List of usage examples for org.jfree.chart.plot XYPlot setRangeMinorGridlineStroke
public void setRangeMinorGridlineStroke(Stroke stroke)
From source file:org.gwaspi.reports.PlinkReportLoader.java
private static void appendToCombinedRangePlot(CombinedRangeXYPlot combinedPlot, String chromosome, XYSeriesCollection seriesCol) {/*from www . j a va 2s . c o m*/ XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(false, true); renderer.setSeriesPaint(0, Color.blue); JFreeChart subchart = ChartFactory.createScatterPlot("", "Chr " + chromosome, "", seriesCol, PlotOrientation.VERTICAL, true, false, false); XYPlot subplot = (XYPlot) subchart.getPlot(); subplot.setRenderer(renderer); subplot.setBackgroundPaint(null); subplot.setDomainGridlineStroke(new BasicStroke(0.0f)); subplot.setDomainMinorGridlineStroke(new BasicStroke(0.0f)); subplot.setDomainGridlinePaint(Color.blue); subplot.setRangeGridlineStroke(new BasicStroke(0.0f)); subplot.setRangeMinorGridlineStroke(new BasicStroke(0.0f)); subplot.setRangeGridlinePaint(Color.blue); NumberAxis chrAxis = (NumberAxis) subplot.getDomainAxis(); chrAxis.setAxisLineVisible(true); chrAxis.setTickLabelsVisible(true); chrAxis.setTickMarksVisible(true); chrAxis.setTickUnit(new NumberTickUnit(10000)); chrAxis.setAutoRangeIncludesZero(false); NumberAxis log10Axis = (NumberAxis) subplot.getRangeAxis(); log10Axis.setTickMarkInsideLength(2.0f); log10Axis.setTickMarkOutsideLength(2.0f); log10Axis.setMinorTickCount(2); log10Axis.setMinorTickMarksVisible(true); log10Axis.setAxisLineVisible(true); log10Axis.setAutoRangeIncludesZero(false); XYItemRenderer lblRenderer = subplot.getRenderer(); MySeriesItemLabelGenerator lblGenerator = new MySeriesItemLabelGenerator(4.0d, chromosome); lblRenderer.setSeriesItemLabelGenerator(0, lblGenerator); lblRenderer.setSeriesItemLabelGenerator(1, lblGenerator); lblRenderer.setSeriesItemLabelFont(0, new Font("Serif", Font.PLAIN, 12)); lblRenderer.setSeriesItemLabelFont(1, new Font("Serif", Font.PLAIN, 12)); lblRenderer.setSeriesPositiveItemLabelPosition(0, new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.BOTTOM_LEFT, TextAnchor.TOP_LEFT, -Math.PI / 4.0)); lblRenderer.setSeriesPositiveItemLabelPosition(1, new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.BOTTOM_LEFT, TextAnchor.TOP_LEFT, -Math.PI / 4.0)); lblRenderer.setSeriesItemLabelsVisible(0, true); lblRenderer.setSeriesItemLabelsVisible(1, true); combinedPlot.add(subplot, 1); }
From source file:org.gwaspi.gui.reports.SampleQAHetzygPlotZoom.java
private JFreeChart createChart(XYDataset dataset) { JFreeChart chart = ChartFactory.createScatterPlot("Heterozygosity vs. Missing Ratio", "Heterozygosity Ratio", "Missing Ratio", dataset, PlotOrientation.VERTICAL, true, false, false); XYPlot plot = (XYPlot) chart.getPlot(); plot.setNoDataMessage("NO DATA"); plot.setDomainZeroBaselineVisible(true); plot.setRangeZeroBaselineVisible(true); // CHART BACKGROUD COLOR chart.setBackgroundPaint(Color.getHSBColor(0.1f, 0.1f, 1.0f)); // Hue, saturation, brightness plot.setBackgroundPaint(PLOT_MANHATTAN_BACKGROUND); // Hue, saturation, brightness 9 // GRIDLINES/*from w ww. j a v a 2 s . c o m*/ plot.setDomainGridlineStroke(new BasicStroke(0.0f)); plot.setDomainMinorGridlineStroke(new BasicStroke(0.0f)); plot.setDomainGridlinePaint(PLOT_MANHATTAN_BACKGROUND.darker().darker()); // Hue, saturation, brightness 7 plot.setDomainMinorGridlinePaint(PLOT_MANHATTAN_BACKGROUND); // Hue, saturation, brightness 9 plot.setRangeGridlineStroke(new BasicStroke(0.0f)); plot.setRangeMinorGridlineStroke(new BasicStroke(0.0f)); plot.setRangeGridlinePaint(PLOT_MANHATTAN_BACKGROUND.darker().darker()); // Hue, saturation, brightness 7 plot.setRangeMinorGridlinePaint(PLOT_MANHATTAN_BACKGROUND.darker()); // Hue, saturation, brightness 8 plot.setDomainMinorGridlinesVisible(true); plot.setRangeMinorGridlinesVisible(true); // DOTS RENDERER XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesPaint(0, PLOT_MANHATTAN_DOTS); // renderer.setSeriesOutlinePaint(0, Color.DARK_GRAY); // renderer.setUseOutlinePaint(true); // Set dot shape of the currently appended Series renderer.setSeriesShape(0, new Rectangle2D.Double(-1, -1, 2, 2)); renderer.setSeriesVisibleInLegend(0, false); // AXIS double maxHetzy = 0.005; for (int i = 0; i < dataset.getItemCount(0); i++) { if (maxHetzy < dataset.getXValue(0, i)) { maxHetzy = dataset.getXValue(0, i); } } NumberAxis hetzyAxis = (NumberAxis) plot.getDomainAxis(); hetzyAxis.setAutoRangeIncludesZero(true); hetzyAxis.setAxisLineVisible(true); hetzyAxis.setTickLabelsVisible(true); hetzyAxis.setTickMarksVisible(true); hetzyAxis.setRange(0, maxHetzy * 1.1); double maxMissrat = 0.005; for (int i = 0; i < dataset.getItemCount(0); i++) { if (maxMissrat < dataset.getYValue(0, i)) { maxMissrat = dataset.getYValue(0, i); } } NumberAxis missratAxis = (NumberAxis) plot.getRangeAxis(); missratAxis.setAutoRangeIncludesZero(true); missratAxis.setAxisLineVisible(true); missratAxis.setTickLabelsVisible(true); missratAxis.setTickMarksVisible(true); missratAxis.setRange(0, maxMissrat * 1.1); // Add significance Threshold to subplot final Marker missingThresholdLine = new ValueMarker(missingThreshold); missingThresholdLine.setPaint(Color.blue); final Marker hetzyThresholdLine = new ValueMarker(hetzyThreshold); hetzyThresholdLine.setPaint(Color.blue); // Add legend to hetzyThreshold hetzyThresholdLine.setLabel("hetzyg. threshold = " + hetzyThreshold); missingThresholdLine.setLabel("missing. threshold = " + missingThreshold); hetzyThresholdLine.setLabelAnchor(RectangleAnchor.TOP_LEFT); hetzyThresholdLine.setLabelTextAnchor(TextAnchor.TOP_RIGHT); missingThresholdLine.setLabelAnchor(RectangleAnchor.BOTTOM_LEFT); missingThresholdLine.setLabelTextAnchor(TextAnchor.TOP_LEFT); plot.addRangeMarker(missingThresholdLine); // THIS FOR MISSING RATIO plot.addDomainMarker(hetzyThresholdLine); // THIS FOR HETZY RATIO // Marker label if below hetzyThreshold XYItemRenderer lblRenderer = plot.getRenderer(); // THRESHOLD AND SELECTED LABEL GENERATOR MySeriesItemLabelGenerator lblGenerator = new MySeriesItemLabelGenerator(hetzyThreshold, missingThreshold); lblRenderer.setSeriesItemLabelGenerator(0, lblGenerator); lblRenderer.setSeriesItemLabelFont(0, new Font("SansSerif", Font.PLAIN, 10)); lblRenderer.setSeriesPositiveItemLabelPosition(0, new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.BOTTOM_LEFT, TextAnchor.BOTTOM_LEFT, 2 * Math.PI)); // TOOLTIP GENERATOR MyXYToolTipGenerator tooltipGenerator = new MyXYToolTipGenerator(); lblRenderer.setBaseToolTipGenerator(tooltipGenerator); lblRenderer.setSeriesItemLabelsVisible(0, true); return chart; }
From source file:org.gwaspi.gui.reports.ManhattanPlotZoom.java
private JFreeChart createChart(XYDataset dataset, ChromosomeKey chr) { JFreeChart chart = ChartFactory.createScatterPlot(null, "", "P value", dataset, PlotOrientation.VERTICAL, true, false, false);/*from w ww.j a v a 2 s. co m*/ XYPlot plot = (XYPlot) chart.getPlot(); plot.setNoDataMessage("NO DATA"); plot.setDomainZeroBaselineVisible(true); plot.setRangeZeroBaselineVisible(true); // CHART BACKGROUD COLOR chart.setBackgroundPaint(Color.getHSBColor(0.1f, 0.1f, 1.0f)); // Hue, saturation, brightness plot.setBackgroundPaint(manhattan_back); // Hue, saturation, brightness 9 // GRIDLINES plot.setDomainGridlineStroke(new BasicStroke(0.0f)); plot.setDomainMinorGridlineStroke(new BasicStroke(0.0f)); plot.setDomainGridlinePaint(manhattan_back.darker().darker()); // Hue, saturation, brightness 7 plot.setDomainMinorGridlinePaint(manhattan_back); // Hue, saturation, brightness 9 plot.setRangeGridlineStroke(new BasicStroke(0.0f)); plot.setRangeMinorGridlineStroke(new BasicStroke(0.0f)); plot.setRangeGridlinePaint(manhattan_back.darker().darker()); // Hue, saturation, brightness 7 plot.setRangeMinorGridlinePaint(manhattan_back.darker()); // Hue, saturation, brightness 8 plot.setDomainMinorGridlinesVisible(true); plot.setRangeMinorGridlinesVisible(true); // DOTS RENDERER XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesPaint(0, manhattan_dot); // renderer.setSeriesOutlinePaint(0, Color.DARK_GRAY); // renderer.setUseOutlinePaint(true); // Set dot shape of the currently appended Series renderer.setSeriesShape(0, new Rectangle2D.Double(0.0, 0.0, 2, 2)); renderer.setSeriesVisibleInLegend(0, false); NumberAxis positionAxis = (NumberAxis) plot.getDomainAxis(); // domainAxis.setAutoRangeIncludesZero(false); // domainAxis.setTickMarkInsideLength(2.0f); // domainAxis.setTickMarkOutsideLength(2.0f); // domainAxis.setMinorTickCount(2); // domainAxis.setMinorTickMarksVisible(true); positionAxis.setLabelAngle(1.0); positionAxis.setAutoRangeIncludesZero(false); positionAxis.setAxisLineVisible(true); positionAxis.setTickLabelsVisible(true); positionAxis.setTickMarksVisible(true); // ADD INVERSE LOG(10) Y AXIS LogAxis logPAxis = new LogAxis("P value"); logPAxis.setBase(10); logPAxis.setInverted(true); logPAxis.setNumberFormatOverride(GenericReportGenerator.FORMAT_P_VALUE); logPAxis.setTickMarkOutsideLength(2.0f); logPAxis.setMinorTickCount(2); logPAxis.setMinorTickMarksVisible(true); logPAxis.setAxisLineVisible(true); logPAxis.setUpperMargin(0); TickUnitSource units = NumberAxis.createIntegerTickUnits(); logPAxis.setStandardTickUnits(units); plot.setRangeAxis(0, logPAxis); // Add significance Threshold to subplot //threshold = 0.5/rdMatrixMetadata.getMarkerSetSize(); // (0.05/10? SNPs => 5*10-?) final Marker thresholdLine = new ValueMarker(threshold); thresholdLine.setPaint(Color.red); // Add legend to threshold thresholdLine.setLabel("P = " + GenericReportGenerator.FORMAT_P_VALUE.format(threshold)); thresholdLine.setLabelAnchor(RectangleAnchor.TOP_RIGHT); thresholdLine.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT); plot.addRangeMarker(thresholdLine); // Marker label if below threshold XYItemRenderer lblRenderer = plot.getRenderer(); // THRESHOLD AND SELECTED LABEL GENERATOR MySeriesItemLabelGenerator lblGenerator = new MySeriesItemLabelGenerator(threshold, chr); lblRenderer.setSeriesItemLabelGenerator(0, lblGenerator); lblRenderer.setSeriesItemLabelFont(0, new Font("SansSerif", Font.PLAIN, 12)); lblRenderer.setSeriesPositiveItemLabelPosition(0, new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.TOP_LEFT, TextAnchor.BOTTOM_LEFT, Math.PI / 4.0)); // TOOLTIP GENERATOR MyXYToolTipGenerator tooltipGenerator = new MyXYToolTipGenerator(chr); lblRenderer.setBaseToolTipGenerator(tooltipGenerator); lblRenderer.setSeriesItemLabelsVisible(0, true); return chart; }