Examples with PurpleCopyNumber com.hartwig.hmftools.common.purple.copynumber.PurpleCopyNumber used on opensource projects

Example 11 with PurpleCopyNumber

use of com.hartwig.hmftools.common.purple.copynumber.PurpleCopyNumber in project hmftools by hartwigmedical.

the class PatientReporter method analyseGenomeData.

@NotNull
private GenomeAnalysis analyseGenomeData(@NotNull final String sample, @NotNull final String runDirectory) throws IOException {
    LOGGER.info(" Loading somatic snv and indels...");
    final List<SomaticVariant> variants = PatientReporterHelper.loadPassedSomaticVariants(sample, runDirectory);
    LOGGER.info("  " + variants.size() + " somatic passed snps, mnps and indels loaded for sample " + sample);
    LOGGER.info(" Analyzing somatic snp/mnp and indels....");
    final VariantAnalysis variantAnalysis = variantAnalyzer().run(variants);
    LOGGER.info(" Loading purity numbers...");
    final PurityContext context = PatientReporterHelper.loadPurity(runDirectory, sample);
    if (context.status().equals(FittedPurityStatus.NO_TUMOR)) {
        LOGGER.warn("PURPLE DID NOT DETECT A TUMOR. Proceed with utmost caution!");
    }
    final FittedPurity purity = context.bestFit();
    final FittedPurityScore purityScore = context.score();
    final List<PurpleCopyNumber> purpleCopyNumbers = PatientReporterHelper.loadPurpleCopyNumbers(runDirectory, sample);
    final List<GeneCopyNumber> panelGeneCopyNumbers = PatientReporterHelper.loadPurpleGeneCopyNumbers(runDirectory, sample).stream().filter(x -> reporterData().panelGeneModel().panel().contains(x.gene())).collect(Collectors.toList());
    LOGGER.info("  " + purpleCopyNumbers.size() + " purple copy number regions loaded for sample " + sample);
    LOGGER.info(" Analyzing purple somatic copy numbers...");
    final PurpleAnalysis purpleAnalysis = ImmutablePurpleAnalysis.builder().gender(context.gender()).status(context.status()).fittedPurity(purity).fittedScorePurity(purityScore).copyNumbers(purpleCopyNumbers).panelGeneCopyNumbers(panelGeneCopyNumbers).build();
    final Path structuralVariantVCF = PatientReporterHelper.findStructuralVariantVCF(runDirectory);
    LOGGER.info(" Loading structural variants...");
    final List<StructuralVariant> structuralVariants = StructuralVariantFileLoader.fromFile(structuralVariantVCF.toString(), true);
    LOGGER.info(" Enriching structural variants with purple data.");
    final List<EnrichedStructuralVariant> enrichedStructuralVariants = purpleAnalysis.enrichStructuralVariants(structuralVariants);
    LOGGER.info(" Analysing structural variants...");
    final StructuralVariantAnalysis structuralVariantAnalysis = structuralVariantAnalyzer().run(enrichedStructuralVariants, false);
    return ImmutableGenomeAnalysis.of(sample, variantAnalysis, purpleAnalysis, structuralVariantAnalysis);
}

Example 12 with PurpleCopyNumber

use of com.hartwig.hmftools.common.purple.copynumber.PurpleCopyNumber in project hmftools by hartwigmedical.

the class PurpleAnalysis method enrichSomaticVariants.

@NotNull
public List<VariantReport> enrichSomaticVariants(@NotNull final List<VariantReport> variants) {
    final List<VariantReport> result = Lists.newArrayList();
    final PurityAdjuster purityAdjuster = new PurityAdjuster(gender(), fittedPurity());
    final GenomeRegionSelector<PurpleCopyNumber> copyNumberSelector = GenomeRegionSelectorFactory.create(copyNumbers());
    for (final VariantReport variantReport : variants) {
        final Optional<PurpleCopyNumber> optionalCopyNumber = copyNumberSelector.select(variantReport.variant());
        if (optionalCopyNumber.isPresent()) {
            final PurpleCopyNumber copyNumber = optionalCopyNumber.get();
            double adjustedVAF = Math.min(1, purityAdjuster.purityAdjustedVAF(copyNumber.chromosome(), copyNumber.averageTumorCopyNumber(), variantReport.alleleFrequency()));
            result.add(ImmutableVariantReport.builder().from(variantReport).baf(copyNumber.descriptiveBAF()).impliedVAF(adjustedVAF).build());
        } else {
            result.add(variantReport);
        }
    }
    return result;
}

Example 13 with PurpleCopyNumber

use of com.hartwig.hmftools.common.purple.copynumber.PurpleCopyNumber in project hmftools by hartwigmedical.

the class LoadStructuralVariants method enrichStructuralVariants.

@NotNull
private static List<EnrichedStructuralVariant> enrichStructuralVariants(@NotNull List<StructuralVariant> variants, @NotNull DatabaseAccess dbAccess, @NotNull String tumorSample) {
    final PurityContext purityContext = dbAccess.readPurityContext(tumorSample);
    if (purityContext == null) {
        LOGGER.warn("Unable to retrieve purple data. Enrichment may be incomplete.");
    }
    final PurityAdjuster purityAdjuster = purityContext == null ? new PurityAdjuster(Gender.FEMALE, 1, 1) : new PurityAdjuster(purityContext.gender(), purityContext.bestFit().purity(), purityContext.bestFit().normFactor());
    final List<PurpleCopyNumber> copyNumberList = dbAccess.readCopynumbers(tumorSample);
    final Multimap<String, PurpleCopyNumber> copyNumbers = Multimaps.index(copyNumberList, PurpleCopyNumber::chromosome);
    return EnrichedStructuralVariantFactory.enrich(variants, purityAdjuster, copyNumbers);
}

Example 14 with PurpleCopyNumber

use of com.hartwig.hmftools.common.purple.copynumber.PurpleCopyNumber in project hmftools by hartwigmedical.

the class CopyNumberCharts method copyNumberPDF.

@NotNull
static JFreeChart copyNumberPDF(@NotNull final List<PurpleCopyNumber> copyNumbers) {
    final XYDataset dataset = ploidyPDF(copyNumbers, PurpleCopyNumber::averageTumorCopyNumber, PurpleCopyNumber::bafCount);
    JFreeChart chart = ChartFactory.createScatterPlot("Copy Number PDF", "Ploidy", "BAF Count", dataset, PlotOrientation.VERTICAL, false, false, false);
    XYBarRenderer renderer = new XYBarRenderer(0.9);
    renderer.setShadowVisible(false);
    renderer.setBarPainter(new StandardXYBarPainter());
    renderer.setSeriesPaint(0, Color.BLUE);
    XYPlot xyPlot = (XYPlot) chart.getPlot();
    xyPlot.getDomainAxis().setRange(0, 10);
    xyPlot.setRenderer(renderer);
    return chart;
}

Example 15 with PurpleCopyNumber

use of com.hartwig.hmftools.common.purple.copynumber.PurpleCopyNumber in project hmftools by hartwigmedical.

the class CopyNumberCharts method createDataset.

@NotNull
private static XYDataset createDataset(@NotNull final List<PurpleCopyNumber> copyNumbers) {
    final List<PurpleCopyNumber> sortedCopyNumbers = Lists.newArrayList(copyNumbers);
    sortedCopyNumbers.sort(Comparator.comparingDouble(PurpleCopyNumber::averageTumorCopyNumber));
    int totalCount = copyNumbers.stream().mapToInt(PurpleCopyNumber::bafCount).sum();
    XYSeries series = new XYSeries("CDF");
    int cumulativeBAFCount = 0;
    for (PurpleCopyNumber sortedCopyNumber : sortedCopyNumbers) {
        cumulativeBAFCount += sortedCopyNumber.bafCount();
        series.add((double) cumulativeBAFCount / totalCount * 100, sortedCopyNumber.averageTumorCopyNumber());
    }
    return new XYSeriesCollection(series);
}