Java Code Examples for org.jfree.chart.plot.XYPlot#setDatasetRenderingOrder()

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, boolean showTitle,
    boolean showLegend, double rt, double precursorMZ) {
  //
  if (dataset == null)
    return null;
  //
  NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat rtForm = MZmineCore.getConfiguration().getRTFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  String title = "";
  if (precursorMZ == 0)
    title = "RT=" + mzForm.format(precursorMZ);
  else
    title = MessageFormat.format("MSMS for m/z={0} RT={1}", mzForm.format(precursorMZ),
        rtForm.format(rt));

  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzForm);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  chart.getTitle().setVisible(showTitle);
  chart.getLegend().setVisible(showLegend);
  //
  if (precursorMZ != 0)
    addPrecursorMarker(chart, precursorMZ);
  return chart;
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, RawDataFile raw, boolean sum,
    String title) {
  //
  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzFormat);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  return chart;
}
 

/**
 * All params can be null.
 *
 * @param min - the minimum number on the left range axis (must be set if max is set)
 * @param max - the maximum number on the left range axis (must be set if min is set)
 * @param method2 - the method to run out of Record, and populates a bar series (right range axis)
 * @param highLightIndex - the index to highlight
 * @return
 * @throws Exception
 */
public JFreeChart makeTimeChart(Double min, Double max, String method2, Integer highLightIndex)
    throws Exception {
  startTms = System.currentTimeMillis();
  endTms = 0;
  XYBarRenderer.setDefaultShadowsVisible(false);
  TimeSeriesCollection data = new TimeSeriesCollection();
  Map<String, TimeSeries> timeSeriesMap = makeTimeSeriesMap(method, recordMap, keyNames);
  for (TimeSeries timeSeries : timeSeriesMap.values()) {
    data.addSeries(timeSeries);
  }
  String yAxisLabel = method;
  String denominator = Record.getDenominator(report.getRecordClass(), method.toLowerCase());
  if (denominator != null) {
    yAxisLabel += " (" + denominator + ")";
  }
  chart = ChartFactory.createTimeSeriesChart(title, "Time", yAxisLabel, data, true, true, true);
  XYPlot plot = (XYPlot) chart.getPlot();
  if (method2 != null) {
    Map<Key, R> recordMap2 = recordMap;
    TimeSeriesCollection data2 = new TimeSeriesCollection();
    if (keyNames.length > 0) {
      recordMap2 = report.getMapAggregatedOn();
    }
    Map<String, TimeSeries> timeSeriesMap2 = makeTimeSeriesMap(method2, recordMap2);
    if (timeSeriesMap2.get("Total (" + method2 + ")") != null) {
      data2.addSeries(timeSeriesMap2.get("Total (" + method2 + ")"));
    }
    String y2AxisLabel = method2;
    String demoninator2 = Record.getDenominator(report.getRecordClass(), method2.toLowerCase());
    if (demoninator2 != null) {
      y2AxisLabel += " (" + demoninator2 + ")";
    }
    NumberAxis axis2 = new NumberAxis(y2AxisLabel);
    XYBarRenderer renderer2 = new XYBarRenderer(0.20);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_RIGHT);
    plot.setDataset(1, data2);
    plot.setRenderer(1, renderer2);
    plot.mapDatasetToRangeAxis(1, 1);
    renderer2.setBarPainter(new StandardXYBarPainter());
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.REVERSE);
  }
  if (min != null && max != null) {
    plot.getRangeAxis(0).setRange(min, max);
  }

  if (highLightIndex != null) {
    chart.getXYPlot().getRenderer().setSeriesStroke(highLightIndex, new BasicStroke(5f));
  }

  XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer();
  renderer.setDefaultShapesVisible(true);
  renderer.setUseFillPaint(true);
  renderer.setDefaultFillPaint(Color.white);

  long diff = endTms - startTms;
  String format;
  if (diff > NINTY_DAYS) {
    format = "MMM-yyyy";
  } else if (diff > TWO_DAYS) {
    format = "dd-MMM";
  } else if (diff > TWO_MINUTES) {
    format = "HH:mm";
  } else {
    format = "HH:mm:ss";
  }
  DateAxis axis = (DateAxis) plot.getDomainAxis();
  axis.setDateFormatOverride(new SimpleDateFormat(format));

  LegendTitle lt = chart.getLegend(0);
  lt.setPosition(RectangleEdge.RIGHT);

  if (displayFrame) {
    ChartFrame frame = new ChartFrame(title, chart);
    frame.pack();
    frame.setVisible(true);
  }

  return chart;
}
 

private static JFreeChart createChart(XYZDataset dataset, double[] mins, double[] maxs, int nPoints, XYDataset xyData) {
    NumberAxis xAxis = new NumberAxis("X");
    xAxis.setRange(mins[0],maxs[0]);


    NumberAxis yAxis = new NumberAxis("Y");
    yAxis.setRange(mins[1], maxs[1]);

    XYBlockRenderer renderer = new XYBlockRenderer();
    renderer.setBlockWidth((maxs[0]-mins[0])/(nPoints-1));
    renderer.setBlockHeight((maxs[1] - mins[1]) / (nPoints - 1));
    PaintScale scale = new GrayPaintScale(0, 1.0);
    renderer.setPaintScale(scale);
    XYPlot plot = new XYPlot(dataset, xAxis, yAxis, renderer);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinesVisible(false);
    plot.setRangeGridlinesVisible(false);
    plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5));
    JFreeChart chart = new JFreeChart("", plot);
    chart.getXYPlot().getRenderer().setSeriesVisibleInLegend(0, false);


    NumberAxis scaleAxis = new NumberAxis("Probability (class 0)");
    scaleAxis.setAxisLinePaint(Color.white);
    scaleAxis.setTickMarkPaint(Color.white);
    scaleAxis.setTickLabelFont(new Font("Dialog", Font.PLAIN, 7));
    PaintScaleLegend legend = new PaintScaleLegend(new GrayPaintScale(),
            scaleAxis);
    legend.setStripOutlineVisible(false);
    legend.setSubdivisionCount(20);
    legend.setAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
    legend.setAxisOffset(5.0);
    legend.setMargin(new RectangleInsets(5, 5, 5, 5));
    legend.setFrame(new BlockBorder(Color.red));
    legend.setPadding(new RectangleInsets(10, 10, 10, 10));
    legend.setStripWidth(10);
    legend.setPosition(RectangleEdge.LEFT);
    chart.addSubtitle(legend);

    ChartUtilities.applyCurrentTheme(chart);

    plot.setDataset(1, xyData);
    XYLineAndShapeRenderer renderer2 = new XYLineAndShapeRenderer();
    renderer2.setBaseLinesVisible(false);
    plot.setRenderer(1, renderer2);

    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

    return chart;
}
 

/**
 * Update the chart
 * 
 * @param dataset1
 * @param dataset2
 * @return
 */
private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYAreaChart("",
			// x axis label
			bundle.getString("frmElevationFilter.labelX"), // "Distance"
			// y axis label
			bundle.getString("frmElevationFilter.labelY1"), // "Elevation"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	// -- Background color
	chart.setBackgroundPaint(Color.white);
	chart.setAntiAlias(true);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis("");// bundle.getString("JPanelAnalysisTimeDist.labelY2")); // "Time"
	// plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	// plot.mapDatasetToRangeAxis(1, 1);
	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	renderer2.setSeriesStroke(0, new BasicStroke(1.0f));
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYAreaChart("",
			// x axis label
			bundle.getString("JPanelAnalysisSpeed.labelX"), // "Distance",
			// y axis label
			bundle.getString("JPanelAnalysisSpeed.labelY"), // "Speed"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	chart.setBackgroundPaint(Color.white); // Panel background color
	chart.setAntiAlias(true);

	XYPlot plot = chart.getXYPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis();
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);

	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createScatterPlot("",
			// x axis label
			bundle.getString("JPanelAnalysisSpeedSlope.labelX"), // "Slope",
			// y axis label
			bundle.getString("JPanelAnalysisSpeedSlope.labelY"), // "Speed",
			// data
			dataset1, PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	chart.setBackgroundPaint(Color.white); // Panel background color
	chart.setAntiAlias(true);

	XYPlot plot = chart.getXYPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);
	plot.setRangeCrosshairLockedOnData(false);

	XYDotRenderer renderer = new XYDotRenderer();
	renderer.setSeriesPaint(0, new Color(0x6B, 0xB2, 0x00));
	renderer.setDotWidth(2);
	renderer.setDotHeight(2);
	plot.setRenderer(renderer);

	NumberAxis rangeAxis2 = new NumberAxis();
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);

	XYAreaRenderer renderer2 = new XYAreaRenderer();
	renderer2.setSeriesPaint(0, new Color(0x99, 0xff, 0x00, 0x80));
	renderer2.setOutline(true);
	renderer2.setSeriesOutlinePaint(0, new Color(0x80, 0x80, 0x80, 0x80));
	renderer2.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(1, renderer2);

	/*
	 * StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	 * renderer2.setSeriesPaint(0, Color.red); plot.setRenderer(1, renderer2);
	 */

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.REVERSE);

	return chart;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYAreaChart("",
			// x axis label
			bundle.getString("JPanelAnalysisTimeDist.labelX"), // "Distance"
			// y axis label
			bundle.getString("JPanelAnalysisTimeDist.labelY1"), // "Elevation"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	// -- Background color
	chart.setBackgroundPaint(Color.white);
	chart.setAntiAlias(true);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis(bundle.getString("JPanelAnalysisTimeDist.labelY2")); // "Time"
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);
	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYLineChart("",
			// x axis label
			bundle.getString("JPanelAnalysisTimeDist.labelX"), // "Distance"
			// y axis label
			bundle.getString("JPanelAnalysisTimeDist.labelY1"), // "Elevation"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	// -- Background color
	chart.setBackgroundPaint(Color.white);
	chart.setAntiAlias(true);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis(bundle.getString("JPanelAnalysisTimeTemperature.labelY2")); // "Time"
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);
	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

public void initialize() {

    final JFreeChart chart = chartNode.getChart();
    final XYPlot plot = chart.getXYPlot();

    // Do not set colors and strokes dynamically. They are instead provided
    // by the dataset and configured in configureRenderer()
    plot.setDrawingSupplier(null);
    plot.setDomainGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
    plot.setRangeGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
    plot.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));
    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
    plot.setDomainCrosshairVisible(false);
    plot.setRangeCrosshairVisible(false);

    // chart properties
    chart.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));

    // legend properties
    LegendTitle legend = chart.getLegend();
    // legend.setItemFont(legendFont);
    legend.setFrame(BlockBorder.NONE);

    // set the X axis (m/z) properties
    NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
    xAxis.setLabel("m/z");
    xAxis.setUpperMargin(0.03);
    xAxis.setLowerMargin(0.03);
    xAxis.setRangeType(RangeType.POSITIVE);
    xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));

    // set the Y axis (intensity) properties
    NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
    yAxis.setLabel("Intensity");
    yAxis.setRangeType(RangeType.POSITIVE);
    yAxis.setAutoRangeIncludesZero(true);

    // set the fixed number formats, because otherwise JFreeChart sometimes
    // shows exponent, sometimes it doesn't
    DecimalFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    xAxis.setNumberFormatOverride(mzFormat);
    DecimalFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
    yAxis.setNumberFormatOverride(intensityFormat);

    chartTitle = chartNode.getChart().getTitle();
    chartTitle.setMargin(5, 0, 0, 0);
    chartTitle.setFont(titleFont);

    chartNode.setCursor(Cursor.CROSSHAIR);

    // Remove the dataset if it is removed from the list
    datasets.addListener((Change<? extends MsSpectrumDataSet> c) -> {
      while (c.next()) {
        if (c.wasRemoved()) {
          for (MsSpectrumDataSet ds : c.getRemoved()) {
            int index = plot.indexOf(ds);
            plot.setDataset(index, null);
          }
        }
      }
    });

    itemLabelsVisible.addListener((prop, oldVal, newVal) -> {
      for (MsSpectrumDataSet dataset : datasets) {
        int datasetIndex = plot.indexOf(dataset);
        XYItemRenderer renderer = plot.getRenderer(datasetIndex);
        renderer.setBaseItemLabelsVisible(newVal);
      }
    });

    legendVisible.addListener((prop, oldVal, newVal) -> {
      legend.setVisible(newVal);
    });

  }
 

@FXML
public void initialize() {

  final JFreeChart chart = chartNode.getChart();
  final XYPlot plot = chart.getXYPlot();

  // Do not set colors and strokes dynamically. They are instead provided
  // by the dataset and configured in configureRenderer()
  plot.setDrawingSupplier(null);
  plot.setDomainGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
  plot.setRangeGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
  plot.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));
  plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
  plot.setDomainCrosshairPaint(JavaFXUtil.convertColorToAWT(crossHairColor));
  plot.setRangeCrosshairPaint(JavaFXUtil.convertColorToAWT(crossHairColor));
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);

  // chart properties
  chart.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));

  // legend properties
  LegendTitle legend = chart.getLegend();
  // legend.setItemFont(legendFont);
  legend.setFrame(BlockBorder.NONE);

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setLabel("Retention time (min)");
  xAxis.setUpperMargin(0.03);
  xAxis.setLowerMargin(0.03);
  xAxis.setRangeType(RangeType.POSITIVE);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setLabel("Intensity");
  yAxis.setRangeType(RangeType.POSITIVE);
  yAxis.setAutoRangeIncludesZero(true);

  // set the fixed number formats, because otherwise JFreeChart sometimes
  // shows exponent, sometimes it doesn't
  DecimalFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
  xAxis.setNumberFormatOverride(mzFormat);
  DecimalFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
  yAxis.setNumberFormatOverride(intensityFormat);

  chartTitle = chartNode.getChart().getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  chartTitle.setText("Chromatogram");

  chartNode.setCursor(Cursor.CROSSHAIR);

  // Remove the dataset if it is removed from the list
  datasets.addListener((Change<? extends ChromatogramPlotDataSet> c) -> {
    while (c.next()) {
      if (c.wasRemoved()) {
        for (ChromatogramPlotDataSet ds : c.getRemoved()) {
          int index = plot.indexOf(ds);
          plot.setDataset(index, null);
        }
      }
    }
  });

  itemLabelsVisible.addListener((prop, oldVal, newVal) -> {
    for (ChromatogramPlotDataSet dataset : datasets) {
      int datasetIndex = plot.indexOf(dataset);
      XYItemRenderer renderer = plot.getRenderer(datasetIndex);
      renderer.setBaseItemLabelsVisible(newVal);
    }
  });

  legendVisible.addListener((prop, oldVal, newVal) -> {
    legend.setVisible(newVal);
  });
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, boolean showTitle,
    boolean showLegend, double rt, double precursorMZ) {
  //
  if (dataset == null)
    return null;
  //
  NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat rtForm = MZmineCore.getConfiguration().getRTFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  String title = "";
  if (precursorMZ == 0)
    title = "RT=" + mzForm.format(precursorMZ);
  else
    title = MessageFormat.format("MSMS for m/z={0} RT={1}", mzForm.format(precursorMZ),
        rtForm.format(rt));

  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzForm);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  chart.getTitle().setVisible(showTitle);
  chart.getLegend().setVisible(showLegend);
  //
  if (precursorMZ != 0)
    addPrecursorMarker(chart, precursorMZ);
  return chart;
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, RawDataFile raw, boolean sum,
    String title) {
  //
  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzFormat);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  return chart;
}
 

public static void main(String[] args) {
    /**
     * Getting time series
     */
    TimeSeries series = CsvTradesLoader.loadBitstampSeries();
    
    /**
     * Creating the OHLC dataset
     */
    OHLCDataset ohlcDataset = createOHLCDataset(series);
    
    /**
     * Creating the additional dataset
     */
    TimeSeriesCollection xyDataset = createAdditionalDataset(series);
    
    /**
     * Creating the chart
     */
    JFreeChart chart = ChartFactory.createCandlestickChart(
            "Bitstamp BTC price",
            "Time",
            "USD",
            ohlcDataset,
            true);
    // Candlestick rendering
    CandlestickRenderer renderer = new CandlestickRenderer();
    renderer.setAutoWidthMethod(CandlestickRenderer.WIDTHMETHOD_SMALLEST);
    XYPlot plot = chart.getXYPlot();
    plot.setRenderer(renderer);
    // Additional dataset
    int index = 1;
    plot.setDataset(index, xyDataset);
    plot.mapDatasetToRangeAxis(index, 0);
    XYLineAndShapeRenderer renderer2 = new XYLineAndShapeRenderer(true, false);
    renderer2.setSeriesPaint(index, Color.blue);
    plot.setRenderer(index, renderer2);
    // Misc
    plot.setRangeGridlinePaint(Color.lightGray);
    plot.setBackgroundPaint(Color.white);
    NumberAxis numberAxis = (NumberAxis) plot.getRangeAxis();
    numberAxis.setAutoRangeIncludesZero(false);
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
    
    /**
     * Displaying the chart
     */
    displayChart(chart);
}