List of usage examples for org.jfree.chart.plot CategoryPlot setDomainGridlinesVisible
public void setDomainGridlinesVisible(boolean visible)
From source file:mzmatch.ipeak.normalisation.VanDeSompele.java
public static void main(String args[]) { try {// w w w . j a va 2 s. c o m 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.AxisOffsetsDemo1.java
private static JFreeChart createChart(String s, CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart(s, "Category", "Value", categorydataset, PlotOrientation.VERTICAL, false, true, false); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setDomainGridlinesVisible(true); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); barrenderer.setSeriesPaint(0, gradientpaint); barrenderer.setSeriesPaint(1, gradientpaint1); barrenderer.setSeriesPaint(2, gradientpaint2); return jfreechart; }
From source file:org.jfree.chart.demo.MouseOverDemo1.java
private static JFreeChart createChart(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Mouseover Demo 1", "Category", "Value", categorydataset, PlotOrientation.VERTICAL, true, true, false); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setDomainGridlinesVisible(true); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); MyBarRenderer mybarrenderer = new MyBarRenderer(); mybarrenderer.setDrawBarOutline(true); categoryplot.setRenderer(mybarrenderer); ChartUtilities.applyCurrentTheme(jfreechart); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); mybarrenderer.setSeriesPaint(0, gradientpaint); mybarrenderer.setSeriesPaint(1, gradientpaint1); mybarrenderer.setSeriesPaint(2, gradientpaint2); return jfreechart; }
From source file:userInterface.ManufactureRole.DecisionChartJPanel.java
private static JFreeChart createChart1(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Vaccine Sales", "Vaccine", "quantity", categorydataset, PlotOrientation.VERTICAL, true, true, false); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setDomainGridlinesVisible(true); categoryplot.setRangeCrosshairVisible(true); categoryplot.setRangeCrosshairPaint(Color.blue); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); barrenderer.setSeriesPaint(0, gradientpaint); barrenderer.setSeriesPaint(1, gradientpaint1); barrenderer.setSeriesPaint(2, gradientpaint2); barrenderer.setLegendItemToolTipGenerator(new StandardCategorySeriesLabelGenerator("Tooltip: {0}")); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions( CategoryLabelPositions.createUpRotationLabelPositions(0.52359877559829882D)); return jfreechart; }
From source file:org.jfree.chart.demo.BarChartDemo11.java
private static JFreeChart createChart(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Open Source Projects By Licence", "Licence", "Project Count", categorydataset, PlotOrientation.HORIZONTAL, false, true, false); jfreechart.setBackgroundPaint(Color.white); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setBackgroundPaint(Color.lightGray); categoryplot.setDomainGridlinePaint(Color.white); categoryplot.setDomainGridlinesVisible(true); categoryplot.setRangeGridlinePaint(Color.white); categoryplot.getDomainAxis().setMaximumCategoryLabelWidthRatio(0.4F); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); barrenderer.setSeriesPaint(0, gradientpaint); return jfreechart; }
From source file:userInterface.StateAdminRole.DecisionChart4JPanel.java
private static JFreeChart createChart1(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Total Vaccinations", "Hospital", "Value", categorydataset, PlotOrientation.VERTICAL, true, true, false); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setDomainGridlinesVisible(true); categoryplot.setRangeCrosshairVisible(true); categoryplot.setRangeCrosshairPaint(Color.blue); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); barrenderer.setSeriesPaint(0, gradientpaint); barrenderer.setSeriesPaint(1, gradientpaint1); barrenderer.setSeriesPaint(2, gradientpaint2); barrenderer.setLegendItemToolTipGenerator(new StandardCategorySeriesLabelGenerator("Tooltip: {0}")); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions( CategoryLabelPositions.createUpRotationLabelPositions(0.52359877559829882D)); return jfreechart; }
From source file:demo.BarChartDemo11.java
/** * Creates a sample chart.// w w w.j a v a 2 s. com * * @param dataset the dataset. * * @return The chart. */ private static JFreeChart createChart(CategoryDataset dataset) { // create the chart... JFreeChart chart = ChartFactory.createBarChart("Open Source Projects By License", "License", "Percent", dataset); chart.removeLegend(); TextTitle source = new TextTitle( "Source: http://www.blackducksoftware.com/resources/data/top-20-licenses (as at 30 Aug 2013)", new Font("Dialog", Font.PLAIN, 9)); source.setPosition(RectangleEdge.BOTTOM); chart.addSubtitle(source); // get a reference to the plot for further customisation... CategoryPlot plot = (CategoryPlot) chart.getPlot(); plot.setOrientation(PlotOrientation.HORIZONTAL); plot.setDomainGridlinesVisible(true); plot.getDomainAxis().setMaximumCategoryLabelWidthRatio(0.8f); // set the range axis to display integers only... NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false); StandardCategoryToolTipGenerator tt = new StandardCategoryToolTipGenerator("{1}: {2} percent", new DecimalFormat("0")); renderer.setBaseToolTipGenerator(tt); // set up gradient paints for series... GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.BLUE, 0.0f, 0.0f, new Color(0, 0, 64)); renderer.setSeriesPaint(0, gp0); return chart; }
From source file:wef.articulab.view.ui.BNCategoryPlot.java
/** * Creates a chart./*from w w w .j a v a2 s. co m*/ * * @return A chart. */ private static JFreeChart createChart() { dataset = createDataset(); NumberAxis rangeAxis1 = new NumberAxis("Value"); rangeAxis1.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); LineAndShapeRenderer renderer = new LineAndShapeRenderer(); renderer.setBaseToolTipGenerator(new StandardCategoryToolTipGenerator()); CategoryPlot subplot = new CategoryPlot(dataset, null, rangeAxis1, renderer); subplot.setDomainGridlinesVisible(true); CategoryAxis domainAxis = new CategoryAxis("Time"); CombinedCategoryPlot plot = new CombinedCategoryPlot(domainAxis, new NumberAxis("Activation")); plot.add(subplot); return new JFreeChart("Social Reasoner Plot", new Font("SansSerif", Font.BOLD, 12), plot, true); }
From source file:userInterface.StateAdminRole.DecisionCartJPanel2.java
private static JFreeChart createChart1(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Order Statistics", "Hospital", "Value", categorydataset, PlotOrientation.VERTICAL, true, true, false); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setDomainGridlinesVisible(true); categoryplot.setRangeCrosshairVisible(true); categoryplot.setRangeCrosshairPaint(Color.blue); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); barrenderer.setSeriesPaint(0, gradientpaint); barrenderer.setSeriesPaint(1, gradientpaint1); barrenderer.setSeriesPaint(2, gradientpaint2); barrenderer.setLegendItemToolTipGenerator(new StandardCategorySeriesLabelGenerator("Tooltip: {0}")); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions( CategoryLabelPositions.createUpRotationLabelPositions(0.52359877559829882D)); return jfreechart; }
From source file:org.jfree.chart.demo.selection.SelectionDemo5Category.java
private static JFreeChart createChart(CategoryDataset dataset, DatasetSelectionExtension<CategoryCursor<String, String>> ext) { // create the chart... JFreeChart chart = ChartFactory.createBarChart("Bar Chart Demo 1", "Category", "Value", dataset); CategoryPlot plot = (CategoryPlot) chart.getPlot(); plot.setDomainGridlinesVisible(true); plot.setRangeCrosshairVisible(true); plot.setRangeCrosshairPaint(Color.blue); // set the range axis to display integers only... NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false);//from w w w . j a va2s.c om // set up gradient paints for series... GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.BLUE, 0.0f, 0.0f, new Color(0, 0, 64)); GradientPaint gp1 = new GradientPaint(0.0f, 0.0f, Color.GREEN, 0.0f, 0.0f, new Color(0, 64, 0)); GradientPaint gp2 = new GradientPaint(0.0f, 0.0f, Color.RED, 0.0f, 0.0f, new Color(64, 0, 0)); renderer.setSeriesPaint(0, gp0); renderer.setSeriesPaint(1, gp1); renderer.setSeriesPaint(2, gp2); renderer.setLegendItemToolTipGenerator(new StandardCategorySeriesLabelGenerator("Tooltip: {0}")); CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 6.0)); //add selection specific rendering IRSUtilities.setSelectedItemPaint(renderer, ext, Color.WHITE); //register plot as selection change listener ext.addChangeListener(plot); return chart; }