List of usage examples for org.jfree.chart.axis LogAxis setLowerBound
public void setLowerBound(double min)
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);/* w w w.j a v a 2 s . com*/ 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:netplot.GenericPlotPanel.java
void genericConfig(JFreeChart chart, XYPlot plot, int plotIndex) { if (!enableLegend) { chart.removeLegend();/*from w ww. ja va 2s . co m*/ } XYItemRenderer xyItemRenderer = plot.getRenderer(); //May also be XYBarRenderer if (xyItemRenderer instanceof XYLineAndShapeRenderer) { XYToolTipGenerator xyToolTipGenerator = xyItemRenderer.getBaseToolTipGenerator(); //If currently an XYLineAndShapeRenderer replace it so that we inc the colour for every plotIndex XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(linesEnabled, shapesEnabled); //Ensure we don't loose the tool tips on the new renderer renderer.setBaseToolTipGenerator(xyToolTipGenerator); renderer.setBasePaint(getPlotColour(plotIndex)); renderer.setSeriesStroke(0, new BasicStroke(lineWidth, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL), true); plot.setRenderer(plotIndex, renderer); } //If we have a new y axis then we need a new data set if (yAxisName != null && yAxisName.length() > 0) { if (logYAxis) { LogAxis yAxis = new LogAxis(yAxisName); yAxis.setAutoRange(false); yAxis.setNumberFormatOverride(new LogFormat(10, "10", true)); yAxis.setRange(minScaleValue, maxScaleValue); yAxis.setLowerBound(minScaleValue); yAxis.setUpperBound(maxScaleValue); plot.setRangeAxis(yAxisIndex, yAxis); plot.setRangeAxisLocation(yAxisIndex, AxisLocation.BOTTOM_OR_LEFT); } else { NumberAxis axis = new NumberAxis(yAxisName); axis.setAutoRangeIncludesZero(zeroOnYScale); if (autoScaleEnabled) { axis.setAutoRange(true); } else { Range range = new Range(minScaleValue, maxScaleValue); axis.setRangeWithMargins(range, true, true); } if (yAxisTickCount > 0) { NumberTickUnit tick = new NumberTickUnit(yAxisTickCount); axis.setTickUnit(tick); } plot.setRangeAxis(yAxisIndex, axis); plot.setRangeAxisLocation(yAxisIndex, AxisLocation.BOTTOM_OR_LEFT); } yAxisIndex++; } plot.mapDatasetToRangeAxis(plotIndex, yAxisIndex - 1); ValueAxis a = plot.getDomainAxis(); if (xAxisName.length() > 0) { a.setLabel(xAxisName); } //We can enable/disable zero on the axis if we have a NumberAxis if (a instanceof NumberAxis) { ((NumberAxis) a).setAutoRangeIncludesZero(zeroOnXScale); } }
From source file:edu.fullerton.viewerplugin.XYPlotter.java
private ChartPanel getPanel(double[][] data) throws WebUtilException { ChartPanel ret = null;//from w w w . j a v a2 s . c om 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:edu.fullerton.viewerplugin.SpectrumPlot.java
private ChartPanel getPanel(ArrayList<ChanDataBuffer> dbufs, boolean compact) throws WebUtilException { ChartPanel ret = null;/* w ww . j a v a 2s.co 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; }