables
dataManager.plotCumulativeTables(PATH_TO_RSCRIPT, PATH_TO_RESOURCES, OUTPUT_DIR);
dataManager.plotCumulativeTables(PATH_TO_RSCRIPT, PATH_TO_RESOURCES, OUTPUT_DIR, MIN_VARIANTS_PER_BIN, MAX_VARIANTS_PER_BIN);
}
}

74
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
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@ -52,11 +52,14 @@ public class AnnotationDataManager {
// Loop over each annotation in the vcf record
final Map<String,String> infoField = variant.getInfoValues();
for( String annotationKey : infoField.keySet() ) {
if( annotationKey.equalsIgnoreCase("AC") ) {
continue; // This annotation isn't a float value
}
final float value = Float.parseFloat( infoField.get( annotationKey ) );
TreeSet<AnnotationDatum> treeSet = data.get( annotationKey );
if( treeSet == null ) { // This annotation hasn't been seen before
treeSet = new TreeSet<AnnotationDatum>( new AnnotationDatum() );
treeSet = new TreeSet<AnnotationDatum>( new AnnotationDatum() ); // AnnotationDatum is a Comparator that orders variants by the value of the Annotation
data.put( annotationKey, treeSet );
}
AnnotationDatum datum = new AnnotationDatum( value );
@ -66,6 +69,7 @@ public class AnnotationDataManager {
treeSet.add(datum);
}
// Decide if it was a Ti or a Tv
if( BaseUtils.isTransition(variant.getReferenceForSNP(), variant.getAlternativeBaseForSNP()) ) {
datum.incrementTi();
} else {
@ -74,21 +78,25 @@ public class AnnotationDataManager {
}
}
public void plotCumulativeTables(final String PATH_TO_RSCRIPT, final String PATH_TO_RESOURCES, final String OUTPUT_DIR) {
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() ) {
/*
PrintStream output;
try {
output = new PrintStream(OUTPUT_DIR + annotationKey + ".dat");
output = new PrintStream(OUTPUT_DIR + annotationKey + ".cumulative.dat");
} catch (FileNotFoundException e) {
throw new StingException("Can't create intermediate output annotation data file.");
}
// Output a header line
output.println("value\tcumulativeTiTv\tnumVariants\tGT");
// Filter SNPs greater than this annotation value
int numTi = 0;
int numTv = 0;
for( AnnotationDatum datum : data.get( annotationKey )) {
for( AnnotationDatum datum : data.get( annotationKey ) ) {
numTi += datum.numTransitions;
numTv += datum.numTransversions;
float titv;
@ -98,6 +106,7 @@ public class AnnotationDataManager {
}
// Filter SNPs less than this annotation value
numTi = 0;
numTv = 0;
Iterator<AnnotationDatum> iter = data.get( annotationKey ).descendingIterator();
@ -111,15 +120,66 @@ public class AnnotationDataManager {
output.println(datum.value + "\t" + titv + "\t" + (numTi+numTv) +"\t0");
}
*/
PrintStream output;
try {
output = new PrintStream(OUTPUT_DIR + annotationKey + ".binned.dat");
} catch (FileNotFoundException e) {
throw new StingException("Can't create intermediate output annotation data file.");
}
// Output a header line
output.println("value\ttitv\tnumVariants\t");
// 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 ) ) {
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));
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));
}
/*
System.out.println(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_CumulativeTiTv.R" + " " +
OUTPUT_DIR + annotationKey + ".dat" + " " + annotationKey);
OUTPUT_DIR + annotationKey + ".cumulative.dat" + " " + OUTPUT_DIR + " " + annotationKey);
try {
Process p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_CumulativeTiTv.R" + " " +
OUTPUT_DIR + annotationKey + ".dat" + " " + annotationKey);
OUTPUT_DIR + annotationKey + ".cumulative.dat"+ " " + OUTPUT_DIR + " " + annotationKey);
} catch (Exception e) {
throw new StingException("Unable to run RScript command");
throw new StingException("Unable to execute RScript command");
}
*/
//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 {
final Process p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTiTv.R" + " " +
OUTPUT_DIR + annotationKey + ".binned.dat" + " " + OUTPUT_DIR + " " + annotationKey +
" " + MIN_VARIANTS_PER_BIN);
} catch (Exception e) {
throw new StingException("Unable to execute RScript command");
}
}
}