Example usage for org.jfree.chart.renderer.category BoxAndWhiskerRenderer setMaximumBarWidth

List of usage examples for org.jfree.chart.renderer.category BoxAndWhiskerRenderer setMaximumBarWidth

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Introduction

In this page you can find the example usage for org.jfree.chart.renderer.category BoxAndWhiskerRenderer setMaximumBarWidth.

Prototype

public void setMaximumBarWidth(double percent)

Source Link

Document

Sets the maximum bar width, which is specified as a percentage of the available space for all bars, and sends a RendererChangeEvent to all registered listeners.

Usage

From source file:wsattacker.plugin.intelligentdos.ui.helper.ChartHelper.java

public static JFreeChart createWhiskerChart(SuccessfulAttack sa) {
    BoxAndWhiskerCategoryDataset boxandwhiskercategorydataset = createDataset(sa);
    final BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
    renderer.setMaximumBarWidth(0.05);
    renderer.setMeanVisible(false);/*from   w  w  w. j  a va  2  s  .c  om*/
    renderer.setSeriesPaint(0, Color.GREEN);
    renderer.setSeriesPaint(1, Color.RED);
    renderer.setSeriesPaint(2, Color.BLUE);

    NumberAxis numberAxis = new NumberAxis("duration in ms");
    CategoryPlot categoryplot = new CategoryPlot(boxandwhiskercategorydataset, new CategoryAxis(""), numberAxis,
            renderer);
    categoryplot.setDomainGridlinesVisible(true);
    categoryplot.setRangePannable(true);
    NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis();
    numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    JFreeChart jFreeChart = new JFreeChart("", new Font("SansSerif", Font.BOLD, 14), categoryplot, true);
    jFreeChart.removeLegend();
    return jFreeChart;
}

From source file:org.gephi.ui.utils.ChartsUtils.java

/**
 * Build a new box-plot from an array of numbers using a default title and yLabel.
 * String dataName will be used for xLabel.
 * @param numbers Numbers for building box-plot
 * @param dataName Name of the numbers data
 * @return Prepared box-plot/*  w  ww  . jav  a2 s. co  m*/
 */
public static JFreeChart buildBoxPlot(final Number[] numbers, final String dataName) {
    if (numbers == null || numbers.length == 0) {
        return null;
    }
    DefaultBoxAndWhiskerCategoryDataset dataset = new DefaultBoxAndWhiskerCategoryDataset();
    final ArrayList<Number> list = new ArrayList<Number>();
    list.addAll(Arrays.asList(numbers));

    final String valuesString = getMessage("ChartsUtils.report.box-plot.values");
    dataset.add(list, valuesString, "");

    final BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
    renderer.setMeanVisible(false);
    renderer.setFillBox(false);
    renderer.setMaximumBarWidth(0.5);

    final CategoryAxis xAxis = new CategoryAxis(dataName);
    final NumberAxis yAxis = new NumberAxis(getMessage("ChartsUtils.report.box-plot.values-range"));
    yAxis.setAutoRangeIncludesZero(false);
    renderer.setBaseToolTipGenerator(new BoxAndWhiskerToolTipGenerator());
    final CategoryPlot plot = new CategoryPlot(dataset, xAxis, yAxis, renderer);
    plot.setRenderer(renderer);

    JFreeChart boxPlot = new JFreeChart(getMessage("ChartsUtils.report.box-plot.title"), plot);
    return boxPlot;
}

From source file:weka.core.ChartUtils.java

/**
 * Create a box plot from summary data (mean, median, q1, q3, min, max,
 * minOutlier, maxOutlier, list of outliers)
 * //from   ww  w.ja va 2s.com
 * @param summary summary data
 * @param outliers list of outlier values
 * @param additionalArgs additional options to the renderer
 * @return a box plot chart
 * @throws Exception if a problem occurs
 */
protected static JFreeChart getBoxPlotFromSummaryData(List<Double> summary, List<Double> outliers,
        List<String> additionalArgs) throws Exception {

    if (summary.size() != 8) {
        throw new Exception("Expected 8 values in the summary argument: mean, median, "
                + "q1, q3, min, max, minOutlier, maxOutlier");
    }

    String plotTitle = "Box Plog";
    String userTitle = getOption(additionalArgs, "-title");
    plotTitle = (userTitle != null) ? userTitle : plotTitle;
    String xLabel = getOption(additionalArgs, "-x-label");
    xLabel = xLabel == null ? "" : xLabel;
    String yLabel = getOption(additionalArgs, "-y-label");
    yLabel = yLabel == null ? "" : yLabel;

    DefaultBoxAndWhiskerCategoryDataset dataset = new DefaultBoxAndWhiskerCategoryDataset();

    Double mean = summary.get(0);
    Double median = summary.get(1);
    Double q1 = summary.get(2);
    Double q3 = summary.get(3);
    Double min = summary.get(4);
    Double max = summary.get(5);
    Double minOutlier = summary.get(6);
    Double maxOutlier = summary.get(7);

    if (mean.isNaN() || median.isNaN() || min.isNaN() || max.isNaN() || q1.isNaN() || q3.isNaN()) {
        throw new Exception("NaN in summary data - can't generate box plot");
    }

    BoxAndWhiskerItem item = new BoxAndWhiskerItem(mean, median, q1, q3, min, max, minOutlier, maxOutlier,
            outliers);

    dataset.add(item, "", "");

    CategoryAxis xAxis = new CategoryAxis();
    NumberAxis yAxis = new NumberAxis();
    yAxis.setAutoRangeIncludesZero(false);
    BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
    renderer.setFillBox(false);
    renderer.setMaximumBarWidth(0.15);

    CategoryPlot plot = new CategoryPlot(dataset, xAxis, yAxis, renderer);

    JFreeChart chart = new JFreeChart(plotTitle, new Font("SansSerif", Font.BOLD, 12), plot, false);

    return chart;
}

From source file:de.hs.mannheim.modUro.controller.diagram.BoxAndWhiskerPlotController.java

/**
 * Plots Data for Chart/*from w  w w . j  av  a2s .  c  om*/
 */
private void boxWhiskerPlot() {
    BoxAndWhiskerCategoryDataset dataset = createDataset();
    CategoryAxis xAxis = new CategoryAxis("Model");
    NumberAxis yAxis = new NumberAxis("Fitness");
    yAxis.setRange(0.0, 1.0);

    BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
    renderer.setFillBox(false);
    renderer.setMaximumBarWidth(0.2);
    renderer.setItemMargin(0.5);
    renderer.setToolTipGenerator(new BoxAndWhiskerToolTipGenerator());
    CategoryPlot plot = new CategoryPlot(dataset, xAxis, yAxis, renderer);
    plot.setOrientation(PlotOrientation.HORIZONTAL);

    final JFreeChart chart = new JFreeChart("Model comparison", new Font("Palatino", Font.BOLD, 14), plot,
            true);
    chart.removeLegend();

    ChartViewer viewer = new ChartViewer(chart, this);
    boxWhiskerPane.setCenter(viewer);
}

From source file:org.jax.bham.test.PhenotypeEffectPlotPanel.java

private void updateChart() {
    BoxAndWhiskerCategoryDataset dataset = this.createDataset();
    JFreeChart chart = ChartFactory.createBoxAndWhiskerChart("Phenotype Effect Plot", "Groups",
            this.phenotypeDataSource.getName(), dataset, true);
    CategoryPlot plot = (CategoryPlot) chart.getPlot();
    BoxAndWhiskerRenderer renderer = (BoxAndWhiskerRenderer) plot.getRenderer();
    renderer.setMaximumBarWidth(0.05);

    this.chartPanel.setChart(chart);
}

From source file:de.hs.mannheim.modUro.reader.BoxAndWhiskersPlotDiagram.java

/**
 * Plots Data for Chart/*from   w ww  .j av a 2 s  .com*/
 */
private void boxWhiskerPlot() {
    BoxAndWhiskerCategoryDataset dataset = createDataset();
    CategoryAxis xAxis = new CategoryAxis("Model");
    NumberAxis yAxis = new NumberAxis("Fitness");
    yAxis.setRange(0.0, 1.0);

    BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
    renderer.setFillBox(false);
    renderer.setMaximumBarWidth(0.2);
    renderer.setItemMargin(0.5);
    renderer.setToolTipGenerator(new BoxAndWhiskerToolTipGenerator());
    CategoryPlot plot = new CategoryPlot(dataset, xAxis, yAxis, renderer);
    plot.setOrientation(PlotOrientation.HORIZONTAL);

    chart = new JFreeChart("Model comparison", new Font("Palatino", Font.BOLD, 14), plot, true);
    chart.removeLegend();
    // boxWhiskerPane.setCenter(viewer);
}

From source file:net.sf.maltcms.chromaui.normalization.spi.charts.PeakGroupBoxPlot.java

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>());
        }/*from www . java2 s. com*/
        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);
        CategoryPlot cp = new CategoryPlot(baw, new CategoryAxis("Treatment Groups"),
                new NumberAxis("Normalized Peak Area"), 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;
}

From source file:net.sf.maltcms.chromaui.normalization.spi.charts.PeakGroupRtBoxPlot.java

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>());
        }/*from ww  w .  j  av  a 2  s.c  o m*/
        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;
}

From source file:gui.TraitViewerDialog.java

@SuppressWarnings("rawtypes")
private ChartPanel getChart(int selectedRow) {

    ArrayList<Float> data = new ArrayList<Float>();
    for (float[] row : tFile.getRows()) {
        if (row[selectedRow + 1] != (float) -99.0) {
            data.add(row[selectedRow + 1]);
        }//from  www. j  a v a 2s  .  com
    }
    BoxAndWhiskerItem a = BoxAndWhiskerCalculator.calculateBoxAndWhiskerStatistics(data);
    java.util.List l = new ArrayList(0);

    a = new BoxAndWhiskerItem(a.getMean(), a.getMedian(), a.getQ1(), a.getQ3(), a.getMinRegularValue(),
            a.getMaxRegularValue(), a.getMinRegularValue(), a.getMaxRegularValue(), l);
    traitstats.setText(showBoxAndWhiskerItem(a));

    DefaultBoxAndWhiskerCategoryDataset ds2 = new DefaultBoxAndWhiskerCategoryDataset();

    ds2.add(a, (Comparable) 1, (Comparable) 1);
    JFreeChart chart = ChartFactory.createBoxAndWhiskerChart(null, null, null, ds2, false);

    chart.removeLegend();

    // XYPlot plot = chart.getXYPlot();
    CategoryPlot plot = chart.getCategoryPlot();
    plot.getDomainAxis().setVisible(false);
    BoxAndWhiskerRenderer b = (BoxAndWhiskerRenderer) plot.getRenderer();
    // b.setFillBox(false);
    b.setSeriesPaint(0, new Color(236, 55, 169));
    b.setSeriesOutlinePaint(1, new Color(131, 79, 112));
    b.setBaseOutlineStroke(new BasicStroke(1.0f));
    // b.get
    b.setWhiskerWidth(0.8);
    b.setBaseOutlinePaint(new Color(84, 144, 201));
    b.setDefaultEntityRadius(2);
    b.setMaximumBarWidth(0.18);

    ChartPanel chartPanel = new ChartPanel(chart);
    chartPanel.setPopupMenu(null);
    return chartPanel;
}

From source file:org.jax.pubarray.server.restful.GraphingResource.java

/**
 * Create a graph for the given configuration
 * @param graphConfiguration/*  ww  w . j ava2  s .  c  om*/
 *          the key
 * @return
 *          the graph
 */
@SuppressWarnings("unchecked")
private JFreeChart createProbeIntensityGraph(ProbeIntensityGraphConfiguration graphConfiguration) {
    try {
        Connection connection = this.getConnection();

        String[] probeIds = graphConfiguration.getProbeIds();
        double[][] probeDataRows = new double[probeIds.length][];
        for (int i = 0; i < probeIds.length; i++) {
            probeDataRows[i] = this.persistenceManager.getDataRowForProbeID(connection, probeIds[i]);
        }

        TableColumnMetadata orderBy = graphConfiguration.getOrderProbesBy();
        final List<Comparable> orderByItems;
        if (orderBy != null) {
            LOG.info("We are ordering by: " + orderBy);
            orderByItems = this.persistenceManager.getDesignDataColumn(connection, orderBy);
        } else {
            orderByItems = null;
        }

        TableMetadata metadata = this.persistenceManager.getDataTableMetadata(connection);
        final CategoryDataset categoryDataset;
        if (graphConfiguration.getGroupReplicates()) {
            switch (graphConfiguration.getGroupedGraphType()) {
            case BOX_PLOT: {
                categoryDataset = new DefaultBoxAndWhiskerCategoryDataset();
            }
                break;

            case SCATTER_PLOT: {
                categoryDataset = new DefaultMultiValueCategoryDataset();
            }
                break;

            default:
                throw new IllegalArgumentException(
                        "don't know how to deal with plot type: " + graphConfiguration.getGroupedGraphType());
            }
        } else {
            categoryDataset = new DefaultCategoryDataset();
        }

        // iterate through all of the selected probesets
        List<QualifiedColumnMetadata> termsOfInterest = Arrays.asList(graphConfiguration.getTermsOfInterest());
        for (int rowIndex = 0; rowIndex < probeDataRows.length; rowIndex++) {
            double[] currRow = probeDataRows[rowIndex];
            assert currRow.length == metadata.getColumnMetadata().length - 1;

            // should we log2 transform the data?
            if (graphConfiguration.getLog2TransformData()) {
                for (int i = 0; i < currRow.length; i++) {
                    currRow[i] = Math.log(currRow[i]) / LOG2_FACTOR;
                }
            }

            // iterate through the columns in the data table (each column
            // represents a different array)
            List<ComparableContainer<Double, Comparable>> rowElemList = new ArrayList<ComparableContainer<Double, Comparable>>();
            for (int colIndex = 0; colIndex < currRow.length; colIndex++) {
                // we use +1 indexing here because we want to skip over
                // the probesetId metadata and get right to the
                // array intensity metadata
                TableColumnMetadata colMeta = metadata.getColumnMetadata()[colIndex + 1];

                // check to see if we need to skip this data
                if (!graphConfiguration.getIncludeDataFromAllArrays()) {
                    // if it's one of the "terms of interest" we will keep
                    // it. we're using a brute force search here
                    boolean keepThisOne = false;
                    for (QualifiedColumnMetadata termOfInterest : termsOfInterest) {
                        if (termOfInterest.getTableName().equals(metadata.getTableName())
                                && termOfInterest.getName().equals(colMeta.getName())) {
                            keepThisOne = true;
                            break;
                        }
                    }

                    if (!keepThisOne) {
                        continue;
                    }
                }

                final String columnName = colMeta.getName();
                final Comparable columnKey;
                if (orderByItems == null) {
                    columnKey = columnName;
                } else {
                    // the ordering will be done on the selected
                    // "order by" design criteria
                    columnKey = new ComparableContainer<String, Comparable>(columnName,
                            orderByItems.get(colIndex), !graphConfiguration.getGroupReplicates());

                    // TODO remove me!!!!
                    System.out.println("For array " + columnName + " the order by " + "value is: "
                            + orderByItems.get(colIndex));
                    // end of remove me
                }

                rowElemList
                        .add(new ComparableContainer<Double, Comparable>(currRow[colIndex], columnKey, false));
            }

            Collections.sort(rowElemList);

            if (graphConfiguration.getGroupReplicates()) {
                switch (graphConfiguration.getGroupedGraphType()) {
                case BOX_PLOT: {
                    DefaultBoxAndWhiskerCategoryDataset dataset = (DefaultBoxAndWhiskerCategoryDataset) categoryDataset;
                    for (int i = 0; i < rowElemList.size(); i++) {
                        List<Double> groupList = new ArrayList<Double>();
                        groupList.add(rowElemList.get(i).getElement());
                        Comparable colKey = rowElemList.get(i).getComparable();

                        i++;
                        for (; i < rowElemList.size()
                                && rowElemList.get(i).getComparable().equals(colKey); i++) {
                            groupList.add(rowElemList.get(i).getElement());
                        }
                        i--;

                        dataset.add(groupList, probeIds[rowIndex], colKey);
                    }
                }
                    break;

                case SCATTER_PLOT: {
                    DefaultMultiValueCategoryDataset dataset = (DefaultMultiValueCategoryDataset) categoryDataset;
                    for (int i = 0; i < rowElemList.size(); i++) {
                        List<Double> groupList = new ArrayList<Double>();
                        groupList.add(rowElemList.get(i).getElement());
                        Comparable colKey = rowElemList.get(i).getComparable();

                        i++;
                        for (; i < rowElemList.size()
                                && rowElemList.get(i).getComparable().equals(colKey); i++) {
                            groupList.add(rowElemList.get(i).getElement());
                        }
                        i--;

                        dataset.add(groupList, probeIds[rowIndex], colKey);
                    }
                }
                    break;
                }
            } else {
                DefaultCategoryDataset dataset = (DefaultCategoryDataset) categoryDataset;
                for (ComparableContainer<Double, Comparable> rowElem : rowElemList) {
                    dataset.addValue(rowElem.getElement(), probeIds[rowIndex], rowElem.getComparable());
                }
            }
        }

        CategoryAxis xAxis = new CategoryAxis();
        if (graphConfiguration.getGroupReplicates() && orderBy != null) {
            xAxis.setLabel(orderBy.getName());
        } else {
            if (orderBy != null) {
                xAxis.setLabel("Arrays (Ordered By " + orderBy.getName() + ")");
            } else {
                xAxis.setLabel("Arrays");
            }
        }
        xAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90);

        final NumberAxis yAxis;
        if (graphConfiguration.getLog2TransformData()) {
            yAxis = new NumberAxis("log2(Intensity)");
        } else {
            yAxis = new NumberAxis("Intensity");
        }
        yAxis.setAutoRange(true);
        yAxis.setAutoRangeIncludesZero(false);

        // TODO: this is a HACK to deal with auto-range bug in JFreeChart
        //       which occurs when doing the grouped scatter plot
        if (graphConfiguration.getGroupReplicates()
                && graphConfiguration.getGroupedGraphType() == GroupedGraphType.SCATTER_PLOT) {
            double minVal = Double.POSITIVE_INFINITY;
            double maxVal = Double.NEGATIVE_INFINITY;
            for (double[] dataRow : probeDataRows) {
                for (double datum : dataRow) {
                    if (datum > maxVal) {
                        maxVal = datum;
                    }

                    if (datum < minVal) {
                        minVal = datum;
                    }
                }

                if (minVal != Double.POSITIVE_INFINITY && maxVal != Double.NEGATIVE_INFINITY
                        && minVal != maxVal) {
                    yAxis.setAutoRange(false);

                    double margin = (maxVal - minVal) * 0.02;
                    Range yRange = new Range(minVal - margin, maxVal + margin);
                    yAxis.setRange(yRange);
                }
            }
        }
        // END HACK

        final CategoryItemRenderer renderer;
        if (graphConfiguration.getGroupReplicates()) {
            switch (graphConfiguration.getGroupedGraphType()) {
            case BOX_PLOT: {
                BoxAndWhiskerRenderer boxRenderer = new BoxAndWhiskerRenderer();
                boxRenderer.setMaximumBarWidth(0.03);
                renderer = boxRenderer;
            }
                break;

            case SCATTER_PLOT: {
                renderer = new ScatterRenderer();
            }
                break;

            default:
                throw new IllegalArgumentException(
                        "don't know how to deal with plot type: " + graphConfiguration.getGroupedGraphType());
            }
        } else {
            renderer = new LineAndShapeRenderer();
        }
        Plot plot = new CategoryPlot(categoryDataset, xAxis, yAxis, renderer);

        return new JFreeChart("Intensity Values", plot);
    } catch (SQLException ex) {
        LOG.log(Level.SEVERE, "failed to generate image", ex);
        return null;
    }
}