Example usage for org.jfree.chart.plot CategoryPlot getRenderer

List of usage examples for org.jfree.chart.plot CategoryPlot getRenderer

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Introduction

In this page you can find the example usage for org.jfree.chart.plot CategoryPlot getRenderer.

Prototype

public CategoryItemRenderer getRenderer()

Source Link

Document

Returns a reference to the renderer for the plot.

Usage

From source file:mzmatch.ipeak.normalisation.VanDeSompele.java

public static void main(String args[]) {
    try {/*from   w w  w .  j  a  v a2  s  .  c  o  m*/
        Tool.init();

        // parse the commandline options
        Options options = new Options();
        CmdLineParser cmdline = new CmdLineParser(options);

        // check whether we need to show the help
        cmdline.parse(args);
        if (options.help) {
            Tool.printHeader(System.out, application, version);
            cmdline.printUsage(System.out, "");
            return;
        }

        if (options.verbose) {
            Tool.printHeader(System.out, application, version);
            cmdline.printOptions();
        }

        // check the command-line parameters
        {
            // if the output directories do not exist, create them
            if (options.output != null)
                Tool.createFilePath(options.output, true);
        }

        // load the data
        if (options.verbose)
            System.out.println("Loading data");
        ParseResult result = PeakMLParser.parse(new FileInputStream(options.input), true);

        Header header = result.header;
        IPeakSet<IPeakSet<? extends IPeak>> peaksets = (IPeakSet<IPeakSet<? extends IPeak>>) result.measurement;

        int nrmeasurements = header.getNrMeasurementInfos();

        // remove the stability factor annotation
        for (IPeak peak : peaksets)
            peak.removeAnnotation("stability factor");

        // load the database
        if (options.verbose)
            System.out.println("Loading the molecule database");
        HashMap<String, Molecule> database = MoleculeIO.parseXml(new FileInputStream(options.database));

        // filter the set to include only identifiable metabolites
        if (options.verbose)
            System.out.println("Creating selection");
        Vector<IPeakSet<? extends IPeak>> selection = new Vector<IPeakSet<? extends IPeak>>();
        for (Molecule molecule : database.values()) {
            double mass = molecule.getMass(Mass.MONOISOTOPIC);
            double delta = PeriodicTable.PPM(mass, options.ppm);

            // get the most intense peak containing all the measurements
            Vector<IPeakSet<? extends IPeak>> neighbourhoud = peaksets.getPeaksInMassRange(mass - delta,
                    mass + delta);
            Collections.sort(neighbourhoud, IPeak.sort_intensity_descending);
            for (IPeakSet<? extends IPeak> neighbour : neighbourhoud)
                if (count(neighbour) == nrmeasurements) {
                    selection.add(neighbour);
                    break;
                }
        }

        // calculate the stability factor for each peak in the selection
        if (options.verbose)
            System.out.println("Calculating stability factors");
        for (int peakid1 = 0; peakid1 < selection.size(); ++peakid1) {
            double stddeviations[] = new double[selection.size()];

            IPeakSet<? extends IPeak> peakset1 = selection.get(peakid1);
            for (int peakid2 = 0; peakid2 < selection.size(); ++peakid2) {
                IPeakSet<? extends IPeak> peakset2 = selection.get(peakid2);

                double values[] = new double[nrmeasurements];
                for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
                    int measurementid1 = peakset1.get(measurementid).getMeasurementID();
                    int setid1 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid1));
                    int measurementid2 = peakset2.get(measurementid).getMeasurementID();
                    int setid2 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid2));
                    if (setid1 != setid2 || measurementid1 != measurementid2)
                        System.err.println("[WARNING]: differing setid or spectrumid for comparison");

                    values[measurementid] = Math.log(peakset1.get(measurementid).getIntensity()
                            / peakset2.get(measurementid).getIntensity()) / Math.log(2);
                }
                stddeviations[peakid2] = Statistical.stddev(values);
            }

            peakset1.addAnnotation("stability factor", Statistical.mean(stddeviations));
        }

        // sort on the stability factor
        Collections.sort(selection, new IPeak.AnnotationAscending("stability factor"));

        // take the top 10% and calculate the geometric mean
        if (options.verbose)
            System.out.println("Calculating normalisation factors");
        int nrselected = (int) (0.1 * selection.size());
        if (nrselected < 10)
            nrselected = (10 < selection.size() ? 10 : selection.size());
        double normalization_factors[] = new double[nrmeasurements];
        for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
            double values[] = new double[nrselected];
            for (int i = 0; i < nrselected; ++i) {
                IPeak peak = selection.get(i).get(measurementid);
                values[i] = peak.getIntensity();
            }
            normalization_factors[measurementid] = Statistical.geomean(values);
        }

        // scale the found normalization factors
        double maxnf = Statistical.max(normalization_factors);
        for (int sampleid = 0; sampleid < nrmeasurements; ++sampleid)
            normalization_factors[sampleid] /= maxnf;

        // write the selection if needed
        if (options.selection != null) {
            if (options.verbose)
                System.out.println("Writing original selection data");

            PeakMLWriter.write(result.header, selection, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection)), null);
        }

        // normalize all the peaks
        if (options.verbose)
            System.out.println("Normalizing all the entries");
        for (IPeakSet<? extends IPeak> peakset : peaksets) {
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
                // TODO why did I do this again ?
                int id = 0;
                int setid = 0;
                int spectrumid = 0;
                for (int i = 0; i < header.getNrSetInfos(); ++i) {
                    SetInfo set = header.getSetInfos().get(i);

                    if (id + set.getNrMeasurementIDs() > measurementid) {
                        setid = i;
                        spectrumid = measurementid - id;
                        break;
                    } else
                        id += set.getNrMeasurementIDs();
                }

                MassChromatogram<Peak> masschromatogram = null;
                for (IPeak p : peakset) {
                    int mymeasurementid = p.getMeasurementID();
                    int mysetid = header.indexOfSetInfo(header.getSetInfoForMeasurementID(mymeasurementid));
                    if (mysetid == setid && mymeasurementid == spectrumid) {
                        masschromatogram = (MassChromatogram<Peak>) p;
                        break;
                    }
                }
                if (masschromatogram == null)
                    continue;

                for (IPeak peak : masschromatogram.getPeaks())
                    peak.setIntensity(peak.getIntensity() / normalization_factors[measurementid]);
            }
        }

        // write the selection if needed
        if (options.selection_normalized != null) {
            if (options.verbose)
                System.out.println("Writing the normalized selection data");

            PeakMLWriter.write(result.header, selection, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection_normalized)), null);
        }

        // write the factors if needed
        if (options.factors != null) {
            if (options.verbose)
                System.out.println("Writing the normalization factors");

            PrintStream out = new PrintStream(options.factors);
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid)
                out.println(header.getMeasurementInfo(measurementid).getLabel() + "\t"
                        + normalization_factors[measurementid]);
        }

        // write the plot if needed
        if (options.img != null) {
            if (options.verbose)
                System.out.println("Writing the graph");

            DefaultCategoryDataset dataset = new DefaultCategoryDataset();
            JFreeChart linechart = ChartFactory.createLineChart(null, "measurement", "normalization factor",
                    dataset, PlotOrientation.VERTICAL, false, // legend
                    false, // tooltips
                    false // urls
            );

            CategoryPlot plot = (CategoryPlot) linechart.getPlot();
            CategoryAxis axis = (CategoryAxis) plot.getDomainAxis();
            axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);
            LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer();

            renderer.setSeriesShapesFilled(0, true);
            renderer.setSeriesShapesVisible(0, true);

            linechart.setBackgroundPaint(Color.WHITE);
            linechart.setBorderVisible(false);
            linechart.setAntiAlias(true);

            plot.setBackgroundPaint(Color.WHITE);
            plot.setDomainGridlinesVisible(true);
            plot.setRangeGridlinesVisible(true);

            // create the datasets
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid)
                dataset.addValue(normalization_factors[measurementid], "",
                        header.getMeasurementInfo(measurementid).getLabel());
            JFreeChartTools.writeAsPDF(new FileOutputStream(options.img), linechart, 800, 500);
        }

        // write the normalized values
        if (options.verbose)
            System.out.println("Writing the normalized data");
        PeakMLWriter.write(result.header, peaksets.getPeaks(), null,
                new GZIPOutputStream(new FileOutputStream(options.output)), null);
    } catch (Exception e) {
        Tool.unexpectedError(e, application);
    }
}

From source file:org.jfree.chart.demo.GradientPaintTransformerDemo1.java

public static JPanel createDemoPanel() {
    JPanel jpanel = new JPanel(new GridLayout(2, 2));
    jpanel.setPreferredSize(new Dimension(800, 600));
    CategoryDataset categorydataset = createDataset();
    JFreeChart jfreechart = createChart("Type: VERTICAL", categorydataset);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer();
    barrenderer.setDrawBarOutline(false);
    barrenderer.setSeriesPaint(0, new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, Color.yellow));
    barrenderer.setSeriesPaint(1, new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, Color.green));
    barrenderer.setGradientPaintTransformer(
            new StandardGradientPaintTransformer(GradientPaintTransformType.VERTICAL));
    ChartPanel chartpanel = new ChartPanel(jfreechart);
    jpanel.add(chartpanel);// w w w .j av  a 2  s . com
    JFreeChart jfreechart1 = createChart("Type: HORIZONTAL", categorydataset);
    CategoryPlot categoryplot1 = (CategoryPlot) jfreechart1.getPlot();
    BarRenderer barrenderer1 = (BarRenderer) categoryplot1.getRenderer();
    barrenderer1.setDrawBarOutline(false);
    barrenderer1.setSeriesPaint(0, new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, Color.yellow));
    barrenderer1.setSeriesPaint(1, new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, Color.green));
    barrenderer1.setGradientPaintTransformer(
            new StandardGradientPaintTransformer(GradientPaintTransformType.HORIZONTAL));
    ChartPanel chartpanel1 = new ChartPanel(jfreechart1);
    jpanel.add(chartpanel1);
    JFreeChart jfreechart2 = createChart("Type: CENTER_VERTICAL", categorydataset);
    CategoryPlot categoryplot2 = (CategoryPlot) jfreechart2.getPlot();
    BarRenderer barrenderer2 = (BarRenderer) categoryplot2.getRenderer();
    barrenderer2.setDrawBarOutline(false);
    barrenderer2.setSeriesPaint(0, new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, Color.yellow));
    barrenderer2.setSeriesPaint(1, new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, Color.green));
    barrenderer2.setGradientPaintTransformer(
            new StandardGradientPaintTransformer(GradientPaintTransformType.CENTER_VERTICAL));
    ChartPanel chartpanel2 = new ChartPanel(jfreechart2);
    jpanel.add(chartpanel2);
    JFreeChart jfreechart3 = createChart("Type: CENTER_HORIZONTAL", categorydataset);
    CategoryPlot categoryplot3 = (CategoryPlot) jfreechart3.getPlot();
    BarRenderer barrenderer3 = (BarRenderer) categoryplot3.getRenderer();
    barrenderer3.setDrawBarOutline(false);
    barrenderer3.setSeriesPaint(0, new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, Color.yellow));
    barrenderer3.setSeriesPaint(1, new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, Color.green));
    barrenderer3.setGradientPaintTransformer(
            new StandardGradientPaintTransformer(GradientPaintTransformType.CENTER_HORIZONTAL));
    ChartPanel chartpanel3 = new ChartPanel(jfreechart3);
    jpanel.add(chartpanel3);
    return jpanel;
}

From source file:org.jfree.chart.demo.MouseOverDemo1.java

public static JPanel createDemoPanel() {
    JFreeChart jfreechart = createChart(createDataset());
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    MyBarRenderer mybarrenderer = (MyBarRenderer) categoryplot.getRenderer();
    MyDemoPanel mydemopanel = new MyDemoPanel(mybarrenderer);
    ChartPanel chartpanel = new ChartPanel(jfreechart);
    mydemopanel.addChart(jfreechart);//from w  w  w  . j a  v  a  2  s. c om
    chartpanel.addChartMouseListener(mydemopanel);
    mydemopanel.add(chartpanel);
    return mydemopanel;
}

From source file:net.imglib2.script.analysis.BarChart.java

static private final void setBarTheme(final JFreeChart chart) {
    CategoryPlot plot = (CategoryPlot) chart.getPlot();
    BarRenderer renderer = (BarRenderer) plot.getRenderer();
    renderer.setSeriesOutlinePaint(0, Color.lightGray);
    renderer.setShadowVisible(false);/*from w  ww.  j  a v  a  2 s. co  m*/
    renderer.setDrawBarOutline(true);
    setBackgroundDefault(chart);
}

From source file:org.jfree.chart.demo.StackedBarChartDemo6.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createStackedBarChart("Stacked Bar Chart Demo 6", "Category", "Value",
            categorydataset, PlotOrientation.HORIZONTAL, true, true, false);
    jfreechart.setBackgroundPaint(Color.white);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setBackgroundPaint(Color.lightGray);
    categoryplot.setRangeGridlinePaint(Color.white);
    StackedBarRenderer stackedbarrenderer = (StackedBarRenderer) categoryplot.getRenderer();
    stackedbarrenderer.setDrawBarOutline(false);
    long l = System.currentTimeMillis();
    stackedbarrenderer.setBase(l);// w w w  .j  a v  a 2  s. c  o  m
    DateAxis dateaxis = new DateAxis("Date");
    dateaxis.setLowerMargin(0.0D);
    categoryplot.setRangeAxis(dateaxis);
    return jfreechart;
}

From source file:com.compomics.pepshell.view.statistics.JFreeChartPanel.java

/**
 * Enable shadow of renderer? JFreeChart 1.0.11 changed the <b>default</b>
 * look by painting shadows for bars. To revert back to the old look, you
 * can disable the shadows with this method.
 *
 * @param chart JFreeChart.//from  w  ww.ja  va2s  .com
 * @param state False, to disable shadow-
 * @since 4.1.0
 */
private static void setShadowVisible(final JFreeChart chart, final boolean state) {
    if (chart != null) {
        final Plot p = chart.getPlot();
        if (p instanceof XYPlot) {
            final XYPlot xyplot = (XYPlot) p;
            final XYItemRenderer xyItemRenderer = xyplot.getRenderer();
            if (xyItemRenderer instanceof XYBarRenderer) {
                final XYBarRenderer br = (XYBarRenderer) xyItemRenderer;
                br.setBarPainter(new StandardXYBarPainter());
                br.setShadowVisible(state);
            }
        } else if (p instanceof CategoryPlot) {
            final CategoryPlot categoryPlot = (CategoryPlot) p;
            final CategoryItemRenderer categoryItemRenderer = categoryPlot.getRenderer();
            if (categoryItemRenderer instanceof BarRenderer) {
                final BarRenderer br = (BarRenderer) categoryItemRenderer;
                br.setBarPainter(new StandardBarPainter());
                br.setShadowVisible(state);
            }
        }
    }
}

From source file:graficos.GraficoGantt.java

private static JFreeChart crearGrafico(IntervalCategoryDataset cjto_datos) {
    JFreeChart grafico = ChartFactory.createGanttChart("Diagrama de Gantt", // Ttulo
            "Actividad", // Ttulo eje x
            "Fecha", // Ttulo eje y
            cjto_datos, // Datos
            true, // Incluir leyenda
            true, // Incluir tooltips
            false // Incluir URLs
    );/*  w  w  w .  jav a  2 s .  c o m*/
    grafico.setBackgroundPaint(new Color(240, 240, 240));
    grafico.getPlot().zoom(0.0);
    CategoryPlot categoriaPlot = (CategoryPlot) grafico.getPlot();
    GanttRenderer renderer = (GanttRenderer) categoriaPlot.getRenderer();
    renderer.setDrawBarOutline(true);
    // GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, new Color(102, 255, 102), 0.0f, 0.0f, new Color(102, 255, 102));
    renderer.setSeriesPaint(0, new Color(48, 239, 48));
    renderer.setSeriesPaint(1, Color.RED);
    grafico.getPlot().setOutlineVisible(true);
    return grafico;
}

From source file:com.pasi.pdfbox.Main.java

private static JFreeChart createBarChart() {
    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    dataset.addValue(7445, "JFreeSVG", "Warm-up");
    dataset.addValue(24448, "Batik", "Warm-up");
    dataset.addValue(4297, "JFreeSVG", "Test");
    dataset.addValue(21022, "Batik", "Test");

    JFreeChart chart = ChartFactory.createBarChart("Performance: JFreeSVG vs Batik", null /* x-axis label*/,
            "Milliseconds" /* y-axis label */, dataset);
    chart.addSubtitle(//from  w  ww . j ava 2 s .co  m
            new TextTitle("Time to generate 1000 charts in SVG " + "format (lower bars = better performance)"));
    chart.setBackgroundPaint(Color.white);
    CategoryPlot plot = (CategoryPlot) chart.getPlot();

    NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
    rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    BarRenderer renderer = (BarRenderer) plot.getRenderer();
    renderer.setDrawBarOutline(false);
    chart.getLegend().setFrame(BlockBorder.NONE);
    return chart;
}

From source file:org.gaixie.micrite.jfreechart.style.BarStyle.java

/**
 * ???/*  w  w w.  java  2  s .c om*/
 * @param chart JFreeChart
 */
public static void styleOne(JFreeChart chart) {
    CategoryPlot categoryplot = (CategoryPlot) chart.getPlot();
    CategoryDataset dca = categoryplot.getDataset();
    //?
    chart.setBackgroundPaint(null);
    if (dca != null) {
        BarRenderer categoryitemrenderer = (BarRenderer) categoryplot.getRenderer();
        // ?
        categoryitemrenderer.setBaseItemLabelGenerator(new StandardCategoryItemLabelGenerator());
        //            categoryitemrenderer.setBaseItemLabelFont(
        //                    new Font("", Font.PLAIN, 15));
        categoryitemrenderer.setBaseItemLabelsVisible(true);
        //tooltip
        categoryplot.getRenderer()
                .setBaseToolTipGenerator(new StandardCategoryToolTipGenerator("{0}={2}", new DecimalFormat()));
        //?
        for (int i = 0; i < dca.getRowCount(); i++) {
            int colorIdx = i % colors.length;
            categoryitemrenderer.setSeriesPaint(i, colors[colorIdx]);
        }
    } else {
        //?
        categoryplot.setNoDataMessage("NO DATA");
    }
}

From source file:org.jfree.chart.demo.AxisOffsetsDemo1.java

private static JFreeChart createChart(String s, CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createBarChart(s, "Category", "Value", categorydataset,
            PlotOrientation.VERTICAL, false, true, false);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setDomainGridlinesVisible(true);
    NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis();
    numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer();
    barrenderer.setDrawBarOutline(false);
    GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64));
    GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0));
    GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0));
    barrenderer.setSeriesPaint(0, gradientpaint);
    barrenderer.setSeriesPaint(1, gradientpaint1);
    barrenderer.setSeriesPaint(2, gradientpaint2);
    return jfreechart;
}