net.sf.maltcms.chromaui.normalization.spi.charts.PeakGroupRtBoxPlot.java Source code

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/* 
 * Maui, Maltcms User Interface. 
 * Copyright (C) 2008-2014, The authors of Maui. All rights reserved.
 *
 * Project website: http://maltcms.sf.net
 *
 * Maui may be used under the terms of either the
 *
 * GNU Lesser General Public License (LGPL)
 * http://www.gnu.org/licenses/lgpl.html
 *
 * or the
 *
 * Eclipse Public License (EPL)
 * http://www.eclipse.org/org/documents/epl-v10.php
 *
 * As a user/recipient of Maui, you may choose which license to receive the code 
 * under. Certain files or entire directories may not be covered by this 
 * dual license, but are subject to licenses compatible to both LGPL and EPL.
 * License exceptions are explicitly declared in all relevant files or in a 
 * LICENSE file in the relevant directories.
 *
 * Maui is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE. Please consult the relevant license documentation
 * for details.
 */
package net.sf.maltcms.chromaui.normalization.spi.charts;

import java.awt.Color;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import lombok.Data;
import net.sf.maltcms.chromaui.charts.ChartCustomizer;
import net.sf.maltcms.chromaui.project.api.IChromAUIProject;
import net.sf.maltcms.chromaui.project.api.descriptors.IPeakAnnotationDescriptor;
import net.sf.maltcms.chromaui.project.api.descriptors.IPeakGroupDescriptor;
import net.sf.maltcms.chromaui.project.api.descriptors.ITreatmentGroupDescriptor;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.CategoryAxis;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.plot.CategoryPlot;
import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer;
import org.jfree.data.statistics.BoxAndWhiskerCalculator;
import org.jfree.data.statistics.BoxAndWhiskerItem;
import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset;

/**
 *
 * @author Nils Hoffmann
 */
@Data
public class PeakGroupRtBoxPlot {

    private final IChromAUIProject project;
    private final Collection<IPeakGroupDescriptor> pgdl;
    private boolean showAreas = true;
    private boolean ignoreNullAndNanValues;

    public List<JFreeChart> createChart() {
        List<JFreeChart> charts = new ArrayList<>();
        LinkedHashSet<ITreatmentGroupDescriptor> treatmentGroups = new LinkedHashSet<>(
                project.getTreatmentGroups());
        List<CategoryPlot> plots = new LinkedList<>();
        for (IPeakGroupDescriptor pgd : pgdl) {
            LinkedHashMap<ITreatmentGroupDescriptor, HashSet<IPeakAnnotationDescriptor>> map = new LinkedHashMap<>();
            for (ITreatmentGroupDescriptor itgd : treatmentGroups) {
                map.put(itgd, new LinkedHashSet<IPeakAnnotationDescriptor>());
            }
            List<IPeakAnnotationDescriptor> descriptors = pgd.getPeakAnnotationDescriptors();

            DefaultBoxAndWhiskerCategoryDataset baw = new DefaultBoxAndWhiskerCategoryDataset();
            for (IPeakAnnotationDescriptor ipad : descriptors) {
                ITreatmentGroupDescriptor treatmentGroup = ipad.getChromatogramDescriptor().getTreatmentGroup();
                HashSet<IPeakAnnotationDescriptor> descr = map.get(treatmentGroup);
                if (descr == null) {
                    descr = new HashSet<>();
                    map.put(treatmentGroup, descr);
                }
                descr.add(ipad);
            }
            List<Color> colors = new LinkedList<>();
            for (ITreatmentGroupDescriptor tgd : map.keySet()) {
                String name = getPeakName(pgd);
                baw.add(createBoxAndWhiskerItem(map.get(tgd)), tgd.getName() + " (" + map.get(tgd).size() + ")",
                        name);
                colors.add(tgd.getColor());
            }
            BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
            renderer.setFillBox(true);
            renderer.setMeanVisible(false);
            renderer.setMedianVisible(true);
            renderer.setArtifactPaint(new Color(0, 0, 0, 128));
            renderer.setMaximumBarWidth(0.1);

            renderer.setUseOutlinePaintForWhiskers(false);
            //            renderer.setAutoPopulateSeriesFillPaint(true);
            //            renderer.setAutoPopulateSeriesPaint(true);
            //            renderer.setAutoPopulateSeriesOutlinePaint(true);
            NumberAxis yAxis = new NumberAxis("Peak Apex Retention Time");
            yAxis.setAutoRange(true);
            yAxis.setAutoRangeIncludesZero(false);
            CategoryPlot cp = new CategoryPlot(baw, new CategoryAxis("Treatment Groups"), yAxis, renderer);
            Logger.getLogger(getClass().getName()).log(Level.INFO, "Setting {0} colors!", colors.size());
            ChartCustomizer.setSeriesColors(cp, 0.6f, colors);
            //            ChartCustomizer.setSeriesColors(cp, 0.9f,colors);
            plots.add(cp);
            JFreeChart chart = new JFreeChart(cp);
            chart.setTitle(
                    "Peak group " + pgd.getDisplayName() + " size: " + pgd.getPeakAnnotationDescriptors().size());
            charts.add(chart);
        }
        //        CategoryAxis ca = new CategoryAxis("Treatment Groups");
        //        NumberAxis va = new NumberAxis("Normalized Peak Area");
        //        CombinedDomainCategoryPlot cdcp = new CombinedDomainCategoryPlot(ca);
        //        for (CategoryPlot cp : plots) {
        //            cp.setRangeAxis(va);
        //            cdcp.add(cp);
        //            break;
        //        }
        //        return new JFreeChart(cdcp);
        return charts;
    }

    protected String getPeakName(IPeakGroupDescriptor pgd) {
        String rt = "mean rt: " + String.format("%.2f", pgd.getMeanApexTime()) + "+/-"
                + String.format("%.2f", pgd.getApexTimeStdDev()) + "; median rt: "
                + String.format("%.2f", pgd.getMedianApexTime()) + ": ";
        LinkedHashMap<String, Integer> names = new LinkedHashMap<>();
        if (!pgd.getDisplayName().equals(pgd.getName())) {
            return rt + pgd.getDisplayName();
        }
        for (IPeakAnnotationDescriptor ipad : pgd.getPeakAnnotationDescriptors()) {
            if (names.containsKey(ipad.getName())) {
                names.put(ipad.getName(), names.get(ipad.getName()) + 1);
            } else {
                names.put(ipad.getName(), 1);
            }
        }
        if (names.isEmpty()) {
            return rt + "<NA>";
        }
        if (names.size() > 1) {
            StringBuilder sb = new StringBuilder();
            for (String key : names.keySet()) {
                sb.append(key);
                sb.append(" (" + names.get(key) + ")");
                sb.append(" | ");
            }
            return rt + sb.replace(sb.length() - 1, sb.length() - 1, "").toString();
        } else {
            return rt + names.keySet().toArray(new String[0])[0];
        }
    }

    protected BoxAndWhiskerItem createBoxAndWhiskerItem(Collection<IPeakAnnotationDescriptor> descriptors) {
        List<Double> values = new LinkedList<>();
        for (IPeakAnnotationDescriptor ipad : descriptors) {
            values.add(ipad.getApexTime());
        }

        //        for (int i = 0; i < 100; i++) {
        //            values.add(1000000 * Math.random());
        //        }
        BoxAndWhiskerItem bawi = BoxAndWhiskerCalculator.calculateBoxAndWhiskerStatistics(values,
                ignoreNullAndNanValues);
        return bawi;
    }
}