Java tutorial
/** * This file is part of Genevar (GENe Expression VARiation) * Copyright (C) 2010 Genome Research Ltd. * * Genevar is free software: you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package sanger.team16.gui.genevar.mqtl.gene; import java.awt.BasicStroke; import java.awt.Color; import java.awt.Dimension; import java.util.List; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.ValueMarker; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.renderer.xy.XYItemRenderer; import org.jfree.data.xy.XYDataset; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import org.jfree.util.ShapeUtilities; import sanger.team16.common.xqtl.QTL; import sanger.team16.gui.jface.BaseJPane; /** * @author Tsun-Po Yang <tpy@sanger.ac.uk> * @link http://www.sanger.ac.uk/Teams/Team16/ */ @SuppressWarnings("serial") public class RegionalPlot extends BaseJPane { public RegionalPlot(String geneChromosome, int geneStart, int distance, double threshold, List<QTL> significances, List<QTL> insignificances) throws ArrayIndexOutOfBoundsException { XYDataset dataset = this.createDataset(significances, insignificances); JFreeChart chart = createChart(geneChromosome, geneStart, distance, threshold, dataset); chart.setBackgroundPaint(Color.white); ChartPanel chartPanel = new ChartPanel(chart); chartPanel.setPreferredSize(new Dimension(680, 175)); this.add(chartPanel); } private XYDataset createDataset(List<QTL> significances, List<QTL> insignificances) { XYSeriesCollection dataset = new XYSeriesCollection(); this.addToDataset(dataset, significances); this.addToDataset(dataset, insignificances); return dataset; } private void addToDataset(XYSeriesCollection dataset, List<QTL> qtls) { int size = qtls.size(); for (int i = 0; i < size; i++) { QTL qtl = qtls.get(i); XYSeries series = new XYSeries(qtl.snp.getName()); series.add(qtl.snp.getPosition(), qtl.getMinusLog10P()); dataset.addSeries(series); } } private JFreeChart createChart(String geneChromosome, int geneStart, int distanceToTSS, double threshold, XYDataset dataset) { JFreeChart chart = ChartFactory.createScatterPlot(null, "Position on chromosome " + geneChromosome + " (bp)", "-log10(P)", dataset, PlotOrientation.VERTICAL, true, true, false); XYPlot plot = (XYPlot) chart.getPlot(); plot.setBackgroundPaint(Color.WHITE); plot.setDomainGridlinePaint(Color.lightGray); //plot.setRangeGridlinePaint(Color.lightGray); //plot.setRangeCrosshairVisible(true); //NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis(); //domainAxis.setRange(geneStart - distance, geneStart + distance); //domainAxis.setUpperMargin(1000); //domainAxis.setLowerMargin(1000); //ValueAxis rangeAxis = plot.getRangeAxis(); //rangeAxis.setUpperMargin(dataset.getYValue(0, 0)/5); //rangeAxis.setLowerBound(0); XYItemRenderer renderer = plot.getRenderer(); int size = dataset.getSeriesCount(); for (int i = 0; i < size; i++) { //int scale = (int) Math.round((255 - (255 * dataset.getYValue(i, 0)) / top) / 1.4); //renderer.setSeriesPaint(i, new Color(255, scale, scale)); renderer.setSeriesPaint(i, new Color(50, 205, 50)); renderer.setSeriesShape(i, ShapeUtilities.createDiamond((float) 3)); renderer.setBaseSeriesVisibleInLegend(false); } ValueMarker upperMarker = new ValueMarker(-Math.log10(threshold)); upperMarker.setPaint(Color.gray); //upperMarker.setLabelOffsetType(LengthAdjustmentType.EXPAND); //upperMarker.setLabel("-log10(10E-4)"); //upperMarker.setLabelPaint(Color.red); //upperMarker.setLabelAnchor(RectangleAnchor.TOP_RIGHT); //upperMarker.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT); float[] f = { 4, 3, 4, 3 }; upperMarker.setStroke(new BasicStroke(1.0f, 1, 1, 0, f, 1.0f)); plot.addRangeMarker(upperMarker); ValueMarker marker = new ValueMarker(0.0); marker.setPaint(Color.lightGray); plot.addRangeMarker(marker); XYSeries series = new XYSeries("Range"); series.add(geneStart - distanceToTSS, -0.05); series.add(geneStart + distanceToTSS, -0.05); ((XYSeriesCollection) dataset).addSeries(series); renderer.setSeriesVisible(dataset.getSeriesCount() - 1, false, false); return chart; } }