edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils.java Source code

Introduction

Here is the source code for edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils.java

Source

/*
 * Copyright (C) 2014 wangqion
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */
package edu.msu.cme.rdp.classifier.train.validation.distance;

import java.awt.BasicStroke;
import java.awt.Font;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.CategoryAxis;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.plot.CategoryPlot;

import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer;
import org.jfree.data.statistics.BoxAndWhiskerItem;
import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;

/**
 *
 * @author wangqion
 */
public class BoxPlotUtils {

    public static void readData(String inFile, File outdir, String xAxisLabel, String yAxisLabel)
            throws IOException {
        XYSeriesCollection dataset = new XYSeriesCollection();
        DefaultBoxAndWhiskerCategoryDataset scatterDataset = new DefaultBoxAndWhiskerCategoryDataset();

        BufferedReader reader = new BufferedReader(new FileReader(inFile));
        String line = reader.readLine();

        while ((line = reader.readLine()) != null) {
            String[] values = line.split("\\t");
            XYSeries series = new XYSeries(values[2]);
            dataset.addSeries(series);

            double average = Double.parseDouble(values[4]);
            int Q1 = Integer.parseInt(values[6]);
            ;
            int median = Integer.parseInt(values[7]);
            int Q3 = Integer.parseInt(values[8]);
            int pct_98 = Integer.parseInt(values[9]);
            int pct_2 = Integer.parseInt(values[10]);
            int minOutlier = 0; // we don't care about the outliers
            int maxOutlier = 0; //

            BoxAndWhiskerItem item = new BoxAndWhiskerItem(average, median, Q1, Q3, pct_2, pct_98, minOutlier,
                    maxOutlier, new ArrayList());
            scatterDataset.add(item, values[2], "");
        }

        String title = new File(inFile).getName();
        int index = title.indexOf(".");
        if (index != -1) {
            title = title.substring(0, index);
        }

        Font lableFont = new Font("Helvetica", Font.BOLD, 28);
        createBoxplot(scatterDataset, new PrintStream(new File(outdir, title + ".boxchart.png")), title, xAxisLabel,
                yAxisLabel, lableFont);

    }

    public static void createBoxplot(DefaultBoxAndWhiskerCategoryDataset scatterDataset, PrintStream outStream,
            String title, String xAxisLabel, String yAxisLabel, Font lableFont) throws IOException {

        CategoryAxis xAxis = new CategoryAxis(xAxisLabel);
        xAxis.setLabelFont(lableFont);
        NumberAxis yAxis = new NumberAxis(yAxisLabel);
        yAxis.setTickLabelFont(lableFont);
        yAxis.setAutoRangeIncludesZero(false);
        yAxis.setRange(0, 100);
        yAxis.setLabelFont(lableFont);

        BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
        renderer.setFillBox(true);
        renderer.setBaseLegendTextFont(lableFont);
        renderer.setStroke(new BasicStroke(5.0f));

        CategoryPlot plot = new CategoryPlot(scatterDataset, xAxis, yAxis, renderer);
        JFreeChart boxchart = new JFreeChart(title, new Font("Helvetica", Font.BOLD, 40), plot, true);

        // higher scale factor gives higher resolution
        ChartUtilities.writeScaledChartAsPNG(outStream, boxchart, 800, 1000, 3, 3);
    }

    public static void main(String[] args) throws IOException {
        String usage = "data.txt outdir xAxisLabel yAxisLabel";
        if (args.length != 4) {
            System.err.println(usage);
            return;
        }
        readData(args[0], new File(args[1]), args[2], args[3]);
    }

}