Added -name argument to AnalyzeAnnotations that allows one to specify the name of the annotation to be used on the plots. Instead of seeing AB and DP, one can add -name AB,AlleleBalance -name DP,Depth
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2742 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin
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62a80f2b6f
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@ -24,7 +24,7 @@ xmax = max(d$value)
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# Plot TiTv ratio as a function of the annotation
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#
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outfile = paste(input, ".TiTv.", annotationName, ".pdf", sep="")
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outfile = paste(input, ".TiTv.pdf", sep="")
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pdf(outfile, height=7, width=7)
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par(cex=1.1)
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plot(all$value,all$titv,xlab=annotationName,ylab="Ti/Tv Ratio",pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
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@ -51,7 +51,7 @@ dev.off()
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# Plot TiTv ratio as a function of the annotation, log scale on the x-axis
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#
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outfile = paste(input, ".TiTv_log.", annotationName, ".pdf", sep="")
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outfile = paste(input, ".TiTv_log.pdf", sep="")
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pdf(outfile, height=7, width=7)
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par(cex=1.1)
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plot(all$value,all$titv,xlab=annotationName,log="x",ylab="Ti/Tv Ratio",pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
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@ -75,7 +75,7 @@ dev.off()
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ymin = min(all$dbsnp)
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ymax = max(all$dbsnp)
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outfile = paste(input, ".truthRate.", annotationName, ".pdf", sep="")
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outfile = paste(input, ".truthRate.pdf", sep="")
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pdf(outfile, height=7, width=7)
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par(cex=1.1)
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yLabel = "DBsnp Rate"
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@ -101,7 +101,7 @@ dev.off()
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# Plot dbsnp and true positive rate as a function of the annotation, log scale on the x-axis
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#
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outfile = paste(input, ".truthRate_log.", annotationName, ".pdf", sep="")
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outfile = paste(input, ".truthRate_log.pdf", sep="")
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pdf(outfile, height=7, width=7)
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par(cex=1.1)
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yLabel = "DBsnp Rate"
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@ -123,7 +123,7 @@ dev.off()
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# Plot histogram of the annotation's value
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#
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outfile = paste(input, "annotationHistogram.", annotationName, ".pdf", sep="")
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outfile = paste(input, ".Histogram.pdf", sep="")
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pdf(outfile, height=7, width=7)
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par(cex=1.1)
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plot(all$value,all$numVariants,xlab=annotationName,ylab="Num variants in bin",type="h",xaxt="n",ps=14);
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@ -32,7 +32,7 @@ import net.sf.samtools.SAMRecord;
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* User: rpoplin
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* Date: Jan 29, 2010
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*
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* The number of previous N bases (along the direction of the read) that contain G's and C's.
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* The number of previous N bases (along the direction of the read) that contain G's and C's. The goal is to correct for dye slippage.
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* Only valid for Illumina reads. Otherwise return -1.
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*/
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@ -11,6 +11,8 @@ import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
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import java.util.HashMap;
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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@ -61,12 +63,14 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
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private int MAX_VARIANTS_PER_BIN = 20000;
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@Argument(fullName = "sampleName", shortName = "sampleName", doc = "If supplied, only process variants found in this sample.", required = false)
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private String SAMPLE_NAME = null;
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@Argument(fullName = "name", shortName = "name", doc = "Labels for the annotations to make plots look nicer. Each name is a separate -name argument. For example, -name DP,Depth -name AB,AlleleBalance", required = false)
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private String[] ANNOTATION_NAMES = null;
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/////////////////////////////
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// Private Member Variables
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/////////////////////////////
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private final AnnotationDataManager dataManager = new AnnotationDataManager();
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private AnnotationDataManager dataManager;
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//---------------------------------------------------------------------------------------------------------------
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//
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@ -76,6 +80,17 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
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public void initialize() {
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// Create a HashMap associating the names of the annotations to full Strings that can be used as labels on plots
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HashMap<String,String> nameMap = null;
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if( ANNOTATION_NAMES != null ) {
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nameMap = new HashMap<String,String>();
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for( String nameLine : ANNOTATION_NAMES ) {
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String[] vals = nameLine.split(",");
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nameMap.put(vals[0],vals[1]);
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}
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}
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dataManager = new AnnotationDataManager( nameMap );
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if( !PATH_TO_RESOURCES.endsWith("/") ) { PATH_TO_RESOURCES = PATH_TO_RESOURCES + "/"; }
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}
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@ -89,13 +104,14 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
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if( tracker != null ) {
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// First find out if this variant is in the truth set
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// First find out if this variant is in the truth sets
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boolean isInTruthSet = false;
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boolean isTrueVariant = false;
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for( ReferenceOrderedDatum rod : tracker.getAllRods() ) {
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if( rod != null && rod.getName().toUpperCase().startsWith("TRUTH") ) {
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isInTruthSet = true;
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// Next see if the truth sets say this site is variant or reference
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if( rod instanceof RodVCF ) {
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if( ((RodVCF) rod).isSNP() ) {
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isTrueVariant = true;
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@ -43,9 +43,11 @@ import java.io.FileNotFoundException;
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public class AnnotationDataManager {
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public final HashMap<String, TreeSet<AnnotationDatum>> data;
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public final HashMap<String,String> nameMap;
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public AnnotationDataManager() {
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public AnnotationDataManager( HashMap<String,String> _nameMap ) {
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data = new HashMap<String, TreeSet<AnnotationDatum>>();
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nameMap = _nameMap;
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}
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public void addAnnotations( final RodVCF variant, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
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@ -136,10 +138,15 @@ public class AnnotationDataManager {
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// Close the PrintStream
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output.close();
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String annotationName = nameMap.get(annotationKey);
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if( annotationName == null ) { // name is not in the map so use the key
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annotationName = annotationKey;
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}
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// Print out the command line to make it clear to the user what is being executed and how one might modify it
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final String rScriptCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTruthMetrics.R" + " " +
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OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationKey + " " + MIN_VARIANTS_PER_BIN;
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OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationName + " " + MIN_VARIANTS_PER_BIN;
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System.out.println( rScriptCommandLine );
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// Execute the RScript command to plot the table of TiTv values
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