List of usage examples for org.jfree.chart.annotations XYShapeAnnotation XYShapeAnnotation
public XYShapeAnnotation(Shape shape, Stroke stroke, Paint outlinePaint, Paint fillPaint)
From source file:gov.nih.nci.rembrandt.web.plots.RBTPrincipalComponentAnalysisPlot.java
/** * This chart uses the XYAnnotation as a glyph to represent * a single pca data point. Glyph shape is determined by survival time. * Survival of more than 10 months is represented by a circle. 10 months or less * is represented by a square. Component1 values are represented by X * Component2 values are represented by Y *//*from ww w . j a va2 s .c o m*/ protected void createGlyphsAndAddToPlot(XYPlot plot) { //for RBT, if its non_tumor, show a diamond meaning "N/A for survival" XYShapeAnnotation glyph; Shape glyphShape; Color glyphColor; PrincipalComponentAnalysisDataPoint pcaPoint; double x, y; for (Iterator i = dataPoints.iterator(); i.hasNext();) { pcaPoint = (PrincipalComponentAnalysisDataPoint) i.next(); x = pcaPoint.getComponentValue(component1); y = pcaPoint.getComponentValue(component2); double survival = pcaPoint.getSurvivalInMonths(); String diseaseName = pcaPoint.getDiseaseName(); if (this.colorBy.equals(PCAcolorByType.NONE)) { Ellipse2D.Double circle = new Ellipse2D.Double(); circle.setFrameFromCenter(x, y, x + 2, y + 2); glyphShape = circle; } else if (diseaseName.equals(RembrandtConstants.NON_TUMOR) || diseaseName.equals("CELL_LINE")) { //glyphShape = ShapeUtilities.createDiamond(new Float(x)); Rectangle2D.Double rect = new Rectangle2D.Double(); rect.setFrameFromCenter(x, y, x + 2, y + 2); glyphShape = rect; Shape gShape = ShapeUtilities.rotateShape(glyphShape, new Double(0.785398163), new Float(x), new Float(y)); glyphShape = gShape; } else if ((survival > 0) && (survival < 10.0)) { Rectangle2D.Double rect = new Rectangle2D.Double(); rect.setFrameFromCenter(x, y, x + 2, y + 2); glyphShape = rect; } else if ((survival > 0) && (survival >= 10.0)) { Ellipse2D.Double circle = new Ellipse2D.Double(); circle.setFrameFromCenter(x, y, x + 2, y + 2); glyphShape = circle; } else { GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf + 3.0f, yf - 3.0f); gp.lineTo(xf - 3.0f, yf - 3.0f); gp.closePath(); glyphShape = gp; } glyphColor = getColorForDataPoint(pcaPoint); glyph = new XYShapeAnnotation(glyphShape, new BasicStroke(1.0f), Color.BLACK, glyphColor); String tooltip = ""; if (pcaPoint.getSurvivalInMonths() <= 0.0) { tooltip = pcaPoint.getSampleId() + " " + pcaPoint.getDiseaseName(); } else { tooltip = pcaPoint.getSampleId() + " " + pcaPoint.getDiseaseName() + " survivalMonths=" + nf.format(pcaPoint.getSurvivalInMonths()); } glyph.setToolTipText(tooltip); plot.addAnnotation(glyph); } }
From source file:gov.nih.nci.caintegrator.ui.graphing.chart.plot.ClinicalPlot.java
private void createGlyphsAndAddToPlot(XYPlot plot) { XYShapeAnnotation glyph;//from w w w .j ava 2s .co m Shape glyphShape; Color glyphColor; ClinicalDataPoint clinicalPoint; String survivalLenStr; double x, y; for (Iterator i = dataPoints.iterator(); i.hasNext();) { clinicalPoint = (ClinicalDataPoint) i.next(); x = clinicalPoint.getFactorValue(factor1); y = clinicalPoint.getFactorValue(factor2); if ((x != ClinicalDataPoint.MISSING_CLINICAL_FACTOR_VALUE) && (y != ClinicalDataPoint.MISSING_CLINICAL_FACTOR_VALUE)) { //Make this a triangle GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf + 1.5f, yf - 1.5f); gp.lineTo(xf - 1.5f, yf - 1.5f); gp.closePath(); glyphShape = gp; //Rectangle2D.Double rect = new Rectangle2D.Double(); //rect.setFrameFromCenter(x,y, x+1,y+1); //glyphShape = rect; glyphColor = getColorForDataPoint(clinicalPoint); glyph = new XYShapeAnnotation(glyphShape, new BasicStroke(1.0f), Color.BLACK, glyphColor); if (clinicalPoint.getSurvivalInMonths() >= 0.0) { survivalLenStr = nf.format(clinicalPoint.getSurvivalInMonths()); } else { survivalLenStr = ""; } String tooltip = clinicalPoint.getPatientId() + " " + clinicalPoint.getDiseaseName() + " survivalMonths=" + survivalLenStr; glyph.setToolTipText(tooltip); plot.addAnnotation(glyph); } } }
From source file:gov.nih.nci.cma.web.graphing.CMAPrincipalComponentAnalysisPlot.java
/** * This chart uses the XYAnnotation as a glyph to represent * a single pca data point. Glyph shape is determined by survival time. * Survival of more than 10 months is represented by a circle. 10 months or less * is represented by a square. Component1 values are represented by X * Component2 values are represented by Y *//*from w w w. ja va 2 s. c o m*/ private void createGlyphsAndAddToPlot(XYPlot plot) { //, double glyphScaleFactor) { XYShapeAnnotation glyph; Shape glyphShape = null; Color glyphColor; NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis(); Range r = domainAxis.getRange(); double upperBound = r.getUpperBound(); double dotSize = 0.7; if (upperBound >= 50 && upperBound <= 100) dotSize = 1d; else if (upperBound > 100 && upperBound <= 150) dotSize = 2d; else if (upperBound > 150 && upperBound <= 200) dotSize = 3d; else if (upperBound > 200) dotSize = 5d; //PrincipalComponentAnalysisDataPoint pcaPoint; double x, y; //for (Iterator i=dataPoints.iterator(); i.hasNext(); ) { for (CMAPCADataPoint pcaPoint : dataPoints) { x = pcaPoint.getComponentValue(component1); y = pcaPoint.getComponentValue(component2); String sampleGroupName = pcaPoint.getSampleGroupName(); String order = sampleGroupNames.get(sampleGroupName); glyphShape = getShapeForDataPoint(order, x, y, dotSize); glyphColor = colorMap.get(order); if (glyphColor == null) glyphColor = Color.black; glyph = new XYShapeAnnotation(glyphShape, new BasicStroke(1.0f), Color.BLACK, glyphColor); String tooltip = ""; tooltip = pcaPoint.getSampleId() + " " + pcaPoint.getSampleGroupName(); glyph.setToolTipText(tooltip); plot.addAnnotation(glyph); } }
From source file:probe.com.view.core.chart4j.VennDiagramPanel.java
/** * Update the plot./*w ww .j a v a 2s . co m*/ */ public void updatePlot() { // plotPanel.removeAll(); tooltipToDatasetMap = new HashMap<String, String>(); DefaultXYZDataset xyzDataset = new DefaultXYZDataset(); chart = ChartFactory.createBubbleChart(null, "X", "Y", xyzDataset, PlotOrientation.VERTICAL, false, true, false); XYPlot plot = chart.getXYPlot(); if (currentVennDiagramType == VennDiagramType.ONE_WAY) { plot.getRangeAxis().setRange(0.86, 1.24); plot.getDomainAxis().setRange(0.85, 1.25); } else if (currentVennDiagramType == VennDiagramType.TWO_WAY) { plot.getRangeAxis().setRange(0.86, 1.24); plot.getDomainAxis().setRange(0.85, 1.25); } else if (currentVennDiagramType == VennDiagramType.THREE_WAY) { plot.getRangeAxis().setRange(0.86, 1.24); plot.getDomainAxis().setRange(0.85, 1.25); } else { plot.getRangeAxis().setRange(-0.04, 0.6); plot.getDomainAxis().setRange(-0.08, 0.7); } plot.getRangeAxis().setVisible(false); plot.getDomainAxis().setVisible(false); double radius = 0.1; Ellipse2D ellipse = new Ellipse2D.Double(1 - radius, 1 - radius, radius + radius, radius + radius); XYShapeAnnotation xyShapeAnnotation = new XYShapeAnnotation(ellipse, new BasicStroke(2f), new Color(140, 140, 140, 150), datasetAColor); // @TODO: make it possible set the line color and width? plot.addAnnotation(xyShapeAnnotation); if (currentVennDiagramType == VennDiagramType.TWO_WAY || currentVennDiagramType == VennDiagramType.THREE_WAY) { ellipse = new Ellipse2D.Double(1 - radius + 0.1, 1 - radius, radius + radius, radius + radius); xyShapeAnnotation = new XYShapeAnnotation(ellipse, new BasicStroke(2f), new Color(140, 140, 140, 150), datasetBColor); plot.addAnnotation(xyShapeAnnotation); } if (currentVennDiagramType == VennDiagramType.THREE_WAY) { ellipse = new Ellipse2D.Double(1 - radius + 0.05, 1 - radius + 0.1, radius + radius, radius + radius); xyShapeAnnotation = new XYShapeAnnotation(ellipse, new BasicStroke(2f), new Color(140, 140, 140, 150), datasetCColor); plot.addAnnotation(xyShapeAnnotation); } XYTextAnnotation anotation; if (currentVennDiagramType == VennDiagramType.ONE_WAY) { anotation = new XYTextAnnotation("" + vennDiagramResults.get("a").size(), 1.0, 1.0); anotation.setToolTipText(groupNames.get("a")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "a"); // legend if (showLegend) { anotation = new XYTextAnnotation(groupNames.get("a"), legendDatasetAThreeWay.getX(), legendDatasetAThreeWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); } } else if (currentVennDiagramType == VennDiagramType.TWO_WAY) { anotation = new XYTextAnnotation("" + vennDiagramResults.get("a").size(), 0.96, 1.0); anotation.setToolTipText(groupNames.get("a")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "a"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("b").size(), 1.14, 1.0); anotation.setToolTipText(groupNames.get("b")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "b"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("ab").size(), 1.05, 1.0); anotation .setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "ab"); // legend if (showLegend) { anotation = new XYTextAnnotation(groupNames.get("a"), legendDatasetAThreeWay.getX(), legendDatasetAThreeWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); anotation = new XYTextAnnotation(groupNames.get("b"), legendDatasetBThreeWay.getX(), legendDatasetBThreeWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); } } else if (currentVennDiagramType == VennDiagramType.THREE_WAY) { anotation = new XYTextAnnotation("" + vennDiagramResults.get("a").size(), 0.96, 0.97); anotation.setToolTipText(groupNames.get("a")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "a"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("b").size(), 1.14, 0.97); anotation.setToolTipText(groupNames.get("b")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "b"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("ab").size(), 1.05, 0.97); anotation .setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "ab"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("c").size(), 1.05, 1.14); anotation.setToolTipText(groupNames.get("c")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "c"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("ac").size(), 0.99, 1.065); anotation.setToolTipText( "<html>" + groupNames.get("a") + " ∩ " + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "ac"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("bc").size(), 1.11, 1.065); anotation .setToolTipText("<html>" + groupNames.get("b") + " ∩ " + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "bc"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("abc").size(), 1.05, 1.036); anotation.setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + " ∩ " + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "abc"); // legend if (showLegend) { anotation = new XYTextAnnotation(groupNames.get("a"), legendDatasetAThreeWay.getX(), legendDatasetAThreeWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); anotation = new XYTextAnnotation(groupNames.get("b"), legendDatasetBThreeWay.getX(), legendDatasetBThreeWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); anotation = new XYTextAnnotation(groupNames.get("c"), legendDatasetCThreeWay.getX(), legendDatasetCThreeWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); } } else if (currentVennDiagramType == VennDiagramType.FOUR_WAY) { XYBoxAnnotation anotation2 = new XYBoxAnnotation(0, 0, 0.2, 0.5, new BasicStroke(2), Color.LIGHT_GRAY, datasetAColor); plot.addAnnotation(anotation2); anotation2 = new XYBoxAnnotation(0.1, 0, 0.3, 0.4, new BasicStroke(2), Color.LIGHT_GRAY, datasetBColor); plot.addAnnotation(anotation2); anotation2 = new XYBoxAnnotation(0, 0.1, 0.4, 0.3, new BasicStroke(2), Color.LIGHT_GRAY, datasetCColor); plot.addAnnotation(anotation2); anotation2 = new XYBoxAnnotation(0, 0, 0.5, 0.2, new BasicStroke(2), Color.LIGHT_GRAY, datasetDColor); plot.addAnnotation(anotation2); anotation = new XYTextAnnotation("" + vennDiagramResults.get("a").size(), 0.15, 0.45); anotation.setToolTipText(groupNames.get("a")); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "a"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("ab").size(), 0.15, 0.35); anotation .setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "ab"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("abc").size(), 0.15, 0.25); anotation.setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + " ∩ " + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "abc"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("abcd").size(), 0.15, 0.15); anotation.setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + " ∩ " + groupNames.get("c") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "abcd"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("abd").size(), 0.15, 0.05); anotation.setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("b") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "abd"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("ac").size(), 0.05, 0.25); anotation .setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "ac"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("acd").size(), 0.05, 0.15); anotation.setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("c") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "acd"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("ad").size(), 0.05, 0.05); anotation .setToolTipText("<html>" + groupNames.get("a") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "ad"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("b").size(), 0.25, 0.35); anotation.setToolTipText("<html>" + groupNames.get("b") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "b"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("bc").size(), 0.25, 0.25); anotation .setToolTipText("<html>" + groupNames.get("b") + " ∩ " + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "bc"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("bcd").size(), 0.25, 0.15); anotation.setToolTipText("<html>" + groupNames.get("b") + " ∩ " + groupNames.get("c") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "bcd"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("bd").size(), 0.25, 0.05); anotation .setToolTipText("<html>" + groupNames.get("b") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "bd"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("c").size(), 0.35, 0.25); anotation.setToolTipText("<html>" + groupNames.get("c") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "c"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("cd").size(), 0.35, 0.15); anotation .setToolTipText("<html>" + groupNames.get("c") + " ∩ " + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "cd"); anotation = new XYTextAnnotation("" + vennDiagramResults.get("d").size(), 0.45, 0.15); anotation.setToolTipText("<html>" + groupNames.get("d") + "</html>"); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeValues)); plot.addAnnotation(anotation); tooltipToDatasetMap.put(anotation.getToolTipText(), "d"); // legend if (showLegend) { anotation = new XYTextAnnotation(groupNames.get("a"), legendDatasetAFourWay.getX(), legendDatasetAFourWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); anotation = new XYTextAnnotation(groupNames.get("b"), legendDatasetBFourWay.getX(), legendDatasetBFourWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); anotation = new XYTextAnnotation(groupNames.get("c"), legendDatasetCFourWay.getX(), legendDatasetCFourWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); anotation = new XYTextAnnotation(groupNames.get("d"), legendDatasetDFourWay.getX(), legendDatasetDFourWay.getY()); anotation.setTextAnchor(TextAnchor.BASELINE_LEFT); anotation.setFont(new Font(anotation.getFont().getFontName(), Font.BOLD, fontSizeLegend)); plot.addAnnotation(anotation); } } // set up the renderer XYBubbleRenderer renderer = new XYBubbleRenderer(XYBubbleRenderer.SCALE_ON_RANGE_AXIS); renderer.setBaseToolTipGenerator(new StandardXYZToolTipGenerator()); plot.setRenderer(renderer); // make all datapoints semitransparent plot.setForegroundAlpha(0.5f); // remove space before/after the domain axis plot.getDomainAxis().setUpperMargin(0); plot.getDomainAxis().setLowerMargin(0); plot.setRangeGridlinePaint(Color.black); // hide unwanted chart details plot.setDomainGridlinesVisible(false); plot.setRangeGridlinesVisible(false); chart.getPlot().setOutlineVisible(false); // set background color chart.getPlot().setBackgroundPaint(Color.WHITE); chart.setBackgroundPaint(Color.WHITE); chartPanel = new ChartPanel(chart); // disable the pop up menu chartPanel.setPopupMenu(null); chartPanel.setBackground(Color.WHITE); // add the plot to the chart // plotPanel.add(chartPanel); // plotPanel.revalidate(); // plotPanel.repaint(); // // this.add(plotPanel); }
From source file:gov.nih.nci.caintegrator.ui.graphing.chart.plot.PrincipalComponentAnalysisPlot.java
/** * This chart uses the XYAnnotation as a glyph to represent * a single pca data point. Glyph shape is determined by survival time. * Survival of more than 10 months is represented by a circle. 10 months or less * is represented by a square. Component1 values are represented by X * Component2 values are represented by Y *//*from w w w . j a va 2 s. c o m*/ protected void createGlyphsAndAddToPlot(XYPlot plot) { XYShapeAnnotation glyph; Shape glyphShape; Color glyphColor; PrincipalComponentAnalysisDataPoint pcaPoint; double x, y; for (Iterator i = dataPoints.iterator(); i.hasNext();) { pcaPoint = (PrincipalComponentAnalysisDataPoint) i.next(); x = pcaPoint.getComponentValue(component1); y = pcaPoint.getComponentValue(component2); double survival = pcaPoint.getSurvivalInMonths(); if ((survival > 0) && (survival < 10.0)) { Rectangle2D.Double rect = new Rectangle2D.Double(); rect.setFrameFromCenter(x, y, x + 2, y + 2); glyphShape = rect; } else if ((survival > 0) && (survival >= 10.0)) { Ellipse2D.Double circle = new Ellipse2D.Double(); circle.setFrameFromCenter(x, y, x + 2, y + 2); glyphShape = circle; } else { //Rectangle2D.Double rect = new Rectangle2D.Double(); //rect.setFrameFromCenter(x,y, x+2,y+2); GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf + 3.0f, yf - 3.0f); gp.lineTo(xf - 3.0f, yf - 3.0f); gp.closePath(); glyphShape = gp; } glyphColor = getColorForDataPoint(pcaPoint); glyph = new XYShapeAnnotation(glyphShape, new BasicStroke(1.0f), Color.BLACK, glyphColor); String tooltip = ""; if (pcaPoint.getSurvivalInMonths() <= 0.0) { tooltip = pcaPoint.getSampleId() + " " + pcaPoint.getDiseaseName(); } else { tooltip = pcaPoint.getSampleId() + " " + pcaPoint.getDiseaseName() + " survivalMonths=" + nf.format(pcaPoint.getSurvivalInMonths()); } glyph.setToolTipText(tooltip); plot.addAnnotation(glyph); } }
From source file:gov.nih.nci.ispy.ui.graphing.chart.plot.ISPYPrincipalComponentAnalysisPlot.java
/** * This chart uses the XYAnnotation as a glyph to represent * a single pca data point. Glyph shape is determined by survival time. * Survival of more than 10 months is represented by a circle. 10 months or less * is represented by a square. Component1 values are represented by X * Component2 values are represented by Y *///from w w w . j av a 2 s .c o m private void createGlyphsAndAddToPlot(XYPlot plot, double glyphScaleFactor) { XYShapeAnnotation glyph; Shape glyphShape = null; Color glyphColor; double glyphSize = 8.0; //pixels double glyphIncrement = (glyphSize * glyphScaleFactor) / 2.0; float gi = (float) glyphIncrement; ISPYPCADataPoint pcaPoint; double x, y; for (Iterator i = dataPoints.iterator(); i.hasNext();) { pcaPoint = (ISPYPCADataPoint) i.next(); x = pcaPoint.getComponentValue(component1); y = pcaPoint.getComponentValue(component2); Double mriPctChange = pcaPoint.getTumorMRIpctChange(); if (mriPctChange == null) { //data is missing Rectangle2D.Double rect = new Rectangle2D.Double(); //rect.setFrameFromCenter(x,y, x+1.25,y+1.25); rect.setFrameFromCenter(x, y, x + glyphIncrement, y + glyphIncrement); glyphShape = rect; } else if (mriPctChange <= -30.0) { //tumor shrank by more than 30% (down arrow) GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf - gi, yf + gi); gp.lineTo(xf + gi, yf + gi); gp.closePath(); glyphShape = gp; } else if (mriPctChange > 0.0) { //tumor size increased (up arrow) GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf + gi, yf - gi); gp.lineTo(xf - gi, yf - gi); gp.closePath(); glyphShape = gp; // Ellipse2D.Double circle = new Ellipse2D.Double(); // circle.setFrameFromCenter(x,y, x+2, y+2); } else if ((mriPctChange > -30.0) && (mriPctChange <= 0.0)) { //no change or reduction in tumor size but less than 30% reduction Ellipse2D.Double circle = new Ellipse2D.Double(); //circle.setFrameFromCenter(x,y,x+1.25,y+1.25); circle.setFrameFromCenter(x, y, x + gi, y + gi); glyphShape = circle; } glyphColor = getColorForDataPoint(pcaPoint); glyph = new XYShapeAnnotation(glyphShape, new BasicStroke(1.0f), Color.BLACK, glyphColor); String tooltip = pcaPoint.toString(); glyph.setToolTipText(tooltip); plot.addAnnotation(glyph); } }
From source file:com.juanhg.icecubes.IceCubesApplet.java
private void drawGlass() { Stroke border = new BasicStroke(3f); gBaseAnnotation = new XYShapeAnnotation(new Ellipse2D.Double(gXLeft, gYBase - 0.5, gXRight - gXLeft, 1), border, Color.BLACK, fluidColor); chartGlass.setAnnotation(gBaseAnnotation); gTopAnnotation = new XYShapeAnnotation(new Ellipse2D.Double(gXLeft, gYTop - 0.5, gXRight - gXLeft, 1), border, Color.BLACK); chartGlass.setAnnotation(gTopAnnotation); gRightAnnotation = new XYLineAnnotation(gXRight, gYBase, gXRight, gYTop, border, Color.black); chartGlass.setAnnotation(gRightAnnotation); gLeftAnnotation = new XYLineAnnotation(gXLeft, gYBase, gXLeft, gYTop, border, Color.black); chartGlass.setAnnotation(gLeftAnnotation); gTopAnnotation = new XYBoxAnnotation(gXLeft, gYBase, gXRight, gYTop / 2, null, null, fluidColor); chartGlass.setAnnotation(gTopAnnotation); updateGlass(IceCubesModel.getV(sliderVol.getValue(), sliderN.getValue())); }
From source file:com.juanhg.icecubes.IceCubesApplet.java
private void updateGlass(double vol) { double surface = vol; Stroke border = new BasicStroke(3f); chartGlass.deleteAnnotation(gBaseAnnotation); gBaseAnnotation = new XYShapeAnnotation(new Ellipse2D.Double(gXLeft, gYBase - 0.5, gXRight - gXLeft, 1), border, Color.BLACK, fluidColor); chartGlass.setAnnotation(gBaseAnnotation); chartGlass.deleteAnnotation(gTopAnnotation); gTopAnnotation = new XYBoxAnnotation(gXLeft, gYBase, gXRight, surface, null, null, fluidColor); chartGlass.setAnnotation(gTopAnnotation); chartGlass.deleteAnnotation(gSurfaceAnnotation); gSurfaceAnnotation = new XYShapeAnnotation( new Ellipse2D.Double(gXLeft, (surface) - 0.5, gXRight - gXLeft, 1), border, Color.BLACK, fluidColor);/* w w w. ja v a 2 s . co m*/ chartGlass.setAnnotation(gSurfaceAnnotation); chartGlass.deleteAnnotation(cube1Annotation); chartGlass.deleteAnnotation(cube2Annotation); chartGlass.deleteAnnotation(cube3Annotation); chartGlass.deleteAnnotation(cube4Annotation); if (sliderVol.getValue() >= 10 || N <= 2) { if (N >= 1) { cube1Annotation = new XYShapeAnnotation( new RoundRectangle2D.Double(cX, surface - 2, getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube1Annotation); if (N >= 2) { cube2Annotation = new XYShapeAnnotation(new RoundRectangle2D.Double(cX + getCubeW() + 0.4, surface - 2, getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube2Annotation); if (N >= 3) { cube3Annotation = new XYShapeAnnotation(new RoundRectangle2D.Double(cX, surface - 2.2 - getCubeH(), getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube3Annotation); if (N >= 4) { cube4Annotation = new XYShapeAnnotation( new RoundRectangle2D.Double(cX + getCubeW() + 0.4, surface - 2.2 - getCubeH(), getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube4Annotation); } } } } } else { if (N >= 1) { cube1Annotation = new XYShapeAnnotation( new RoundRectangle2D.Double(cX, gYBase, getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube1Annotation); if (N >= 2) { cube2Annotation = new XYShapeAnnotation(new RoundRectangle2D.Double(cX + getCubeW() + 0.4, gYBase, getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube2Annotation); if (N >= 3) { cube3Annotation = new XYShapeAnnotation(new RoundRectangle2D.Double(cX, gYBase + getCubeH(), getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube3Annotation); if (N >= 4) { cube4Annotation = new XYShapeAnnotation( new RoundRectangle2D.Double(cX + getCubeW() + 0.4, gYBase + getCubeH(), getCubeW(), getCubeH(), archeight, archwidth), border, Color.BLACK, cubeColor); chartGlass.setAnnotation(cube4Annotation); } } } } } }
From source file:gov.nih.nci.ispy.ui.graphing.chart.plot.ISPYCorrelationScatterPlot.java
private void createGlyphsAndAddToPlot(XYPlot plot, double xScale, double yScale) { XYShapeAnnotation glyph;//www . j a va 2 s.c om Shape glyphShape = null; Color glyphColor; //double glyphSize = 8.0; //pixels double glyphIncrementX = (glyphSize * xScale) / 2.0; double glyphIncrementY = (glyphSize * yScale) / 2.0; float gi_x = (float) glyphIncrementX; float gi_y = (float) glyphIncrementY; PatientData pd; double x, y; Double mriPctChange = null; for (ISPYPlotPoint corrPoint : dataPoints) { x = corrPoint.getX(); y = corrPoint.getY(); mriPctChange = corrPoint.getMRITumorPctChange(); if (mriPctChange == null) { //data is missing Rectangle2D.Double rect = new Rectangle2D.Double(); //rect.setFrameFromCenter(x,y, x+1.25,y+1.25); rect.setFrameFromCenter(x, y, x + glyphIncrementX, y + glyphIncrementY); glyphShape = rect; } else if (mriPctChange <= -30.0) { //tumor shrank by more than 30% (down arrow) GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf - gi_x, yf + gi_y); gp.lineTo(xf + gi_x, yf + gi_y); gp.closePath(); glyphShape = gp; } else if (mriPctChange > 0.0) { //tumor size increased (up arrow) GeneralPath gp = new GeneralPath(); float xf = (float) x; float yf = (float) y; //make a triangle gp.moveTo(xf, yf); gp.lineTo(xf + gi_x, yf - gi_y); gp.lineTo(xf - gi_x, yf - gi_y); gp.closePath(); glyphShape = gp; // Ellipse2D.Double circle = new Ellipse2D.Double(); // circle.setFrameFromCenter(x,y, x+2, y+2); } else if ((mriPctChange > -30.0) && (mriPctChange <= 0.0)) { //no change or reduction in tumor size but less than 30% reduction Ellipse2D.Double circle = new Ellipse2D.Double(); //circle.setFrameFromCenter(x,y,x+1.25,y+1.25); circle.setFrameFromCenter(x, y, x + gi_x, y + gi_y); glyphShape = circle; } //glyphColor = Color.BLUE; //later can set color based on glyphColor = getColorForDataPoint(corrPoint); glyph = new XYShapeAnnotation(glyphShape, new BasicStroke(1.0f), Color.BLACK, glyphColor); String tooltip = corrPoint.getTag(); glyph.setToolTipText(tooltip); plot.addAnnotation(glyph); } }
From source file:mio_de_pso.MainForm.java
private void viewIndividuals(Individual[] population, XYPlot plot) { double annotationSize = (((x1Max - x1Min) * 0.02) + ((x2Max - x2Min) * 0.02)) / 2; for (int i = 0; i < population.length; ++i) { XYShapeAnnotation annotation = new XYShapeAnnotation( new Ellipse2D.Double(population[i].getPosition("x1"), population[i].getPosition("x2"), annotationSize, annotationSize), new BasicStroke(1.0f), Color.LIGHT_GRAY, Color.LIGHT_GRAY); plot.addAnnotation(annotation);//from w w w. j a va 2 s . c o m } }