List of usage examples for org.jfree.chart.axis LogAxis setMinorTickCount
public void setMinorTickCount(int count)
From source file:org.gwaspi.reports.PlinkReportLoaderCombined.java
private static void appendToCombinedRangePlot(CombinedRangeXYPlot combinedPlot, String chromosome, XYSeriesCollection tempChrData, boolean showlables) { XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(false, true); renderer.setSeriesPaint(0, Color.blue); renderer.setSeriesPaint(1, Color.red); renderer.setSeriesVisibleInLegend(0, showlables); renderer.setSeriesVisibleInLegend(1, showlables); //renderer.setBaseShape(new Ellipse2D.Float(0, 0, 2,2), false); if (combinedPlot.getSubplots().isEmpty()) { LogAxis rangeAxis = new LogAxis("P value"); rangeAxis.setBase(10);/*from w w w.ja v a 2 s . c o m*/ rangeAxis.setInverted(true); rangeAxis.setNumberFormatOverride(GenericReportGenerator.FORMAT_P_VALUE); rangeAxis.setTickMarkOutsideLength(2.0f); rangeAxis.setMinorTickCount(2); rangeAxis.setMinorTickMarksVisible(true); rangeAxis.setAxisLineVisible(true); rangeAxis.setAutoRangeMinimumSize(0.0000005); rangeAxis.setLowerBound(1d); //rangeAxis.setAutoRangeIncludesZero(false); combinedPlot.setRangeAxis(0, rangeAxis); } JFreeChart subchart = ChartFactory.createScatterPlot("", "Chr " + chromosome, "", tempChrData, PlotOrientation.VERTICAL, true, false, false); XYPlot subplot = (XYPlot) subchart.getPlot(); subplot.setRenderer(renderer); subplot.setBackgroundPaint(null); final Marker thresholdLine = new ValueMarker(0.0000005); thresholdLine.setPaint(Color.red); if (showlables) { thresholdLine.setLabel("P = 510??"); } thresholdLine.setLabelAnchor(RectangleAnchor.TOP_RIGHT); thresholdLine.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT); subplot.addRangeMarker(thresholdLine); NumberAxis chrAxis = (NumberAxis) subplot.getDomainAxis(); chrAxis.setAxisLineVisible(false); chrAxis.setTickLabelsVisible(false); chrAxis.setTickMarksVisible(false); chrAxis.setAutoRangeIncludesZero(false); //combinedPlot.setGap(0); combinedPlot.add(subplot, 1); }
From source file:org.gwaspi.reports.GenericReportGenerator.java
private static void appendToCombinedRangeManhattanPlot(CombinedRangeXYPlot combinedPlot, String chromosome, XYSeriesCollection currChrSC, boolean showlables, double threshold, Color background, Color backgroundAlternative, Color main) { XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(false, true); // Set dot shape of the currently appended Series renderer.setSeriesPaint(currChrSC.getSeriesCount() - 1, main); renderer.setSeriesVisibleInLegend(currChrSC.getSeriesCount() - 1, showlables); renderer.setSeriesShape(currChrSC.getSeriesCount() - 1, new Rectangle2D.Double(-1.0, -1.0, 2.0, 2.0)); // Set range axis if (combinedPlot.getSubplots().isEmpty()) { LogAxis rangeAxis = new LogAxis("P value"); rangeAxis.setBase(10);/*from w w w . ja v a2 s. c om*/ rangeAxis.setInverted(true); rangeAxis.setNumberFormatOverride(FORMAT_P_VALUE); rangeAxis.setTickMarkOutsideLength(2.0f); rangeAxis.setMinorTickCount(2); rangeAxis.setMinorTickMarksVisible(true); rangeAxis.setAxisLineVisible(true); rangeAxis.setUpperMargin(0); TickUnitSource units = NumberAxis.createIntegerTickUnits(); rangeAxis.setStandardTickUnits(units); combinedPlot.setRangeAxis(0, rangeAxis); } // Build subchart JFreeChart subchart = ChartFactory.createScatterPlot("", "Chr " + chromosome, "", currChrSC, PlotOrientation.VERTICAL, false, false, false); // Get subplot from subchart XYPlot subplot = (XYPlot) subchart.getPlot(); subplot.setRenderer(renderer); subplot.setBackgroundPaint(null); // CHART BACKGROUD COLOR if (combinedPlot.getSubplots().size() % 2 == 0) { subplot.setBackgroundPaint(background); // Hue, saturation, brightness } else { subplot.setBackgroundPaint(backgroundAlternative); // Hue, saturation, brightness } // Add significance Threshold to subplot final Marker thresholdLine = new ValueMarker(threshold); thresholdLine.setPaint(Color.red); // Add legend to hetzyThreshold if (showlables) { thresholdLine.setLabel("P = " + FORMAT_P_VALUE.format(threshold)); } thresholdLine.setLabelAnchor(RectangleAnchor.TOP_RIGHT); thresholdLine.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT); subplot.addRangeMarker(thresholdLine); // Chromosome Axis Labels NumberAxis chrAxis = (NumberAxis) subplot.getDomainAxis(); chrAxis.setLabelAngle(1.0); chrAxis.setAutoRangeIncludesZero(false); chrAxis.setAxisLineVisible(true); chrAxis.setTickLabelsVisible(false); chrAxis.setTickMarksVisible(false); // chrAxis.setNumberFormatOverride(Report_Analysis.FORMAT_SCIENTIFIC); // TickUnitSource units = NumberAxis.createIntegerTickUnits(); // chrAxis.setStandardTickUnits(units); //combinedPlot.setGap(0); combinedPlot.add(subplot, 1); }
From source file:net.sf.mzmine.modules.visualization.scatterplot.scatterplotchart.ScatterPlotChart.java
public ScatterPlotChart(ScatterPlotTopPanel topPanel, PeakList peakList) { super(null, true); this.peakList = peakList; this.topPanel = topPanel; // initialize the chart by default time series chart from factory chart = ChartFactory.createXYLineChart("", // title "", // x-axis label "", // y-axis label null, // data set PlotOrientation.VERTICAL, // orientation false, // create legend false, // generate tooltips false // generate URLs );// w ww . j a va2s . c o m chart.setBackgroundPaint(Color.white); setChart(chart); // disable maximum size (we don't want scaling) setMaximumDrawWidth(Integer.MAX_VALUE); setMaximumDrawHeight(Integer.MAX_VALUE); // set the plot properties plot = chart.getXYPlot(); plot.setBackgroundPaint(Color.white); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD); plot.setDomainGridlinePaint(gridColor); plot.setRangeGridlinePaint(gridColor); // Set the domain log axis LogAxis logAxisDomain = new LogAxis(); logAxisDomain.setMinorTickCount(1); logAxisDomain.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat()); logAxisDomain.setAutoRange(true); plot.setDomainAxis(logAxisDomain); // Set the range log axis LogAxis logAxisRange = new LogAxis(); logAxisRange.setMinorTickCount(1); logAxisRange.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat()); logAxisRange.setAutoRange(true); plot.setRangeAxis(logAxisRange); // Set crosshair properties plot.setDomainCrosshairVisible(true); plot.setRangeCrosshairVisible(true); plot.setDomainCrosshairPaint(crossHairColor); plot.setRangeCrosshairPaint(crossHairColor); plot.setDomainCrosshairStroke(crossHairStroke); plot.setRangeCrosshairStroke(crossHairStroke); // Create data sets; mainDataSet = new ScatterPlotDataSet(peakList); plot.setDataset(0, mainDataSet); diagonalLineDataset = new DiagonalLineDataset(); plot.setDataset(1, diagonalLineDataset); // Create renderers mainRenderer = new ScatterPlotRenderer(); plot.setRenderer(0, mainRenderer); diagonalLineRenderer = new DiagonalLineRenderer(); plot.setRenderer(1, diagonalLineRenderer); // Set tooltip properties ttm = new ComponentToolTipManager(); ttm.registerComponent(this); setDismissDelay(Integer.MAX_VALUE); setInitialDelay(0); // add items to popup menu TODO: add other Show... items JPopupMenu popupMenu = getPopupMenu(); popupMenu.addSeparator(); GUIUtils.addMenuItem(popupMenu, "Show Chromatogram", this, "TIC"); }
From source file:edu.fullerton.viewerplugin.XYPlotter.java
private ChartPanel getPanel(double[][] data) throws WebUtilException { ChartPanel ret = null;// www .j a v a 2 s . co m try { XYSeries xys; XYSeriesCollection mtds = new XYSeriesCollection(); String mylegend = legend == null || legend.isEmpty() ? "series 1" : legend; xys = new XYSeries(legend); int len = data.length; double minx = Double.MAX_VALUE; double maxx = Double.MIN_VALUE; double miny = Double.MAX_VALUE; double maxy = Double.MIN_VALUE; boolean gotZeroX = false; boolean gotZeroY = false; for (int i = 0; i < len; i++) { double x = data[i][0]; double y = data[i][1]; if (x == 0) { gotZeroX = true; } else { minx = Math.min(minx, x); maxx = Math.max(maxx, x); } if (y == 0) { gotZeroY = true; } else { miny = Math.min(miny, y); maxy = Math.max(maxy, y); } } // this kludge lets us plot a 0 on a log axis double fakeZeroX = 0.; double fakeZeroY = 0.; if (gotZeroX) { if (logXaxis) { fakeZeroX = minx / 10; } else { minx = Math.min(0, minx); maxx = Math.max(0, maxx); } } if (gotZeroY) { if (logYaxis) { fakeZeroY = miny / 10; } else { miny = Math.min(0, miny); maxy = Math.max(0, maxy); } } for (int i = 0; i < len; i++) { double x = data[i][0]; double y = data[i][1]; x = x == 0 ? fakeZeroX : x; y = y == 0 ? fakeZeroY : y; xys.add(x, y); } mtds.addSeries(xys); DefaultXYDataset ds = new DefaultXYDataset(); int exp; if (maxy == 0. && miny == 0.) { miny = -1.; exp = 0; logYaxis = false; } else { maxy = maxy > miny ? maxy : miny * 10; exp = PluginSupport.scaleRange(mtds, miny, maxy); if (!logYaxis && exp > 0) { yLabel += " x 1e-" + Integer.toString(exp); } } JFreeChart chart = ChartFactory.createXYLineChart(title, xLabel, yLabel, ds, PlotOrientation.VERTICAL, true, false, false); org.jfree.chart.plot.XYPlot plot = (org.jfree.chart.plot.XYPlot) chart.getPlot(); if (logYaxis) { LogAxis rangeAxis = new LogAxis(yLabel); double smallest = miny * Math.pow(10, exp); rangeAxis.setSmallestValue(smallest); rangeAxis.setMinorTickCount(9); LogAxisNumberFormat lanf = new LogAxisNumberFormat(); lanf.setExp(exp); rangeAxis.setNumberFormatOverride(lanf); rangeAxis.setRange(smallest, maxy * Math.pow(10, exp)); plot.setRangeAxis(rangeAxis); } if (logXaxis) { LogAxis domainAxis = new LogAxis(xLabel); domainAxis.setMinorTickCount(9); domainAxis.setSmallestValue(minx); domainAxis.setNumberFormatOverride(new LogAxisNumberFormat()); plot.setDomainAxis(domainAxis); } ValueAxis domainAxis = plot.getDomainAxis(); if (fmin != null && fmin > 0) { domainAxis.setLowerBound(fmin); } if (fmax != null && fmax > 0) { domainAxis.setUpperBound(fmax); } plot.setDomainAxis(domainAxis); plot.setDataset(0, mtds); // Set the line thickness XYLineAndShapeRenderer r = (XYLineAndShapeRenderer) plot.getRenderer(); BasicStroke str = new BasicStroke(lineThickness); int n = plot.getSeriesCount(); for (int i = 0; i < n; i++) { r.setSeriesStroke(i, str); } if (legend == null || legend.isEmpty()) { chart.removeLegend(); } ret = new ChartPanel(chart); } catch (Exception ex) { throw new WebUtilException("Creating spectrum plot" + ex.getLocalizedMessage()); } return ret; }
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 va2 s .c o 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; }
From source file:edu.fullerton.viewerplugin.SpectrumPlot.java
private ChartPanel getPanel(ArrayList<ChanDataBuffer> dbufs, boolean compact) throws WebUtilException { ChartPanel ret = null;// w ww. java 2 s . c o m try { float tfsMax = 0; for (ChanDataBuffer buf : dbufs) { ChanInfo ci = buf.getChanInfo(); float fs = ci.getRate(); tfsMax = Math.max(fs, tfsMax); } setFsMax(tfsMax); String gtitle = getTitle(dbufs, compact); int nbuf = dbufs.size(); XYSeries[] xys = new XYSeries[nbuf]; XYSeriesCollection mtds = new XYSeriesCollection(); int cnum = 0; compact = dbufs.size() > 2 ? false : compact; float bw = 1.f; for (ChanDataBuffer dbuf : dbufs) { String legend = getLegend(dbuf, compact); xys[cnum] = new XYSeries(legend); bw = calcSpectrum(xys[cnum], dbuf); mtds.addSeries(xys[cnum]); } DefaultXYDataset ds = new DefaultXYDataset(); String yLabel = pwrScale.toString(); DecimalFormat dform = new DecimalFormat("0.0###"); String xLabel; xLabel = String.format("Frequency Hz - (bw: %1$s, #fft: %2$,d, s/fft: %3$.2f, ov: %4$.2f)", dform.format(bw), nfft, secperfft, overlap); Double minx, miny, maxx, maxy; Double[] rng = new Double[4]; if (fmin <= 0) { fmin = bw; } float searchFmax = fmax; if (fmax <= 0 || fmax == Float.MAX_VALUE) { fmax = tfsMax / 2; searchFmax = tfsMax / 2 * 0.8f; } PluginSupport.getRangeLimits(mtds, rng, 2, fmin, searchFmax); minx = rng[0]; miny = rng[1]; maxx = rng[2]; maxy = rng[3]; findSmallest(mtds); int exp; if (maxy == 0. && miny == 0.) { miny = -1.; exp = 0; logYaxis = false; } else { miny = miny > 0 ? miny : smallestY; maxy = maxy > 0 ? maxy : miny * 10; exp = PluginSupport.scaleRange(mtds, miny, maxy); if (!logYaxis) { yLabel += " x 1e-" + Integer.toString(exp); } } JFreeChart chart = ChartFactory.createXYLineChart(gtitle, xLabel, yLabel, ds, PlotOrientation.VERTICAL, true, false, false); XYPlot plot = (XYPlot) chart.getPlot(); if (logYaxis) { LogAxis rangeAxis = new LogAxis(yLabel); double smallest = miny * Math.pow(10, exp); rangeAxis.setSmallestValue(smallest); rangeAxis.setMinorTickCount(9); LogAxisNumberFormat lanf = new LogAxisNumberFormat(); lanf.setExp(exp); rangeAxis.setNumberFormatOverride(lanf); rangeAxis.setRange(smallest, maxy * Math.pow(10, exp)); rangeAxis.setStandardTickUnits(LogAxis.createLogTickUnits(Locale.US)); plot.setRangeAxis(rangeAxis); plot.setRangeGridlinesVisible(true); plot.setRangeGridlinePaint(Color.BLACK); } if (logXaxis) { LogAxis domainAxis = new LogAxis(xLabel); domainAxis.setBase(2); domainAxis.setMinorTickCount(9); domainAxis.setMinorTickMarksVisible(true); domainAxis.setSmallestValue(smallestX); domainAxis.setNumberFormatOverride(new LogAxisNumberFormat()); //domainAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); plot.setDomainAxis(domainAxis); plot.setDomainGridlinesVisible(true); plot.setDomainGridlinePaint(Color.BLACK); } ValueAxis domainAxis = plot.getDomainAxis(); if (fmin > Float.MIN_VALUE) { domainAxis.setLowerBound(fmin); } if (fmax != Float.MAX_VALUE) { domainAxis.setUpperBound(fmax); } plot.setDomainAxis(domainAxis); plot.setDataset(0, mtds); plot.setDomainGridlinePaint(Color.DARK_GRAY); plot.setRangeGridlinePaint(Color.DARK_GRAY); // Set the line thickness XYLineAndShapeRenderer r = (XYLineAndShapeRenderer) plot.getRenderer(); BasicStroke str = new BasicStroke(lineThickness); int n = plot.getSeriesCount(); for (int i = 0; i < n; i++) { r.setSeriesStroke(i, str); } plot.setBackgroundPaint(Color.WHITE); if (compact) { chart.removeLegend(); } ret = new ChartPanel(chart); } catch (Exception ex) { throw new WebUtilException("Creating spectrum plot" + ex.getLocalizedMessage()); } return ret; }