Examples with ProbeLoading ubic.gemma.model.analysis.expression.pca.ProbeLoading used on opensource projects

Example 1 with ProbeLoading

use of ubic.gemma.model.analysis.expression.pca.ProbeLoading in project Gemma by PavlidisLab.

the class SVDServiceHelperImpl method getTopLoadedVectors.

@Override
public Map<ProbeLoading, DoubleVectorValueObject> getTopLoadedVectors(ExpressionExperiment ee, int component, int count) {
    PrincipalComponentAnalysis pca = principalComponentAnalysisService.loadForExperiment(ee);
    Map<ProbeLoading, DoubleVectorValueObject> result = new HashMap<>();
    if (pca == null) {
        return result;
    }
    List<ProbeLoading> topLoadedProbes = principalComponentAnalysisService.getTopLoadedProbes(ee, component, count);
    if (topLoadedProbes == null) {
        SVDServiceHelperImpl.log.warn("No probes?");
        return result;
    }
    Map<Long, ProbeLoading> probes = new LinkedHashMap<>();
    Set<CompositeSequence> p = new HashSet<>();
    for (ProbeLoading probeLoading : topLoadedProbes) {
        CompositeSequence probe = probeLoading.getProbe();
        probes.put(probe.getId(), probeLoading);
        p.add(probe);
    }
    if (probes.isEmpty())
        return result;
    assert probes.size() <= count;
    Collection<ExpressionExperiment> ees = new HashSet<>();
    ees.add(ee);
    Collection<DoubleVectorValueObject> dvVos = processedExpressionDataVectorService.getProcessedDataArraysByProbe(ees, p);
    if (dvVos.isEmpty()) {
        SVDServiceHelperImpl.log.warn("No vectors came back from the call; check the Gene2CS table?");
        return result;
    }
    // note that this might have come from a cache.
    /*
         * This is actually expected, because we go through the genes.
         */
    BioAssayDimension bioAssayDimension = pca.getBioAssayDimension();
    assert bioAssayDimension != null;
    assert !bioAssayDimension.getBioAssays().isEmpty();
    for (DoubleVectorValueObject vct : dvVos) {
        ProbeLoading probeLoading = probes.get(vct.getDesignElement().getId());
        if (probeLoading == null) {
            /*
                 * This is okay, we will skip this probe. It was another probe for a gene that _was_ highly loaded.
                 */
            continue;
        }
        assert bioAssayDimension.getBioAssays().size() == vct.getData().length;
        vct.setRank(probeLoading.getLoadingRank().doubleValue());
        vct.setExpressionExperiment(new ExpressionExperimentValueObject(ee));
        result.put(probeLoading, vct);
    }
    if (result.isEmpty()) {
        SVDServiceHelperImpl.log.warn("No results, something went wrong; there were " + dvVos.size() + " vectors to start but they all got filtered out.");
    }
    return result;
}

Example 2 with ProbeLoading

use of ubic.gemma.model.analysis.expression.pca.ProbeLoading in project Gemma by PavlidisLab.

the class DEDVController method handleRequestInternal.

/**
 * Handle case of text export of the results.
 */
@RequestMapping("/downloadDEDV.html")
protected ModelAndView handleRequestInternal(HttpServletRequest request) {
    StopWatch watch = new StopWatch();
    watch.start();
    // might not be any
    Collection<Long> geneIds = ControllerUtils.extractIds(request.getParameter("g"));
    // might not be there
    Collection<Long> eeIds = ControllerUtils.extractIds(request.getParameter("ee"));
    ModelAndView mav = new ModelAndView(new TextView());
    if (eeIds == null || eeIds.isEmpty()) {
        mav.addObject("text", "Input empty for finding DEDVs: " + geneIds + " and " + eeIds);
        return mav;
    }
    String threshSt = request.getParameter("thresh");
    String resultSetIdSt = request.getParameter("rs");
    Double thresh = 100.0;
    if (StringUtils.isNotBlank(threshSt)) {
        try {
            thresh = Double.parseDouble(threshSt);
        } catch (NumberFormatException e) {
            throw new RuntimeException("Threshold was not a valid value: " + threshSt);
        }
    }
    Map<ExpressionExperimentValueObject, Map<Long, Collection<DoubleVectorValueObject>>> result;
    if (request.getParameter("pca") != null) {
        int component = Integer.parseInt(request.getParameter("component"));
        Long eeId = eeIds.iterator().next();
        Map<ProbeLoading, DoubleVectorValueObject> topLoadedVectors = this.svdService.getTopLoadedVectors(eeId, component, thresh.intValue());
        if (topLoadedVectors == null)
            return null;
        mav.addObject("text", format4File(topLoadedVectors.values()));
        return mav;
    }
    /*
         * The following should be set if we're viewing diff. ex results.
         */
    Long resultSetId = null;
    if (StringUtils.isNumeric(resultSetIdSt)) {
        resultSetId = Long.parseLong(resultSetIdSt);
    }
    if (resultSetId != null) {
        /*
             * Diff ex case.
             */
        Long eeId = eeIds.iterator().next();
        Collection<DoubleVectorValueObject> diffExVectors = processedExpressionDataVectorService.getDiffExVectors(resultSetId, thresh, MAX_RESULTS_TO_RETURN);
        if (diffExVectors == null || diffExVectors.isEmpty()) {
            mav.addObject("text", "No results");
            return mav;
        }
        /*
             * Organize the vectors in the same way expected by the ee+gene type of request.
             */
        ExpressionExperimentValueObject ee = expressionExperimentService.loadValueObject(expressionExperimentService.load(eeId));
        result = new HashMap<>();
        Map<Long, Collection<DoubleVectorValueObject>> gmap = new HashMap<>();
        for (DoubleVectorValueObject dv : diffExVectors) {
            for (Long g : dv.getGenes()) {
                if (!gmap.containsKey(g)) {
                    gmap.put(g, new HashSet<DoubleVectorValueObject>());
                }
                gmap.get(g).add(dv);
            }
        }
        result.put(ee, gmap);
    } else {
        // Generic listing.
        result = getDEDV(eeIds, geneIds);
    }
    if (result == null || result.isEmpty()) {
        mav.addObject("text", "No results");
        return mav;
    }
    mav.addObject("text", format4File(result));
    watch.stop();
    Long time = watch.getTime();
    if (time > 100) {
        log.info("Retrieved and Formated" + result.keySet().size() + " DEDVs for eeIDs: " + eeIds + " and GeneIds: " + geneIds + " in : " + time + " ms.");
    }
    return mav;
}

Example 3 with ProbeLoading

use of ubic.gemma.model.analysis.expression.pca.ProbeLoading in project Gemma by PavlidisLab.

the class PrincipalComponentAnalysisServiceImpl method create.

@Override
@Transactional
public PrincipalComponentAnalysis create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore) {
    PrincipalComponentAnalysis pca = PrincipalComponentAnalysis.Factory.newInstance();
    int actualNumberOfComponentsStored = Math.min(numComponentsToStore, v.columns());
    pca.setNumComponentsStored(actualNumberOfComponentsStored);
    pca.setBioAssayDimension(bad);
    pca.setMaxNumProbesPerComponent(numLoadingsToStore);
    pca.setExperimentAnalyzed(ee);
    /*
         * deal with U. We keep only the first numComponentsToStore components for the first numLoadingsToStore genes.
         */
    for (int i = 0; i < actualNumberOfComponentsStored; i++) {
        List<CompositeSequence> inOrder = u.sortByColumnAbsoluteValues(i, true);
        for (int j = 0; j < Math.min(u.rows(), numLoadingsToStore) - 1; j++) {
            CompositeSequence probe = inOrder.get(j);
            ProbeLoading plr = ProbeLoading.Factory.newInstance(i + 1, u.getRowByName(probe)[i], j, probe);
            pca.getProbeLoadings().add(plr);
        }
    }
    /*
         * deal with V. note we store all of it.
         */
    ByteArrayConverter bac = new ByteArrayConverter();
    for (int i = 0; i < v.columns(); i++) {
        double[] column = v.getColumn(i);
        byte[] eigenVectorBytes = bac.doubleArrayToBytes(column);
        int componentNumber = i + 1;
        log.debug(componentNumber);
        Eigenvector evec = Eigenvector.Factory.newInstance(componentNumber, eigenVectorBytes);
        pca.getEigenVectors().add(evec);
    }
    /*
         * Deal with eigenvalues; note we store all of them.
         */
    double sum = 0.0;
    List<Eigenvalue> eigv = new ArrayList<>();
    for (int i = 0; i < eigenvalues.length; i++) {
        double d = eigenvalues[i];
        sum += d;
        Eigenvalue ev = Eigenvalue.Factory.newInstance();
        ev.setComponentNumber(i + 1);
        ev.setValue(d);
        eigv.add(ev);
    }
    for (int i = 0; i < eigenvalues.length; i++) {
        Eigenvalue eigenvalue = eigv.get(i);
        eigenvalue.setVarianceFraction(eigenvalue.getValue() / sum);
        pca.getEigenValues().add(eigenvalue);
    }
    return this.principalComponentAnalysisDao.create(pca);
}

Example 4 with ProbeLoading

use of ubic.gemma.model.analysis.expression.pca.ProbeLoading in project Gemma by PavlidisLab.

the class DEDVController method getDEDVForPcaVisualization.

/**
 * AJAX
 */
public VisualizationValueObject[] getDEDVForPcaVisualization(Long eeId, int component, int count) {
    StopWatch watch = new StopWatch();
    watch.start();
    Map<ProbeLoading, DoubleVectorValueObject> topLoadedVectors = this.svdService.getTopLoadedVectors(eeId, component, count);
    if (topLoadedVectors == null)
        return null;
    Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> layouts;
    Collection<DoubleVectorValueObject> values = topLoadedVectors.values();
    if (values.isEmpty()) {
        return null;
    }
    layouts = experimentalDesignVisualizationService.sortVectorDataByDesign(values);
    return makeVisCollection(values, null, null, layouts);
}