Examples with RSessionWrapper net.sf.mzmine.util.R.RSessionWrapper used on opensource projects

Example 1 with RSessionWrapper

use of net.sf.mzmine.util.R.RSessionWrapper in project mzmine2 by mzmine.

the class HeatMapTask method run.

public void run() {
    errorMsg = null;
    setStatus(TaskStatus.PROCESSING);
    logger.info("Heat map plot");
    if (plegend) {
        newPeakList = groupingDataset(selectedParameter, referenceGroup.toString());
    } else {
        newPeakList = modifySimpleDataset(selectedParameter, referenceGroup.toString());
    }
    if (newPeakList.length == 0 || newPeakList[0].length == 0) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("The data for heat map is empty.");
        return;
    }
    try {
        // Load gplots library
        String[] reqPackages = { "gplots" };
        rSession = new RSessionWrapper(this.rEngineType, "HeatMap analysis module", reqPackages, null);
        rSession.open();
        finishedPercentage = 0.3f;
        if (outputType.contains("png")) {
            if (height < 500 || width < 500) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage("Figure height or width is too small. " + "Minimun height and width is 500.");
                return;
            }
        }
        rSession.eval("dataset<- matrix(\"\",nrow =" + newPeakList[0].length + ",ncol=" + newPeakList.length + ")");
        if (plegend) {
            rSession.eval("stars<- matrix(\"\",nrow =" + newPeakList[0].length + ",ncol=" + newPeakList.length + ")");
        }
        // assing the values to the matrix
        for (int row = 0; row < newPeakList[0].length; row++) {
            for (int column = 0; column < newPeakList.length; column++) {
                int r = row + 1;
                int c = column + 1;
                double value = newPeakList[column][row];
                if (plegend) {
                    String pValue = pValueMatrix[column][row];
                    rSession.eval("stars[" + r + "," + c + "] = \"" + pValue + "\"");
                }
                if (!Double.isInfinite(value) && !Double.isNaN(value)) {
                    rSession.eval("dataset[" + r + "," + c + "] = " + value);
                } else {
                    rSession.eval("dataset[" + r + "," + c + "] = NA");
                }
            }
        }
        finishedPercentage = 0.4f;
        rSession.eval("dataset <- apply(dataset, 2, as.numeric)");
        // Assign row names to the data set
        rSession.assign("rowNames", rowNames);
        rSession.eval("rownames(dataset)<-rowNames");
        // Assign column names to the data set
        rSession.assign("colNames", colNames);
        rSession.eval("colnames(dataset)<-colNames");
        finishedPercentage = 0.5f;
        // Remove the rows with too many NA's. The distances between
        // rows can't be calculated if the rows don't have
        // at least one sample in common.
        rSession.eval("d <- as.matrix(dist(dataset))");
        rSession.eval("d[upper.tri(d)] <- 0");
        rSession.eval("naindices <- na.action(na.omit(d))");
        rSession.eval("if (! is.null(naindices)) dataset <- dataset[-naindices,]");
        finishedPercentage = 0.8f;
        String marginParameter = "margins = c(" + columnMargin + "," + rowMargin + ")";
        rSession.eval("br<-c(seq(from=min(dataset,na.rm=T),to=0,length.out=256)," + "seq(from=0.00001,to=max(dataset,na.rm=T),length.out=256))", false);
        // Convert the path to R-compatible string
        final String escapedOutputFileName = Rsession.toRpath(outputFile);
        // Possible output file types
        if (outputType.contains("pdf")) {
            rSession.eval("pdf(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ")");
        } else if (outputType.contains("fig")) {
            rSession.eval("xfig(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ", horizontal = FALSE, pointsize = 12)");
        } else if (outputType.contains("svg")) {
            // Load RSvgDevice library
            rSession.loadPackage("RSvgDevice");
            rSession.eval("devSVG(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ")");
        } else if (outputType.contains("png")) {
            rSession.eval("png(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ")");
        }
        if (plegend) {
            rSession.eval("heatmap.2(dataset," + marginParameter + ", trace=\"none\", col=bluered(length(br)-1)," + " breaks=br, cellnote=stars, notecol=\"black\"" + ", notecex=" + starSize + ", na.color=\"grey\")", false);
        } else {
            rSession.eval("heatmap.2(dataset," + marginParameter + ", trace=\"none\", col=bluered(length(br)-1)," + " breaks=br, na.color=\"grey\")", false);
        }
        rSession.eval("dev.off()", false);
        // Stands for a (void) collect!
        this.rSession.runOnlyOnline();
        // Done: Refresh R code stack
        this.rSession.clearCode();
        finishedPercentage = 1.0;
        // Turn off R instance, once task ended gracefully.
        if (!isCanceled())
            rSession.close(false);
    } catch (RSessionWrapperException e) {
        if (!isCanceled()) {
            errorMsg = "'R computing error' during heatmap generation. \n" + e.getMessage();
        }
    } catch (Exception e) {
        if (!isCanceled()) {
            errorMsg = "'Unknown error' during heatmap generation. \n" + e.getMessage();
        }
    }
    // Turn off R instance, once task ended UNgracefully.
    try {
        if (!isCanceled())
            if (rSession != null)
                rSession.close(isCanceled());
    } catch (RSessionWrapperException e) {
        if (!isCanceled()) {
            // Do not override potential previous error message.
            if (errorMsg == null) {
                errorMsg = e.getMessage();
            }
        } else {
        // User canceled: Silent.
        }
    }
    // Report error.
    if (errorMsg != null) {
        setErrorMessage(errorMsg);
        setStatus(TaskStatus.ERROR);
    } else {
        setStatus(TaskStatus.FINISHED);
    }
}

Example 2 with RSessionWrapper

use of net.sf.mzmine.util.R.RSessionWrapper in project mzmine2 by mzmine.

the class DeconvolutionTask method run.

@Override
public void run() {
    errorMsg = null;
    if (!isCanceled()) {
        setStatus(TaskStatus.PROCESSING);
        LOG.info("Started peak deconvolution on " + originalPeakList);
        // Check raw data files.
        if (originalPeakList.getNumberOfRawDataFiles() > 1) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Peak deconvolution can only be performed on feature lists with a single raw data file");
        } else {
            try {
                // Peak resolver.
                final MZmineProcessingStep<PeakResolver> resolver = parameters.getParameter(PEAK_RESOLVER).getValue();
                if (resolver.getModule().getRequiresR()) {
                    // Check R availability, by trying to open the
                    // connection.
                    String[] reqPackages = resolver.getModule().getRequiredRPackages();
                    String[] reqPackagesVersions = resolver.getModule().getRequiredRPackagesVersions();
                    String callerFeatureName = resolver.getModule().getName();
                    REngineType rEngineType = resolver.getModule().getREngineType(resolver.getParameterSet());
                    this.rSession = new RSessionWrapper(rEngineType, callerFeatureName, reqPackages, reqPackagesVersions);
                    this.rSession.open();
                } else {
                    this.rSession = null;
                }
                // Deconvolve peaks.
                newPeakList = resolvePeaks(originalPeakList, this.rSession);
                if (!isCanceled()) {
                    // Add new peaklist to the project.
                    project.addPeakList(newPeakList);
                    // Add quality parameters to peaks
                    QualityParameters.calculateQualityParameters(newPeakList);
                    // Remove the original peaklist if requested.
                    if (parameters.getParameter(AUTO_REMOVE).getValue()) {
                        project.removePeakList(originalPeakList);
                    }
                    setStatus(TaskStatus.FINISHED);
                    LOG.info("Finished peak recognition on " + originalPeakList);
                }
                // Turn off R instance.
                if (this.rSession != null)
                    this.rSession.close(false);
            } catch (RSessionWrapperException e) {
                errorMsg = "'R computing error' during CentWave detection. \n" + e.getMessage();
            } catch (Exception e) {
                errorMsg = "'Unknown error' during CentWave detection. \n" + e.getMessage();
            } catch (Throwable t) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage(t.getMessage());
                LOG.log(Level.SEVERE, "Peak deconvolution error", t);
            }
            // Turn off R instance, once task ended UNgracefully.
            try {
                if (this.rSession != null && !isCanceled())
                    rSession.close(isCanceled());
            } catch (RSessionWrapperException e) {
                if (!isCanceled()) {
                    // Do not override potential previous error message.
                    if (errorMsg == null) {
                        errorMsg = e.getMessage();
                    }
                } else {
                // User canceled: Silent.
                }
            }
            // Report error.
            if (errorMsg != null) {
                setErrorMessage(errorMsg);
                setStatus(TaskStatus.ERROR);
            }
        }
    }
}

Example 3 with RSessionWrapper

use of net.sf.mzmine.util.R.RSessionWrapper in project mzmine2 by mzmine.

the class CameraSearchTask method cameraSearch.

/**
 * Perform CAMERA search.
 *
 * @param rawFile raw data file of feature list to process.
 */
private void cameraSearch(final RawDataFile rawFile) {
    LOG.finest("Detecting peaks.");
    errorMsg = null;
    try {
        String[] reqPackages = { "CAMERA" };
        String[] reqPackagesVersions = { CAMERA_VERSION };
        this.rSession = new RSessionWrapper(this.rEngineType, "Camera search feature", reqPackages, reqPackagesVersions);
        this.rSession.open();
        // Create empty peaks matrix.
        this.rSession.eval("columnHeadings <- c('mz','mzmin','mzmax','rt','rtmin','rtmax','into','intb','maxo','sn')");
        this.rSession.eval("peaks <- matrix(nrow=0, ncol=length(columnHeadings))");
        this.rSession.eval("colnames(peaks) <- columnHeadings");
        // Initialize.
        final Feature[] peaks = peakList.getPeaks(rawFile);
        progress = 0.0;
        // Initialize scan map.
        final Map<Scan, Set<DataPoint>> peakDataPointsByScan = new HashMap<Scan, Set<DataPoint>>(rawFile.getNumOfScans(MS_LEVEL));
        int dataPointCount = 0;
        for (final int scanNumber : rawFile.getScanNumbers(MS_LEVEL)) {
            // Create a set to hold data points (sorted by m/z).
            final Set<DataPoint> dataPoints = new TreeSet<DataPoint>(ASCENDING_MASS_SORTER);
            // Add a dummy data point.
            dataPoints.add(new SimpleDataPoint(0.0, 0.0));
            dataPointCount++;
            // Map the set.
            peakDataPointsByScan.put(rawFile.getScan(scanNumber), dataPoints);
        }
        // Add peaks.
        // 80 percents for building peaks list.
        double progressInc = 0.8 / (double) peaks.length;
        for (final Feature peak : peaks) {
            // Get peak data.
            Range<Double> rtRange = null;
            Range<Double> intRange = null;
            final double mz = peak.getMZ();
            // Get the peak's data points per scan.
            for (final int scanNumber : peak.getScanNumbers()) {
                final Scan scan = rawFile.getScan(scanNumber);
                if (scan.getMSLevel() != MS_LEVEL) {
                    throw new IllegalStateException("CAMERA can only process feature lists from MS-level " + MS_LEVEL);
                }
                // Copy the data point.
                final DataPoint dataPoint = peak.getDataPoint(scanNumber);
                if (dataPoint != null) {
                    final double intensity = dataPoint.getIntensity();
                    peakDataPointsByScan.get(scan).add(new SimpleDataPoint(mz, intensity));
                    dataPointCount++;
                    // Update RT & intensity range.
                    final double rt = scan.getRetentionTime();
                    if (rtRange == null) {
                        rtRange = Range.singleton(rt);
                        intRange = Range.singleton(intensity);
                    } else {
                        rtRange = rtRange.span(Range.singleton(rt));
                        intRange = intRange.span(Range.singleton(intensity));
                    }
                }
            }
            // Set peak values.
            final double area = peak.getArea();
            final double maxo = intRange == null ? peak.getHeight() : intRange.upperEndpoint();
            final double rtMin = (rtRange == null ? peak.getRawDataPointsRTRange() : rtRange).lowerEndpoint();
            final double rtMax = (rtRange == null ? peak.getRawDataPointsRTRange() : rtRange).upperEndpoint();
            // Add peak row.
            this.rSession.eval(// mz
            "peaks <- rbind(peaks, c(" + mz + ", " + mz + // mzmin: use the same as mz.
            ", " + mz + // mzmax: use the same as mz.
            ", " + peak.getRT() + // rt
            ", " + rtMin + // rtmin
            ", " + rtMax + // rtmax
            ", " + area + // into: peak area.
            ", " + area + // intb: doesn't affect result, use area.
            ", " + maxo + // maxo
            ", " + SIGNAL_TO_NOISE + "))", false);
            progress += progressInc;
        }
        // 20 percents (5*4) for building pseudo-isotopes groups.
        progressInc = 0.05;
        // Create R vectors.
        final int scanCount = peakDataPointsByScan.size();
        final double[] scanTimes = new double[scanCount];
        final int[] scanIndices = new int[scanCount];
        final double[] masses = new double[dataPointCount];
        final double[] intensities = new double[dataPointCount];
        // Fill vectors.
        int scanIndex = 0;
        int pointIndex = 0;
        for (final int scanNumber : rawFile.getScanNumbers(MS_LEVEL)) {
            final Scan scan = rawFile.getScan(scanNumber);
            scanTimes[scanIndex] = scan.getRetentionTime();
            scanIndices[scanIndex] = pointIndex + 1;
            scanIndex++;
            for (final DataPoint dataPoint : peakDataPointsByScan.get(scan)) {
                masses[pointIndex] = dataPoint.getMZ();
                intensities[pointIndex] = dataPoint.getIntensity();
                pointIndex++;
            }
        }
        // Set vectors.
        this.rSession.assign("scantime", scanTimes);
        this.rSession.assign("scanindex", scanIndices);
        this.rSession.assign("mass", masses);
        this.rSession.assign("intensity", intensities);
        // Construct xcmsRaw object
        this.rSession.eval("xRaw <- new(\"xcmsRaw\")");
        this.rSession.eval("xRaw@tic <- intensity");
        this.rSession.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE);
        this.rSession.eval("xRaw@scanindex <- as.integer(scanindex)");
        this.rSession.eval("xRaw@env$mz <- mass");
        this.rSession.eval("xRaw@env$intensity <- intensity");
        // Create the xcmsSet object.
        this.rSession.eval("xs <- new(\"xcmsSet\")");
        // Set peaks.
        this.rSession.eval("xs@peaks <- peaks");
        // Set file (dummy) file path.
        this.rSession.eval("xs@filepaths  <- ''");
        // Set sample name.
        this.rSession.assign("sampleName", peakList.getName());
        this.rSession.eval("sampnames(xs) <- sampleName");
        // Create an empty xsAnnotate.
        this.rSession.eval("an <- xsAnnotate(xs, sample=1)");
        // Group by RT.
        this.rSession.eval("an <- groupFWHM(an, sigma=" + fwhmSigma + ", perfwhm=" + fwhmPercentage + ')');
        progress += progressInc;
        switch(parameters.getParameter(CameraSearchParameters.ORDER).getValue()) {
            case CameraSearchParameters.GROUP_CORR_FIRST:
                // Split groups by correlating peak shape (need to set xraw to raw
                // data).
                this.rSession.eval("an <- groupCorr(an, calcIso=FALSE, xraw=xRaw, cor_eic_th=" + corrThreshold + ", pval=" + corrPValue + ')');
                progress += progressInc;
                // Identify isotopes.
                this.rSession.eval("an <- findIsotopes(an, maxcharge=" + isoMaxCharge + ", maxiso=" + isoMaxCount + ", ppm=" + isoMassTolerance.getPpmTolerance() + ", mzabs=" + isoMassTolerance.getMzTolerance() + ')');
                progress += progressInc;
                break;
            default:
                // case CameraSearchParameters.FIND_ISOTOPES_FIRST
                // Identify isotopes.
                this.rSession.eval("an <- findIsotopes(an, maxcharge=" + isoMaxCharge + ", maxiso=" + isoMaxCount + ", ppm=" + isoMassTolerance.getPpmTolerance() + ", mzabs=" + isoMassTolerance.getMzTolerance() + ')');
                // this.rSession.eval("write.csv(getPeaklist(an),
                // file='/Users/aleksandrsmirnov/test_camera.csv')");
                progress += progressInc;
                // Split groups by correlating peak shape (need to set xraw to raw
                // data).
                this.rSession.eval("an <- groupCorr(an, calcIso=" + String.valueOf(calcIso).toUpperCase() + ", xraw=xRaw, cor_eic_th=" + corrThreshold + ", pval=" + corrPValue + ')');
                progress += progressInc;
        }
        this.rSession.eval("an <- findAdducts(an, polarity='" + polarity + "')");
        // Get the feature list.
        this.rSession.eval("peakList <- getPeaklist(an)");
        // Extract the pseudo-spectra and isotope annotations from the peak
        // list.
        rSession.eval("pcgroup <- as.integer(peakList$pcgroup)");
        rSession.eval("isotopes <- peakList$isotopes");
        rSession.eval("adducts <- peakList$adduct");
        final int[] spectra = (int[]) rSession.collect("pcgroup");
        final String[] isotopes = (String[]) rSession.collect("isotopes");
        final String[] adducts = (String[]) rSession.collect("adducts");
        // Done: Refresh R code stack
        this.rSession.clearCode();
        // Add identities.
        if (spectra != null) {
            addPseudoSpectraIdentities(peaks, spectra, isotopes, adducts);
        }
        progress += progressInc;
        // Turn off R instance, once task ended gracefully.
        if (!this.userCanceled)
            this.rSession.close(false);
    } catch (RSessionWrapperException e) {
        if (!this.userCanceled) {
            errorMsg = "'R computing error' during CAMERA search. \n" + e.getMessage();
            e.printStackTrace();
        }
    } catch (Exception e) {
        if (!this.userCanceled) {
            errorMsg = "'Unknown error' during CAMERA search. \n" + e.getMessage();
            e.printStackTrace();
        }
    }
    // Turn off R instance, once task ended UNgracefully.
    try {
        if (!this.userCanceled)
            this.rSession.close(this.userCanceled);
    } catch (RSessionWrapperException e) {
        if (!this.userCanceled) {
            // Do not override potential previous error message.
            if (errorMsg == null) {
                errorMsg = e.getMessage();
            }
        } else {
        // User canceled: Silent.
        }
    }
    // Report error.
    if (errorMsg != null) {
        setErrorMessage(errorMsg);
        setStatus(TaskStatus.ERROR);
    }
}

Example 4 with RSessionWrapper

use of net.sf.mzmine.util.R.RSessionWrapper in project mzmine2 by mzmine.

the class BaselineCorrectionTask method run.

@Override
public void run() {
    errorMsg = null;
    // Update the status of this task.
    setStatus(TaskStatus.PROCESSING);
    try {
        // Check R availability, by trying to open the connection.
        String[] reqPackages = this.baselineCorrectorProcStep.getModule().getRequiredRPackages();
        String callerFeatureName = this.baselineCorrectorProcStep.getModule().getName();
        this.rSession = new RSessionWrapper(rEngineType, callerFeatureName, reqPackages, null);
        this.rSession.open();
        this.baselineCorrectorProcStep.getModule().initProgress(origDataFile);
        final RawDataFile correctedDataFile = this.baselineCorrectorProcStep.getModule().correctDatafile(this.rSession, origDataFile, baselineCorrectorProcStep.getParameterSet(), this.commonParameters);
        // If this task was canceled, stop processing.
        if (!isCanceled() && correctedDataFile != null) {
            this.correctedDataFile = correctedDataFile;
            // Add the newly created file to the project
            this.project.addFile(this.correctedDataFile);
            // Remove the original data file if requested.
            if (removeOriginal) {
                project.removeFile(origDataFile);
            }
            // Set task status to FINISHED
            setStatus(TaskStatus.FINISHED);
            LOG.info("Baseline corrected " + origDataFile.getName());
        }
        // Turn off R instance, once task ended gracefully.
        if (!isCanceled())
            this.rSession.close(false);
    } catch (IOException | RSessionWrapperException e) {
        if (!isCanceled()) {
            errorMsg = "'R computing error' during baseline correction. \n" + e.getMessage();
        }
    } catch (Exception e) {
        if (!isCanceled()) {
            errorMsg = "'Unknown error' during baseline correction. \n" + e.getMessage();
        }
    }
    this.baselineCorrectorProcStep.getModule().setAbortProcessing(origDataFile, true);
    // Turn off R instance, once task ended UNgracefully.
    try {
        if (!isCanceled())
            this.rSession.close(isCanceled());
    } catch (RSessionWrapperException e) {
        if (!isCanceled()) {
            // Do not override potential previous error message.
            if (errorMsg == null) {
                errorMsg = e.getMessage();
            }
        } else {
        // User canceled: Silent.
        }
    }
    // Report error.
    if (errorMsg != null) {
        setErrorMessage(errorMsg);
        setStatus(TaskStatus.ERROR);
    }
    // ...
    this.baselineCorrectorProcStep.getModule().clearProgress(origDataFile);
}

Example 5 with RSessionWrapper

use of net.sf.mzmine.util.R.RSessionWrapper in project mzmine2 by mzmine.

the class PeakResolverSetupDialog method parametersChanged.

@Override
public void parametersChanged() {
    if (preview != null && preview.isSelected()) {
        final PeakListRow previewRow = (PeakListRow) comboPeak.getSelectedItem();
        if (previewRow != null) {
            LOG.finest("Loading new preview peak " + previewRow);
            ticPlot.removeAllTICDataSets();
            ticPlot.addTICDataset(new ChromatogramTICDataSet(previewRow.getPeaks()[0]));
            // Auto-range to axes.
            ticPlot.getXYPlot().getDomainAxis().setAutoRange(true);
            ticPlot.getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
            ticPlot.getXYPlot().getRangeAxis().setAutoRange(true);
            ticPlot.getXYPlot().getRangeAxis().setAutoTickUnitSelection(true);
            updateParameterSetFromComponents();
            // If there is some illegal value, do not load the preview but
            // just exit.
            ArrayList<String> errors = new ArrayList<String>();
            if (!parameterSet.checkParameterValues(errors)) {
                LOG.fine("Illegal parameter value: " + errors);
                return;
            }
            // Load the intensities and RTs into array.
            final Feature previewPeak = previewRow.getPeaks()[0];
            // Resolve peaks.
            Feature[] resolvedPeaks = {};
            RSessionWrapper rSession;
            try {
                if (peakResolver.getRequiresR()) {
                    // Check R availability, by trying to open the
                    // connection.
                    String[] reqPackages = peakResolver.getRequiredRPackages();
                    String[] reqPackagesVersions = peakResolver.getRequiredRPackagesVersions();
                    String callerFeatureName = peakResolver.getName();
                    REngineType rEngineType = peakResolver.getREngineType(parameters);
                    rSession = new RSessionWrapper(rEngineType, callerFeatureName, reqPackages, reqPackagesVersions);
                    rSession.open();
                } else {
                    rSession = null;
                }
                CenterFunction mzCenterFunction = new CenterFunction(CenterMeasure.MEDIAN);
                // preview doesn't show msms scans
                // set it to be default searching range
                resolvedPeaks = peakResolver.resolvePeaks(previewPeak, parameters, rSession, mzCenterFunction, 0, 0);
                // Turn off R instance.
                if (rSession != null)
                    rSession.close(false);
            } catch (RSessionWrapperException e) {
                throw new IllegalStateException(e.getMessage());
            } catch (Throwable t) {
                LOG.log(Level.SEVERE, "Peak deconvolution error", t);
                MZmineCore.getDesktop().displayErrorMessage(this, t.toString());
            }
            // Add resolved peaks to TIC plot.
            final int peakCount = Math.min(MAX_PEAKS, resolvedPeaks.length);
            for (int i = 0; i < peakCount; i++) {
                final XYDataset peakDataSet = new PeakDataSet(resolvedPeaks[i]);
                ticPlot.addPeakDataset(peakDataSet);
            }
            // Check peak count.
            if (resolvedPeaks.length > MAX_PEAKS) {
                // MZmineCore.getDesktop().displayMessage(this,
                // "Too many peaks detected, please adjust parameter values");
                MZmineCore.getDesktop().displayMessage(this, "Too many peaks detected. Not all of the peaks might be displayed");
            }
        }
    }
}