List of usage examples for org.jfree.chart ChartRenderingInfo clear
public void clear()
From source file:gov.nih.nci.rembrandt.web.graphing.data.GeneExpressionPlot.java
public static HashMap generateBarChart(String gene, String reporter, HttpSession session, PrintWriter pw, GeneExpressionDataSetType geType) { String log2Filename = null;/* w ww . j a va 2s .com*/ String rawFilename = null; String medianFilename = null; String bwFilename = ""; String legendHtml = null; HashMap charts = new HashMap(); PlotSize ps = PlotSize.MEDIUM; final String geneName = gene; final String alg = geType.equals(GeneExpressionDataSetType.GeneExpressionDataSet) ? RembrandtConstants.REPORTER_SELECTION_AFFY : RembrandtConstants.REPORTER_SELECTION_UNI; try { InstitutionCriteria institutionCriteria = InsitutionAccessHelper.getInsititutionCriteria(session); final GenePlotDataSet gpds = new GenePlotDataSet(gene, reporter, institutionCriteria, geType, session.getId()); //final GenePlotDataSet gpds = new GenePlotDataSet(gene, institutionCriteria,GeneExpressionDataSetType.GeneExpressionDataSet ); //LOG2 Dataset DefaultStatisticalCategoryDataset dataset = (DefaultStatisticalCategoryDataset) gpds.getLog2Dataset(); //RAW Dataset CategoryDataset meanDataset = (CategoryDataset) gpds.getRawDataset(); //B&W dataset DefaultBoxAndWhiskerCategoryDataset bwdataset = (DefaultBoxAndWhiskerCategoryDataset) gpds .getBwdataset(); //Median dataset CategoryDataset medianDataset = (CategoryDataset) gpds.getMedianDataset(); charts.put("diseaseSampleCountMap", gpds.getDiseaseSampleCountMap()); //IMAGE Size Control if (bwdataset != null && bwdataset.getRowCount() > 5) { ps = PlotSize.LARGE; } else { ps = PlotSize.MEDIUM; } //SMALL/MEDIUM == 650 x 400 //LARGE == 1000 x 400 //put as external Props? int imgW = 650; if (ps == PlotSize.LARGE) { imgW = new BigDecimal(bwdataset.getRowCount()).multiply(new BigDecimal(75)).intValue() > 1000 ? new BigDecimal(bwdataset.getRowCount()).multiply(new BigDecimal(75)).intValue() : 1000; } JFreeChart bwChart = null; //B&W plot CategoryAxis xAxis = new CategoryAxis("Disease Type"); NumberAxis yAxis = new NumberAxis("Log2 Expression Intensity"); yAxis.setAutoRangeIncludesZero(true); BoxAndWhiskerCoinPlotRenderer bwRenderer = null; // BoxAndWhiskerRenderer bwRenderer = new BoxAndWhiskerRenderer(); if (reporter != null) { //single reporter, show the coins bwRenderer = new BoxAndWhiskerCoinPlotRenderer(gpds.getCoinHash()); bwRenderer.setDisplayCoinCloud(true); bwRenderer.setDisplayMean(false); bwRenderer.setDisplayAllOutliers(true); bwRenderer.setToolTipGenerator(new CategoryToolTipGenerator() { public String generateToolTip(CategoryDataset dataset, int series, int item) { String tt = ""; NumberFormat formatter = new DecimalFormat(".####"); String key = ""; //String s = formatter.format(-1234.567); // -001235 if (dataset instanceof DefaultBoxAndWhiskerCategoryDataset) { DefaultBoxAndWhiskerCategoryDataset ds = (DefaultBoxAndWhiskerCategoryDataset) dataset; try { String med = formatter.format(ds.getMedianValue(series, item)); tt += "Median: " + med + "<br/>"; tt += "Mean: " + formatter.format(ds.getMeanValue(series, item)) + "<br/>"; tt += "Q1: " + formatter.format(ds.getQ1Value(series, item)) + "<br/>"; tt += "Q3: " + formatter.format(ds.getQ3Value(series, item)) + "<br/>"; tt += "Max: " + formatter.format( FaroutOutlierBoxAndWhiskerCalculator.getMaxFaroutOutlier(ds, series, item)) + "<br/>"; tt += "Min: " + formatter.format( FaroutOutlierBoxAndWhiskerCalculator.getMinFaroutOutlier(ds, series, item)) + "<br/>"; //tt += "<br/><br/>Please click on the box and whisker to view a plot for this reporter.<br/>"; //tt += "X: " + ds.getValue(series, item).toString()+"<br/>"; //tt += "<br/><a href=\\\'#\\\' id=\\\'"+ds.getRowKeys().get(series)+"\\\' onclick=\\\'alert(this.id);return false;\\\'>"+ds.getRowKeys().get(series)+" plot</a><br/><br/>"; key = ds.getRowKeys().get(series).toString(); } catch (Exception e) { } } return tt; } }); } else { //groups, dont show coins bwRenderer = new BoxAndWhiskerCoinPlotRenderer(); bwRenderer.setDisplayAllOutliers(true); bwRenderer.setToolTipGenerator(new CategoryToolTipGenerator() { public String generateToolTip(CategoryDataset dataset, int series, int item) { String tt = ""; NumberFormat formatter = new DecimalFormat(".####"); String key = ""; //String s = formatter.format(-1234.567); // -001235 if (dataset instanceof DefaultBoxAndWhiskerCategoryDataset) { DefaultBoxAndWhiskerCategoryDataset ds = (DefaultBoxAndWhiskerCategoryDataset) dataset; try { String med = formatter.format(ds.getMedianValue(series, item)); tt += "Median: " + med + "<br/>"; tt += "Mean: " + formatter.format(ds.getMeanValue(series, item)) + "<br/>"; tt += "Q1: " + formatter.format(ds.getQ1Value(series, item)) + "<br/>"; tt += "Q3: " + formatter.format(ds.getQ3Value(series, item)) + "<br/>"; tt += "Max: " + formatter.format( FaroutOutlierBoxAndWhiskerCalculator.getMaxFaroutOutlier(ds, series, item)) + "<br/>"; tt += "Min: " + formatter.format( FaroutOutlierBoxAndWhiskerCalculator.getMinFaroutOutlier(ds, series, item)) + "<br/>"; tt += "<br/><br/>Please click on the box and whisker to view a plot for this reporter.<br/>"; //tt += "X: " + ds.getValue(series, item).toString()+"<br/>"; //tt += "<br/><a href=\\\'#\\\' id=\\\'"+ds.getRowKeys().get(series)+"\\\' onclick=\\\'alert(this.id);return false;\\\'>"+ds.getRowKeys().get(series)+" plot</a><br/><br/>"; key = ds.getRowKeys().get(series).toString(); } catch (Exception e) { } } return "onclick=\"popCoin('" + geneName + "','" + key + "', '" + alg + "');\" | " + tt; } }); } bwRenderer.setFillBox(false); CategoryPlot bwPlot = new CategoryPlot(bwdataset, xAxis, yAxis, bwRenderer); bwChart = new JFreeChart(bwPlot); // JFreeChart bwChart = new JFreeChart( // null /*"Gene Expression Plot (" + gene.toUpperCase() + ")"*/, // new Font("SansSerif", Font.BOLD, 14), // bwPlot, // true // ); bwChart.setBackgroundPaint(java.awt.Color.white); //bwChart.getTitle().setHorizontalAlignment(TextTitle.DEFAULT_HORIZONTAL_ALIGNMENT.LEFT); bwChart.removeLegend(); //END BW plot // create the chart...for LOG2 dataset JFreeChart log2Chart = ChartFactory.createBarChart( null /*"Gene Expression Plot (" + gene.toUpperCase() + ")"*/, // chart // title "Groups", // domain axis label "Log2 Expression Intensity", // range axis label dataset, // data PlotOrientation.VERTICAL, // orientation true, // include legend true, // tooltips? false // URLs? ); //create the chart .... for RAW dataset JFreeChart meanChart = ChartFactory.createBarChart( null /*"Gene Expression Plot (" + gene.toUpperCase() + ")"*/, // chart // title "Groups", // domain axis label "Mean Expression Intensity", // range axis label meanDataset, // data PlotOrientation.VERTICAL, // orientation true, // include legend true, // tooltips? false // URLs? ); // create the chart .... for Median dataset JFreeChart medianChart = ChartFactory.createBarChart( null /*"Gene Expression Plot (" + gene.toUpperCase() + ")"*/, // chart // title "Groups", // domain axis label "Median Expression Intensity", // range axis label medianDataset, // data PlotOrientation.VERTICAL, // orientation true, // include legend true, // tooltips? false // URLs? ); log2Chart.setBackgroundPaint(java.awt.Color.white); // lets start some customization to retro fit w/jcharts lookand feel CategoryPlot log2Plot = log2Chart.getCategoryPlot(); CategoryAxis log2Axis = log2Plot.getDomainAxis(); log2Axis.setLowerMargin(0.02); // two percent log2Axis.setCategoryMargin(0.20); // 20 percent log2Axis.setUpperMargin(0.02); // two percent // same for our fake chart - just to get the tooltips meanChart.setBackgroundPaint(java.awt.Color.white); CategoryPlot meanPlot = meanChart.getCategoryPlot(); CategoryAxis meanAxis = meanPlot.getDomainAxis(); meanAxis.setLowerMargin(0.02); // two percent meanAxis.setCategoryMargin(0.20); // 20 percent meanAxis.setUpperMargin(0.02); // two percent // median plot medianChart.setBackgroundPaint(java.awt.Color.white); CategoryPlot medianPlot = medianChart.getCategoryPlot(); CategoryAxis medianAxis = medianPlot.getDomainAxis(); medianAxis.setLowerMargin(0.02); // two percent medianAxis.setCategoryMargin(0.20); // 20 percent medianAxis.setUpperMargin(0.02); // two percent // customise the renderer... StatisticalBarRenderer log2Renderer = new StatisticalBarRenderer(); // BarRenderer renderer = (BarRenderer) plot.getRenderer(); log2Renderer.setItemMargin(0.01); // one percent log2Renderer.setDrawBarOutline(true); log2Renderer.setOutlinePaint(Color.BLACK); log2Renderer.setToolTipGenerator(new CategoryToolTipGenerator() { public String generateToolTip(CategoryDataset dataset, int series, int item) { HashMap pv = gpds.getPValuesHashMap(); HashMap std_d = gpds.getStdDevMap(); String currentPV = (String) pv .get(dataset.getRowKey(series) + "::" + dataset.getColumnKey(item)); String stdDev = (String) std_d .get(dataset.getRowKey(series) + "::" + dataset.getColumnKey(item)); return "Probeset : " + dataset.getRowKey(series) + "<br/>Intensity : " + new DecimalFormat("0.0000").format(dataset.getValue(series, item)) + "<br/>" + RembrandtConstants.PVALUE + " : " + currentPV + "<br/>Std. Dev.: " + stdDev + "<br/>"; } }); log2Plot.setRenderer(log2Renderer); // customize the renderer BarRenderer meanRenderer = (BarRenderer) meanPlot.getRenderer(); meanRenderer.setItemMargin(0.01); // one percent meanRenderer.setDrawBarOutline(true); meanRenderer.setOutlinePaint(Color.BLACK); meanRenderer.setToolTipGenerator(new CategoryToolTipGenerator() { public String generateToolTip(CategoryDataset dataset, int series, int item) { HashMap pv = gpds.getPValuesHashMap(); HashMap std_d = gpds.getStdDevMap(); String currentPV = (String) pv .get(dataset.getRowKey(series) + "::" + dataset.getColumnKey(item)); String stdDev = (String) std_d .get(dataset.getRowKey(series) + "::" + dataset.getColumnKey(item)); return "Probeset : " + dataset.getRowKey(series) + "<br/>Intensity : " + new DecimalFormat("0.0000").format(dataset.getValue(series, item)) + "<br/>" + RembrandtConstants.PVALUE + ": " + currentPV + "<br/>"; //"<br/>Std. Dev.: " + stdDev + "<br/>"; } }); meanPlot.setRenderer(meanRenderer); // customize the renderer BarRenderer medianRenderer = (BarRenderer) medianPlot.getRenderer(); medianRenderer.setItemMargin(0.01); // one percent medianRenderer.setDrawBarOutline(true); medianRenderer.setOutlinePaint(Color.BLACK); medianRenderer.setToolTipGenerator(new CategoryToolTipGenerator() { public String generateToolTip(CategoryDataset dataset, int series, int item) { HashMap pv = gpds.getPValuesHashMap(); HashMap std_d = gpds.getStdDevMap(); String currentPV = (String) pv .get(dataset.getRowKey(series) + "::" + dataset.getColumnKey(item)); String stdDev = (String) std_d .get(dataset.getRowKey(series) + "::" + dataset.getColumnKey(item)); return "Probeset : " + dataset.getRowKey(series) + "<br/>Intensity : " + new DecimalFormat("0.0000").format(dataset.getValue(series, item)) + "<br/>" + RembrandtConstants.PVALUE + ": " + currentPV + "<br/>"; //"<br/>Std. Dev.: " + stdDev + "<br/>"; } }); // LegendTitle lg = chart.getLegend(); medianPlot.setRenderer(medianRenderer); // lets generate a custom legend - assumes theres only one source? LegendItemCollection lic = log2Chart.getLegend().getSources()[0].getLegendItems(); legendHtml = LegendCreator.buildLegend(lic, "Probesets"); log2Chart.removeLegend(); meanChart.removeLegend(); medianChart.removeLegend(); //bwChart.removeLegend(); // <-- do this above // Write the chart image to the temporary directory ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection()); // BW if (bwChart != null) { int bwwidth = new BigDecimal(1.5).multiply(new BigDecimal(imgW)).intValue(); bwFilename = ServletUtilities.saveChartAsPNG(bwChart, bwwidth, 400, info, session); CustomOverlibToolTipTagFragmentGenerator ttip = new CustomOverlibToolTipTagFragmentGenerator(); String toolTip = " href='javascript:void(0);' alt='GeneChart JFreechart Plot' "; ttip.setExtra(toolTip); //must have href for area tags to have cursor:pointer ChartUtilities.writeImageMap(pw, bwFilename, info, ttip, new StandardURLTagFragmentGenerator()); info.clear(); // lose the first one info = new ChartRenderingInfo(new StandardEntityCollection()); } //END BW log2Filename = ServletUtilities.saveChartAsPNG(log2Chart, imgW, 400, info, session); CustomOverlibToolTipTagFragmentGenerator ttip = new CustomOverlibToolTipTagFragmentGenerator(); String toolTip = " alt='GeneChart JFreechart Plot' "; ttip.setExtra(toolTip); //must have href for area tags to have cursor:pointer ChartUtilities.writeImageMap(pw, log2Filename, info, ttip, new StandardURLTagFragmentGenerator()); // clear the first one and overwrite info with our second one - no // error bars info.clear(); // lose the first one info = new ChartRenderingInfo(new StandardEntityCollection()); rawFilename = ServletUtilities.saveChartAsPNG(meanChart, imgW, 400, info, session); // Write the image map to the PrintWriter // can use a different writeImageMap to pass tooltip and URL custom ttip = new CustomOverlibToolTipTagFragmentGenerator(); toolTip = " alt='GeneChart JFreechart Plot' "; ttip.setExtra(toolTip); //must have href for area tags to have cursor:pointer ChartUtilities.writeImageMap(pw, rawFilename, info, ttip, new StandardURLTagFragmentGenerator()); info.clear(); // lose the first one info = new ChartRenderingInfo(new StandardEntityCollection()); medianFilename = ServletUtilities.saveChartAsPNG(medianChart, imgW, 400, info, session); // Write the image map to the PrintWriter // can use a different writeImageMap to pass tooltip and URL custom ttip = new CustomOverlibToolTipTagFragmentGenerator(); toolTip = " alt='GeneChart JFreechart Plot' "; ttip.setExtra(toolTip); //must have href for area tags to have cursor:pointer ChartUtilities.writeImageMap(pw, medianFilename, info, ttip, new StandardURLTagFragmentGenerator()); // ChartUtilities.writeImageMap(pw, filename, info, true); pw.flush(); } catch (Exception e) { System.out.println("Exception - " + e.toString()); e.printStackTrace(System.out); log2Filename = "public_error_500x300.png"; } // return filename; charts.put("errorBars", log2Filename); charts.put("noErrorBars", rawFilename); charts.put("medianBars", medianFilename); charts.put("bwFilename", bwFilename); charts.put("legend", legendHtml); charts.put("size", ps.toString()); return charts; }
From source file:gov.nih.nci.cma.web.graphing.PCAPlot.java
public String generatePCAPlotChart(String components, HttpServletRequest request, PrintWriter pw) { String finalURLpath = null; //imageHandler.getFinalURLPath(); try {// w w w . jav a2 s. c o m //check the components to see which graph to get CMAPrincipalComponentAnalysisPlot plot = null; if (components.equalsIgnoreCase("PC1vsPC2")) { plot = new CMAPrincipalComponentAnalysisPlot(pcaData, PCAcomponent.PC2, PCAcomponent.PC1, sampleGroupNames); } if (components.equalsIgnoreCase("PC1vsPC3")) { plot = new CMAPrincipalComponentAnalysisPlot(pcaData, PCAcomponent.PC3, PCAcomponent.PC1, sampleGroupNames); } if (components.equalsIgnoreCase("PC2vsPC3")) { plot = new CMAPrincipalComponentAnalysisPlot(pcaData, PCAcomponent.PC3, PCAcomponent.PC2, sampleGroupNames); } chart = plot.getChart(); ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection()); // BW if (chart != null) { //int bwwidth = new BigDecimal(1.5).multiply(new BigDecimal(imgW)).intValue(); finalURLpath = ServletUtilities.saveChartAsPNG(chart, 500, 400, info, request.getSession()); CustomOverlibToolTipTagFragmentGenerator ttip = new CustomOverlibToolTipTagFragmentGenerator(); ttip.setExtra(" href='javascript:void(0);' "); //must have href for area tags to have cursor:pointer //ChartUtilities.writeImageMap(pw, finalURLpath, info, // ttip, // new StandardURLTagFragmentGenerator()); //ChartUtilities.writeImageMap(pw, finalURLpath, info, true); pw.write(ImageMapUtil.getBoundingRectImageMapTag(finalURLpath, false, info)); info.clear(); // lose the first one info = new ChartRenderingInfo(new StandardEntityCollection()); } pw.flush(); } catch (IOException e) { logger.error(e); } catch (Exception e) { logger.error(e); } catch (Throwable t) { logger.error(t); } return finalURLpath; }
From source file:gov.nih.nci.cma.web.graphing.GEPlot.java
public String generateBWLog2IntensityChart(String xAxisLabel, String yAxisLabel, HttpSession session, PrintWriter pw, boolean isCoinPlot) { String bwFilename = ""; //PlotSize ps = PlotSize.MEDIUM; JFreeChart bwChart = null;/*w w w . j av a 2 s .c om*/ try { //IMAGE Size Control CategoryAxis xAxis = new CategoryAxis(xAxisLabel); xAxis.setCategoryLabelPositions(CategoryLabelPositions.DOWN_45); NumberAxis yAxis = new NumberAxis(yAxisLabel); yAxis.setAutoRangeIncludesZero(true); BoxAndWhiskerCoinPlotRenderer bwRenderer = null; CategoryPlot bwPlot = null; if (isCoinPlot) { Map<String, List<Double>> groupMap = rawDataMap.get(reporterName); DefaultBoxAndWhiskerCategoryDataset smallBwdataset = new DefaultBoxAndWhiskerCategoryDataset(); int row = 0; int column = 0; HashMap<String, List> caIntegatorCoinList = new HashMap<String, List>(); for (String group : groupList) { smallBwdataset.add(groupMap.get(group), reporterName, group); caIntegatorCoinList.put(row + "_" + column++, groupMap.get(group)); } bwRenderer = new BoxAndWhiskerCoinPlotRenderer(caIntegatorCoinList); bwRenderer.setDisplayAllOutliers(true); bwRenderer.setDisplayCoinCloud(true); bwRenderer.setDisplayMean(false); bwRenderer.setFillBox(false); bwRenderer.setPlotColor(null); bwPlot = new CategoryPlot(smallBwdataset, xAxis, yAxis, bwRenderer); if (groupList.size() < 6) imgW = 200; } else { bwRenderer = new BoxAndWhiskerCoinPlotRenderer(); bwRenderer.setDisplayAllOutliers(true); bwRenderer.setBaseToolTipGenerator(new CategoryToolTipGenerator() { public String generateToolTip(CategoryDataset dataset, int series, int item) { String tt = ""; NumberFormat formatter = new DecimalFormat(".####"); String key = ""; //String s = formatter.format(-1234.567); // -001235 if (dataset instanceof DefaultBoxAndWhiskerCategoryDataset) { DefaultBoxAndWhiskerCategoryDataset ds = (DefaultBoxAndWhiskerCategoryDataset) dataset; try { String med = formatter.format(ds.getMedianValue(series, item)); tt += "Median: " + med + "<br/>"; tt += "Mean: " + formatter.format(ds.getMeanValue(series, item)) + "<br/>"; tt += "Q1: " + formatter.format(ds.getQ1Value(series, item)) + "<br/>"; tt += "Q3: " + formatter.format(ds.getQ3Value(series, item)) + "<br/>"; tt += "Max: " + formatter.format( FaroutOutlierBoxAndWhiskerCalculator.getMaxFaroutOutlier(ds, series, item)) + "<br/>"; tt += "Min: " + formatter.format( FaroutOutlierBoxAndWhiskerCalculator.getMinFaroutOutlier(ds, series, item)) + "<br/>"; tt += "<br/><br/>Please click on the box and whisker to view a plot for this reporter.<br/>"; key = ds.getRowKeys().get(series).toString(); } catch (Exception e) { } } String returnString = "onclick=\"popCoin('" + geneSymbol + "','" + key + "');\" | "; return returnString + tt; } }); bwRenderer.setFillBox(false); bwPlot = new CategoryPlot(bwdataset, xAxis, yAxis, bwRenderer); } bwChart = new JFreeChart(bwPlot); bwChart.setBackgroundPaint(java.awt.Color.white); LegendTitle title = bwChart.getLegend(); LegendItemSource[] sources = title.getSources(); legendItemCollection = sources[0].getLegendItems(); bwChart.removeLegend(); // Write the chart image to the temporary directory ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection()); // BW if (bwChart != null) { //int bwwidth = new BigDecimal(1.5).multiply(new BigDecimal(imgW)).intValue(); bwFilename = ServletUtilities.saveChartAsPNG(bwChart, imgW, 400, info, session); CustomOverlibToolTipTagFragmentGenerator ttip = new CustomOverlibToolTipTagFragmentGenerator(); ttip.setExtra(" href='javascript:void(0);' "); //must have href for area tags to have cursor:pointer ChartUtilities.writeImageMap(pw, bwFilename, info, ttip, new StandardURLTagFragmentGenerator()); info.clear(); // lose the first one info = new ChartRenderingInfo(new StandardEntityCollection()); } //END BW pw.flush(); } catch (Exception e) { System.out.println("Exception - " + e.toString()); e.printStackTrace(System.out); } // return filename; //charts.put("errorBars", log2Filename); //charts.put("noErrorBars", rawFilename); //charts.put("bwFilename", bwFilename); //charts.put("legend", legendHtml); //charts.put("size", ps.toString()); return bwFilename; }