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

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

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Introduction

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

Prototype

public CategoryAxis getDomainAxis()

Source Link

Document

Returns the domain axis for the plot.

Usage

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

public static void main(String args[]) {
    try {//  ww w  .  j a  v a  2  s  .  com
        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.EventFrequencyDemo1.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createBarChart("Event Frequency Demo", "Category", "Value",
            categorydataset, PlotOrientation.HORIZONTAL, true, true, false);
    jfreechart.setBackgroundPaint(new Color(255, 255, 204));
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.getDomainAxis().setMaximumCategoryLabelWidthRatio(10F);
    categoryplot.setRangeAxis(new DateAxis("Date"));
    StandardCategoryToolTipGenerator standardcategorytooltipgenerator = new StandardCategoryToolTipGenerator("",
            DateFormat.getDateInstance());
    LineAndShapeRenderer lineandshaperenderer = new LineAndShapeRenderer(false, true);
    lineandshaperenderer.setBaseToolTipGenerator(standardcategorytooltipgenerator);
    categoryplot.setRenderer(lineandshaperenderer);
    return jfreechart;
}

From source file:org.jfree.chart.demo.StackedBarChart3DDemo5.java

private static JFreeChart createChart(int i, CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createStackedBarChart3D("Chart " + (i + 1), "Category", "Value",
            categorydataset, PlotOrientation.VERTICAL, false, false, false);
    jfreechart.setBackgroundPaint(Color.white);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.getDomainAxis().setMaximumCategoryLabelLines(2);
    categoryplot.setBackgroundPaint(Color.lightGray);
    categoryplot.setAxisOffset(new RectangleInsets(5D, 5D, 5D, 5D));
    categoryplot.setDomainGridlinePaint(Color.white);
    categoryplot.setRangeGridlinePaint(Color.white);
    ValueAxis valueaxis = categoryplot.getRangeAxis();
    valueaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    return jfreechart;
}

From source file:com.ouc.cpss.view.EmpSaleChartBuilder.java

private static JFreeChart createJFreeChart(CategoryDataset dataset) {
    /**/*from   w ww.j  a  va2  s  . c o  m*/
     * JFreeChart
     */
    //?     
    StandardChartTheme standardChartTheme = new StandardChartTheme("CN");
    //     
    standardChartTheme.setExtraLargeFont(new Font("", Font.BOLD, 20));
    //    
    standardChartTheme.setRegularFont(new Font("", Font.PLAIN, 15));
    //?     
    standardChartTheme.setLargeFont(new Font("", Font.PLAIN, 15));
    //?   
    ChartFactory.setChartTheme(standardChartTheme);
    //?
    JFreeChart jfreeChart = ChartFactory.createBarChart3D("", "", "?", dataset,
            PlotOrientation.VERTICAL, true, false, false);
    /**
     * JFreeChart
     */
    jfreeChart.setTitle(new TextTitle("", new Font("", Font.BOLD + Font.ITALIC, 20)));
    CategoryPlot plot = (CategoryPlot) jfreeChart.getPlot();
    CategoryAxis categoryAxis = plot.getDomainAxis();
    categoryAxis.setLabelFont(new Font("", Font.ROMAN_BASELINE, 12));

    return jfreeChart;
}

From source file:com.ohalo.cn.awt.JFreeChartTest2.java

public static JFreeChart createChart(CategoryDataset dataset) // ?
{
    JFreeChart chart = ChartFactory.createBarChart("hi", "", "?", dataset,
            PlotOrientation.VERTICAL, true, true, false); // JFreeChart
    chart.setTitle(new TextTitle("??", new Font("", Font.BOLD + Font.ITALIC, 20)));// ???hi?
    CategoryPlot plot = (CategoryPlot) chart.getPlot();// ?plot
    CategoryAxis categoryAxis = plot.getDomainAxis();// ??
    categoryAxis.setLabelFont(new Font("", Font.BOLD, 12));// ??
    return chart;
}

From source file:org.jfree.chart.demo.GanttDemo3.java

private static JFreeChart createChart(IntervalCategoryDataset intervalcategorydataset) {
    JFreeChart jfreechart = ChartFactory.createGanttChart("Gantt Chart Demo", "Task", "Date",
            intervalcategorydataset, true, true, false);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.getDomainAxis().setMaximumCategoryLabelWidthRatio(10F);
    DateAxis dateaxis = (DateAxis) categoryplot.getRangeAxis();
    dateaxis.setUpperMargin(0.20000000000000001D);
    GanttRenderer ganttrenderer = (GanttRenderer) categoryplot.getRenderer();
    ganttrenderer.setDrawBarOutline(false);
    ganttrenderer.setBaseItemLabelGenerator(new MyLabelGenerator(new SimpleDateFormat("d-MMM")));
    ganttrenderer.setBaseItemLabelsVisible(true);
    ganttrenderer.setBasePositiveItemLabelPosition(
            new ItemLabelPosition(ItemLabelAnchor.OUTSIDE3, TextAnchor.CENTER_LEFT));
    return jfreechart;
}

From source file:org.jfree.chart.demo.StackedAreaChartDemo1.java

public static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createStackedAreaChart("Stacked Area Chart", "Category", "Value",
            categorydataset, PlotOrientation.VERTICAL, true, true, false);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setForegroundAlpha(0.85F);
    CategoryAxis categoryaxis = categoryplot.getDomainAxis();
    categoryaxis.setLowerMargin(0.0D);// w  w  w  .  j  ava  2s .c  om
    categoryaxis.setUpperMargin(0.0D);
    categoryaxis.setCategoryMargin(0.0D);
    NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis();
    numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    CategoryItemRenderer categoryitemrenderer = categoryplot.getRenderer();
    categoryitemrenderer.setBaseItemLabelsVisible(true);
    return jfreechart;
}

From source file:org.jfree.chart.demo.CategoryLabelPositionsDemo1.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createBarChart("CategoryLabelPositionsDemo1", "Category", "Value",
            categorydataset, PlotOrientation.VERTICAL, false, false, false);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    CategoryAxis categoryaxis = categoryplot.getDomainAxis();
    categoryaxis.setMaximumCategoryLabelLines(0x7fffffff);
    categoryaxis.setCategoryLabelPositions(
            CategoryLabelPositions.createUpRotationLabelPositions(0.78539816339744828D));
    return jfreechart;
}

From source file:storybook.ui.chart.jfreechart.ChartUtil.java

public static void hideDomainAxis(CategoryPlot paramCategoryPlot) {
    CategoryAxis localCategoryAxis = paramCategoryPlot.getDomainAxis();
    localCategoryAxis.setTickMarksVisible(false);
    localCategoryAxis.setTickLabelsVisible(false);
}

From source file:com.ouc.cpss.view.ChartProBuilder.java

private static JFreeChart createJFreeChart(CategoryDataset dataset) {
    /**//from ww  w  . ja va 2 s.  c  o m
     * JFreeChart
     */
    //?     
    StandardChartTheme standardChartTheme = new StandardChartTheme("CN");
    //     
    standardChartTheme.setExtraLargeFont(new Font("", Font.BOLD, 20));
    //    
    standardChartTheme.setRegularFont(new Font("", Font.PLAIN, 15));
    //?     
    standardChartTheme.setLargeFont(new Font("", Font.PLAIN, 15));
    //?   
    ChartFactory.setChartTheme(standardChartTheme);
    //?
    // ?
    JFreeChart jfreeChart = null;
    if (choice == 1) {
        jfreeChart = ChartFactory.createBarChart3D("? -- ?TOP10", "",
                "?", dataset, PlotOrientation.VERTICAL, true, false, false);
        /**
          * JFreeChart
          */
        jfreeChart.setTitle(new TextTitle("? -- ?TOP10",
                new Font("", Font.BOLD + Font.ITALIC, 20)));
        CategoryPlot plot = (CategoryPlot) jfreeChart.getPlot();
        CategoryAxis categoryAxis = plot.getDomainAxis();
        categoryAxis.setLabelFont(new Font("", Font.ROMAN_BASELINE, 12));
    } else {
        jfreeChart = ChartFactory.createBarChart3D("? -- ?TOP10", "",
                "?", dataset, PlotOrientation.VERTICAL, true, false, false);
        jfreeChart.setTitle(new TextTitle("? -- ?TOP10",
                new Font("", Font.BOLD + Font.ITALIC, 20)));
        CategoryPlot plot = (CategoryPlot) jfreeChart.getPlot();
        CategoryAxis categoryAxis = plot.getDomainAxis();
        categoryAxis.setLabelFont(new Font("", Font.ROMAN_BASELINE, 12));
    }
    return jfreeChart;
}