Examples with ValueAxis org.jfree.chart.axis.ValueAxis used on opensource projects

Example 21 with ValueAxis

use of org.jfree.chart.axis.ValueAxis in project nimbus by nimbus-org.

the class CombinedDomainXYPlotFactoryService method createPlot.

// PlotFactoryのJavaDoc
public Plot createPlot(PlotCondition[] plotConditions) throws PlotCreateException {
    CombinedDomainXYPlot combinedPlot = (CombinedDomainXYPlot) copyXYPlot();
    if (plotConditions == null || plotConditions.length == 0) {
        return combinedPlot;
    }
    for (int i = 0; i < subPlotFactoryServices.size(); i++) {
        PlotFactory plotFactory = (PlotFactory) subPlotFactoryServices.get(i);
        Plot plot = plotFactory.createPlot(plotConditions);
        if (plot != null && plot instanceof XYPlot) {
            XYPlot xyPlot = (XYPlot) plot;
            combinedPlot.add(xyPlot, xyPlot.getWeight());
        }
    }
    XYPlotConditionImpl xyPlotCondition = mergeXYPlotCondition(plotConditions);
    if (domainAxisServiceNames != null && domainAxisServiceNames.length > 0) {
        for (int i = 0; i < domainAxisServiceNames.length; i++) {
            ValueAxis domainAxis = (ValueAxis) ServiceManagerFactory.getServiceObject(domainAxisServiceNames[i]);
            if (xyPlotCondition != null) {
                // 横軸ラベルフォント
                if (xyPlotCondition.getDefaultDomainAxisLabelFontName() != null || xyPlotCondition.getDefaultDomainAxisLabelFontStyle() != Integer.MIN_VALUE || xyPlotCondition.getDefaultDomainAxisLabelFontSize() != Integer.MIN_VALUE) {
                    domainAxis.setLabelFont(mergeFont(domainAxis.getLabelFont(), xyPlotCondition.getDefaultDomainAxisLabelFontName(), xyPlotCondition.getDefaultDomainAxisLabelFontStyle(), xyPlotCondition.getDefaultDomainAxisLabelFontSize()));
                } else if (xyPlotCondition.getDomainAxisLabelFontName(i) != null || xyPlotCondition.getDomainAxisLabelFontStyle(i) != Integer.MIN_VALUE || xyPlotCondition.getDomainAxisLabelFontSize(i) != Integer.MIN_VALUE) {
                    domainAxis.setLabelFont(mergeFont(domainAxis.getLabelFont(), xyPlotCondition.getDomainAxisLabelFontName(i), xyPlotCondition.getDomainAxisLabelFontStyle(i), xyPlotCondition.getDomainAxisLabelFontSize(i)));
                }
                // 横軸Tickラベルフォント
                if (xyPlotCondition.getDefaultDomainAxisTickLabelFontName() != null || xyPlotCondition.getDefaultDomainAxisTickLabelFontStyle() != Integer.MIN_VALUE || xyPlotCondition.getDefaultDomainAxisTickLabelFontSize() != Integer.MIN_VALUE) {
                    domainAxis.setTickLabelFont(mergeFont(domainAxis.getTickLabelFont(), xyPlotCondition.getDefaultDomainAxisTickLabelFontName(), xyPlotCondition.getDefaultDomainAxisTickLabelFontStyle(), xyPlotCondition.getDefaultDomainAxisTickLabelFontSize()));
                } else if (xyPlotCondition.getDomainAxisTickLabelFontName(i) != null || xyPlotCondition.getDomainAxisTickLabelFontStyle(i) != Integer.MIN_VALUE || xyPlotCondition.getDomainAxisTickLabelFontSize(i) != Integer.MIN_VALUE) {
                    domainAxis.setTickLabelFont(mergeFont(domainAxis.getTickLabelFont(), xyPlotCondition.getDomainAxisTickLabelFontName(i), xyPlotCondition.getDomainAxisTickLabelFontStyle(i), xyPlotCondition.getDomainAxisTickLabelFontSize(i)));
                }
            }
            combinedPlot.setDomainAxis(i, domainAxis);
        }
    }
    if (getTickUnitAdjusters() != null) {
        // 目盛り調節
        TickUnitAdjuster[] adjusters = getTickUnitAdjusters();
        for (int i = 0; i < adjusters.length; i++) {
            adjusters[i].adjust(combinedPlot);
        }
    }
    return combinedPlot;
}

Example 22 with ValueAxis

use of org.jfree.chart.axis.ValueAxis in project mafscaling by vimsh.

the class MafRescale method createGraghPanel.

private void createGraghPanel(JPanel dataPanel) {
    JFreeChart chart = ChartFactory.createScatterPlot(null, null, null, null, PlotOrientation.VERTICAL, false, true, false);
    chart.setBorderVisible(true);
    mafChartPanel = new MafChartPanel(chart, this);
    GridBagConstraints gbl_chartPanel = new GridBagConstraints();
    gbl_chartPanel.anchor = GridBagConstraints.PAGE_START;
    gbl_chartPanel.insets = insets0;
    gbl_chartPanel.fill = GridBagConstraints.BOTH;
    gbl_chartPanel.weightx = 1.0;
    gbl_chartPanel.weighty = 1.0;
    gbl_chartPanel.gridx = 0;
    gbl_chartPanel.gridy = 2;
    dataPanel.add(mafChartPanel.getChartPanel(), gbl_chartPanel);
    XYSplineRenderer lineRenderer = new XYSplineRenderer(3);
    lineRenderer.setUseFillPaint(true);
    lineRenderer.setBaseToolTipGenerator(new StandardXYToolTipGenerator(StandardXYToolTipGenerator.DEFAULT_TOOL_TIP_FORMAT, new DecimalFormat("0.00"), new DecimalFormat("0.00")));
    Stroke stroke = new BasicStroke(2.0f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 1.0f, null, 0.0f);
    lineRenderer.setSeriesStroke(0, stroke);
    lineRenderer.setSeriesStroke(1, stroke);
    lineRenderer.setSeriesPaint(0, new Color(201, 0, 0));
    lineRenderer.setSeriesPaint(1, new Color(0, 0, 255));
    lineRenderer.setSeriesShape(0, ShapeUtilities.createDiamond((float) 2.5));
    lineRenderer.setSeriesShape(1, ShapeUtilities.createUpTriangle((float) 2.5));
    ValueAxis mafvDomain = new NumberAxis(XAxisName);
    ValueAxis mafgsRange = new NumberAxis(YAxisName);
    XYSeriesCollection lineDataset = new XYSeriesCollection();
    lineDataset.addSeries(currMafData);
    lineDataset.addSeries(corrMafData);
    XYPlot plot = chart.getXYPlot();
    plot.setRangePannable(true);
    plot.setDomainPannable(true);
    plot.setDomainGridlinePaint(Color.DARK_GRAY);
    plot.setRangeGridlinePaint(Color.DARK_GRAY);
    plot.setBackgroundPaint(new Color(224, 224, 224));
    plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
    plot.setDataset(0, lineDataset);
    plot.setRenderer(0, lineRenderer);
    plot.setDomainAxis(0, mafvDomain);
    plot.setRangeAxis(0, mafgsRange);
    plot.mapDatasetToDomainAxis(0, 0);
    plot.mapDatasetToRangeAxis(0, 0);
    LegendTitle legend = new LegendTitle(plot.getRenderer());
    legend.setItemFont(new Font("Arial", 0, 10));
    legend.setPosition(RectangleEdge.TOP);
    chart.addLegend(legend);
}

Example 23 with ValueAxis

use of org.jfree.chart.axis.ValueAxis in project mafscaling by vimsh.

the class LogView method createGraghPanel.

private void createGraghPanel() {
    JFreeChart chart = ChartFactory.createXYLineChart(null, null, null, null, PlotOrientation.VERTICAL, false, true, false);
    chartPanel = new ChartPanel(chart, true, true, true, true, true);
    chartPanel.setFocusable(true);
    chartPanel.setAutoscrolls(true);
    chartPanel.setPopupMenu(null);
    chart.setBackgroundPaint(chartColor);
    rpmDataset = new XYSeriesCollection();
    rpmPlotRenderer = new XYLineAndShapeRenderer();
    dataset = new XYSeriesCollection();
    plotRenderer = new XYLineAndShapeRenderer();
    NumberAxis xAxis = new NumberAxis();
    xAxis.setTickLabelsVisible(false);
    xAxis.setTickLabelPaint(Color.WHITE);
    xAxis.setAutoRangeIncludesZero(false);
    NumberAxis yAxis = new NumberAxis();
    yAxis.setTickLabelsVisible(false);
    yAxis.setTickLabelPaint(Color.WHITE);
    yAxis.setAutoRangeIncludesZero(false);
    NumberAxis y2Axis = new NumberAxis();
    y2Axis.setTickLabelsVisible(false);
    y2Axis.setTickLabelPaint(Color.WHITE);
    y2Axis.setAutoRangeIncludesZero(false);
    plot = chartPanel.getChart().getXYPlot();
    plot.setRangePannable(true);
    plot.setDomainPannable(true);
    plot.setDomainGridlinePaint(Color.LIGHT_GRAY);
    plot.setRangeGridlinePaint(Color.LIGHT_GRAY);
    plot.setBackgroundPaint(chartBgColor);
    plot.setDataset(0, rpmDataset);
    plot.setRenderer(0, rpmPlotRenderer);
    plot.setDomainAxis(0, xAxis);
    plot.setRangeAxis(0, yAxis);
    plot.mapDatasetToDomainAxis(0, 0);
    plot.mapDatasetToRangeAxis(0, 0);
    plot.setDataset(1, dataset);
    plot.setRenderer(1, plotRenderer);
    plot.setRangeAxis(1, y2Axis);
    plot.mapDatasetToDomainAxis(1, 0);
    plot.mapDatasetToRangeAxis(1, 1);
    LegendTitle legend = new LegendTitle(plot);
    legend.setItemFont(new Font("Arial", 0, 10));
    legend.setPosition(RectangleEdge.TOP);
    legend.setItemPaint(Color.WHITE);
    chart.addLegend(legend);
    xMarker = new XYDomainMutilineAnnotation();
    xMarker.setDefaultPaint(Color.WHITE);
    plot.addAnnotation(xMarker);
    chartMouseListener = new ChartMouseListener() {

        @Override
        public void chartMouseMoved(ChartMouseEvent event) {
            try {
                Rectangle2D dataArea = chartPanel.getChartRenderingInfo().getPlotInfo().getDataArea();
                Point2D p = chartPanel.translateScreenToJava2D(event.getTrigger().getPoint());
                double x = plot.getDomainAxis().java2DToValue(p.getX(), dataArea, plot.getDomainAxisEdge());
                boolean isLeft = (p.getX() < (dataArea.getMaxX() - dataArea.getMinX()) / 2) ? true : false;
                if (setMarkers(x, isLeft)) {
                    try {
                        int selectedCol = logDataTable.getTable().getSelectedColumn();
                        if (selectedCol < 0)
                            selectedCol = 0;
                        if (logPlayWindow == null || startMarker != null || endMarker != null) {
                            logDataTable.getTable().setRowSelectionInterval((int) x, (int) x);
                            logDataTable.getTable().changeSelection((int) x, selectedCol, false, false);
                        } else {
                            logPlayWindow.setProgressBar((int) x);
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            } catch (Exception e) {
                e.printStackTrace();
            }
        }

        @Override
        public void chartMouseClicked(ChartMouseEvent event) {
            chartPanel.requestFocusInWindow();
            if (logPlayWindow == null)
                return;
            if (xMarker.count() == 0)
                return;
            Rectangle2D dataArea = chartPanel.getChartRenderingInfo().getPlotInfo().getDataArea();
            Point2D p = chartPanel.translateScreenToJava2D(event.getTrigger().getPoint());
            double x = plot.getDomainAxis().java2DToValue(p.getX(), dataArea, plot.getDomainAxisEdge());
            if (x < 0 || (int) x >= logDataTable.getRowCount())
                return;
            if (SwingUtilities.isLeftMouseButton(event.getTrigger())) {
                if (startMarker == null) {
                    startMarker = new ValueMarker(x);
                    startMarker.setPaint(Color.GREEN);
                    startMarker.setStroke(new BasicStroke(1.5f));
                    plot.addDomainMarker(startMarker);
                } else {
                    plot.removeDomainMarker(startMarker);
                    startMarker = null;
                }
            } else if (SwingUtilities.isRightMouseButton(event.getTrigger())) {
                if (endMarker == null) {
                    endMarker = new ValueMarker(x);
                    endMarker.setPaint(Color.GREEN);
                    endMarker.setStroke(new BasicStroke(1.5f));
                    plot.addDomainMarker(endMarker);
                } else {
                    plot.removeDomainMarker(endMarker);
                    endMarker = null;
                }
            }
            chartPanel.repaint();
            logPlayWindow.setStartEndArea(startMarker, endMarker);
        }
    };
    chartPanel.addChartMouseListener(chartMouseListener);
    chartPanel.addKeyListener(new KeyListener() {

        public void keyPressed(KeyEvent e) {
            if (!chartPanel.hasFocus())
                return;
            int keyCode = e.getKeyCode();
            if (keyCode < KeyEvent.VK_LEFT || keyCode > KeyEvent.VK_DOWN)
                return;
            ValueAxis axis = null;
            if (keyCode == KeyEvent.VK_LEFT || keyCode == KeyEvent.VK_RIGHT)
                axis = ((XYPlot) chartPanel.getChart().getXYPlot()).getDomainAxis();
            else
                axis = ((XYPlot) chartPanel.getChart().getXYPlot()).getRangeAxis();
            if (axis != null) {
                double delta = (axis.getUpperBound() - axis.getLowerBound()) / 100.0;
                if (keyCode == KeyEvent.VK_LEFT || keyCode == KeyEvent.VK_DOWN)
                    axis.setRange(axis.getLowerBound() - delta, axis.getUpperBound() - delta);
                else if (keyCode == KeyEvent.VK_UP || keyCode == KeyEvent.VK_RIGHT)
                    axis.setRange(axis.getLowerBound() + delta, axis.getUpperBound() + delta);
            }
        }

        public void keyReleased(KeyEvent arg0) {
        }

        public void keyTyped(KeyEvent arg0) {
        }
    });
}

Example 24 with ValueAxis

use of org.jfree.chart.axis.ValueAxis in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method writeDetailedFactorAnalysis.

private boolean writeDetailedFactorAnalysis(ExpressionExperiment ee, OutputStream os) throws Exception {
    SVDValueObject svdo = svdService.getSvdFactorAnalysis(ee.getId());
    if (svdo == null)
        return false;
    if (svdo.getFactors().isEmpty() && svdo.getDates().isEmpty()) {
        return false;
    }
    Map<Integer, Map<Long, Double>> factorCorrelations = svdo.getFactorCorrelations();
    // Map<Integer, Map<Long, Double>> factorPvalues = svdo.getFactorPvalues();
    Map<Integer, Double> dateCorrelations = svdo.getDateCorrelations();
    assert ee.getId().equals(svdo.getId());
    // need the experimental design
    ee = expressionExperimentService.thawLite(ee);
    int maxWidth = 30;
    Map<Long, String> efs = this.getFactorNames(ee, maxWidth);
    Map<Long, ExperimentalFactor> efIdMap = EntityUtils.getIdMap(ee.getExperimentalDesign().getExperimentalFactors());
    Collection<Long> continuousFactors = new HashSet<>();
    for (ExperimentalFactor ef : ee.getExperimentalDesign().getExperimentalFactors()) {
        boolean isContinous = ExperimentalDesignUtils.isContinuous(ef);
        if (isContinous) {
            continuousFactors.add(ef.getId());
        }
    }
    /*
         * Make plots of the dates vs. PCs, factors vs. PCs.
         */
    int MAX_COMP = 3;
    Map<Long, List<JFreeChart>> charts = new LinkedHashMap<>();
    ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme());
    /*
         * FACTORS
         */
    String componentShorthand = "PC";
    for (Integer component : factorCorrelations.keySet()) {
        if (component >= MAX_COMP)
            break;
        String xaxisLabel = componentShorthand + (component + 1);
        for (Long efId : factorCorrelations.get(component).keySet()) {
            /*
                 * Should not happen.
                 */
            if (!efs.containsKey(efId)) {
                log.warn("No experimental factor with id " + efId);
                continue;
            }
            if (!svdo.getFactors().containsKey(efId)) {
                // this should not happen.
                continue;
            }
            boolean isCategorical = !continuousFactors.contains(efId);
            Map<Long, String> categories = new HashMap<>();
            if (isCategorical) {
                this.getCategories(efIdMap, efId, categories);
            }
            if (!charts.containsKey(efId)) {
                charts.put(efId, new ArrayList<JFreeChart>());
            }
            Double a = factorCorrelations.get(component).get(efId);
            // unique?
            String plotname = (efs.get(efId) == null ? "?" : efs.get(efId)) + " " + xaxisLabel;
            if (a != null && !Double.isNaN(a)) {
                String title = plotname + " " + String.format("%.2f", a);
                List<Double> values = svdo.getFactors().get(efId);
                Double[] eigenGene = this.getEigenGene(svdo, component);
                assert values.size() == eigenGene.length;
                /*
                     * Plot eigengene vs values, add correlation to the plot
                     */
                JFreeChart chart;
                if (isCategorical) {
                    /*
                         * Categorical factor
                         */
                    // use the absolute value of the correlation, since direction is arbitrary.
                    title = plotname + " " + String.format("r=%.2f", Math.abs(a));
                    DefaultMultiValueCategoryDataset dataset = new DefaultMultiValueCategoryDataset();
                    /*
                         * What this code does is organize the factor values by the groups.
                         */
                    Map<String, List<Double>> groupedValues = new TreeMap<>();
                    for (int i = 0; i < values.size(); i++) {
                        Long fvId = values.get(i).longValue();
                        String fvValue = categories.get(fvId);
                        if (fvValue == null) {
                            // is this all we need to do?
                            continue;
                        }
                        if (!groupedValues.containsKey(fvValue)) {
                            groupedValues.put(fvValue, new ArrayList<Double>());
                        }
                        groupedValues.get(fvValue).add(eigenGene[i]);
                        if (log.isDebugEnabled())
                            log.debug(fvValue + " " + values.get(i));
                    }
                    for (String key : groupedValues.keySet()) {
                        dataset.add(groupedValues.get(key), plotname, key);
                    }
                    // don't show the name of the X axis: it's redundant with the title.
                    NumberAxis rangeAxis = new NumberAxis(xaxisLabel);
                    rangeAxis.setAutoRangeIncludesZero(false);
                    // rangeAxis.setAutoRange( false );
                    rangeAxis.setAutoRangeMinimumSize(4.0);
                    // rangeAxis.setRange( new Range( -2, 2 ) );
                    CategoryPlot plot = new CategoryPlot(dataset, new CategoryAxis(null), rangeAxis, new ScatterRenderer());
                    plot.setRangeGridlinesVisible(false);
                    plot.setDomainGridlinesVisible(false);
                    chart = new JFreeChart(title, new Font("SansSerif", Font.BOLD, 12), plot, false);
                    ScatterRenderer renderer = (ScatterRenderer) plot.getRenderer();
                    float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP);
                    renderer.setSeriesFillPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f));
                    renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
                    renderer.setUseOutlinePaint(false);
                    renderer.setUseFillPaint(true);
                    renderer.setBaseFillPaint(Color.white);
                    CategoryAxis domainAxis = plot.getDomainAxis();
                    domainAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);
                } else {
                    /*
                         * Continuous value factor
                         */
                    DefaultXYDataset series = new DefaultXYDataset();
                    series.addSeries(plotname, new double[][] { ArrayUtils.toPrimitive(values.toArray(new Double[] {})), ArrayUtils.toPrimitive(eigenGene) });
                    // don't show x-axis label, which would otherwise be efs.get( efId )
                    chart = ChartFactory.createScatterPlot(title, null, xaxisLabel, series, PlotOrientation.VERTICAL, false, false, false);
                    XYPlot plot = chart.getXYPlot();
                    plot.setRangeGridlinesVisible(false);
                    plot.setDomainGridlinesVisible(false);
                    XYItemRenderer renderer = plot.getRenderer();
                    renderer.setBasePaint(Color.white);
                    renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
                    float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP);
                    renderer.setSeriesPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f));
                    plot.setRenderer(renderer);
                }
                chart.getTitle().setFont(new Font("SansSerif", Font.BOLD, 12));
                charts.get(efId).add(chart);
            }
        }
    }
    /*
         * DATES
         */
    charts.put(-1L, new ArrayList<JFreeChart>());
    for (Integer component : dateCorrelations.keySet()) {
        String xaxisLabel = componentShorthand + (component + 1);
        List<Date> dates = svdo.getDates();
        if (dates.isEmpty())
            break;
        long secspan = ubic.basecode.util.DateUtil.numberOfSecondsBetweenDates(dates);
        if (component >= MAX_COMP)
            break;
        Double a = dateCorrelations.get(component);
        if (a != null && !Double.isNaN(a)) {
            Double[] eigenGene = svdo.getvMatrix().getColObj(component);
            /*
                 * Plot eigengene vs values, add correlation to the plot
                 */
            TimeSeries series = new TimeSeries("Dates vs. eigen" + (component + 1));
            int i = 0;
            for (Date d : dates) {
                // if span is less than an hour, retain the minute.
                if (secspan < 60 * 60) {
                    series.addOrUpdate(new Minute(d), eigenGene[i++]);
                } else {
                    series.addOrUpdate(new Hour(d), eigenGene[i++]);
                }
            }
            TimeSeriesCollection dataset = new TimeSeriesCollection();
            dataset.addSeries(series);
            JFreeChart chart = ChartFactory.createTimeSeriesChart("Dates: " + xaxisLabel + " " + String.format("r=%.2f", a), null, xaxisLabel, dataset, false, false, false);
            XYPlot xyPlot = chart.getXYPlot();
            chart.getTitle().setFont(new Font("SansSerif", Font.BOLD, 12));
            // standard renderer makes lines.
            XYDotRenderer renderer = new XYDotRenderer();
            renderer.setBaseFillPaint(Color.white);
            renderer.setDotHeight(3);
            renderer.setDotWidth(3);
            // has no effect, need dotheight.
            renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
            float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP);
            renderer.setSeriesPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f));
            ValueAxis domainAxis = xyPlot.getDomainAxis();
            domainAxis.setVerticalTickLabels(true);
            xyPlot.setRenderer(renderer);
            xyPlot.setRangeGridlinesVisible(false);
            xyPlot.setDomainGridlinesVisible(false);
            charts.get(-1L).add(chart);
        }
    }
    /*
         * Plot in a grid, with each factor as a column. FIXME What if we have too many factors to fit on the screen?
         */
    int columns = (int) Math.ceil(charts.size());
    int perChartSize = ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX;
    BufferedImage image = new BufferedImage(columns * perChartSize, MAX_COMP * perChartSize, BufferedImage.TYPE_INT_ARGB);
    Graphics2D g2 = image.createGraphics();
    int currentX = 0;
    int currentY = 0;
    for (Long id : charts.keySet()) {
        for (JFreeChart chart : charts.get(id)) {
            this.addChartToGraphics(chart, g2, currentX, currentY, perChartSize, perChartSize);
            if (currentY + perChartSize < MAX_COMP * perChartSize) {
                currentY += perChartSize;
            } else {
                currentY = 0;
                currentX += perChartSize;
            }
        }
    }
    os.write(ChartUtilities.encodeAsPNG(image));
    return true;
}

Example 25 with ValueAxis

use of org.jfree.chart.axis.ValueAxis in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method writeMeanVariance.

/**
 * @param os  response output stream
 * @param mvr MeanVarianceRelation object to plot
 * @return true if mvr data points were plotted
 */
private boolean writeMeanVariance(OutputStream os, MeanVarianceRelation mvr, Double size) throws Exception {
    // if number of datapoints > THRESHOLD then alpha = TRANSLUCENT, else alpha = OPAQUE
    final int THRESHOLD = 1000;
    final int TRANSLUCENT = 50;
    final int OPAQUE = 255;
    // Set maximum plot range to Y_MAX + YRANGE * OFFSET to leave some extra white space
    final double OFFSET_FACTOR = 0.05f;
    // set the final image size to be the minimum of MAX_IMAGE_SIZE_PX or size
    final int MAX_IMAGE_SIZE_PX = 5;
    if (mvr == null) {
        return false;
    }
    // get data points
    XYSeriesCollection collection = this.getMeanVariance(mvr);
    if (collection.getSeries().size() == 0) {
        return false;
    }
    ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme());
    JFreeChart chart = ChartFactory.createScatterPlot("", "mean (log2)", "variance (log2)", collection, PlotOrientation.VERTICAL, false, false, false);
    // adjust colors and shapes
    XYRegressionRenderer renderer = new XYRegressionRenderer();
    renderer.setBasePaint(Color.white);
    int alpha = collection.getSeries(0).getItemCount() > THRESHOLD ? TRANSLUCENT : OPAQUE;
    renderer.setSeriesPaint(0, new Color(0, 0, 0, alpha));
    renderer.setSeriesPaint(1, Color.red);
    renderer.setSeriesStroke(1, new BasicStroke(1));
    renderer.setSeriesShape(0, new Ellipse2D.Double(4, 4, 4, 4));
    renderer.setSeriesShapesFilled(0, false);
    renderer.setSeriesLinesVisible(0, false);
    renderer.setSeriesLinesVisible(1, true);
    renderer.setSeriesShapesVisible(1, false);
    XYPlot plot = chart.getXYPlot();
    plot.setRenderer(renderer);
    plot.setRangeGridlinesVisible(false);
    plot.setDomainGridlinesVisible(false);
    // adjust the chart domain and ranges
    double yRange = collection.getSeries(0).getMaxY() - collection.getSeries(0).getMinY();
    double xRange = collection.getSeries(0).getMaxX() - collection.getSeries(0).getMinX();
    double ybuffer = (yRange) * OFFSET_FACTOR;
    double xbuffer = (xRange) * OFFSET_FACTOR;
    double newYMin = collection.getSeries(0).getMinY() - ybuffer;
    double newYMax = collection.getSeries(0).getMaxY() + ybuffer;
    double newXMin = collection.getSeries(0).getMinX() - xbuffer;
    double newXMax = collection.getSeries(0).getMaxX() + xbuffer;
    ValueAxis yAxis = new NumberAxis("Variance");
    yAxis.setRange(newYMin, newYMax);
    ValueAxis xAxis = new NumberAxis("Mean");
    xAxis.setRange(newXMin, newXMax);
    chart.getXYPlot().setRangeAxis(yAxis);
    chart.getXYPlot().setDomainAxis(xAxis);
    int finalSize = (int) Math.min(MAX_IMAGE_SIZE_PX * ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX, size * ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX);
    ChartUtilities.writeChartAsPNG(os, chart, finalSize, finalSize);
    return true;
}