/*
* Create roc curve graph
*/
package biodiscml;
import java.awt.Color;
import java.io.File;
import java.util.ArrayList;
import java.util.TreeMap;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.DeviationRenderer;
import org.jfree.chart.title.LegendTitle;
import org.jfree.data.xy.XYDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import org.jfree.ui.RectangleEdge;
import org.jfree.ui.RectangleInsets;
import utils.Weka_module;
import weka.classifiers.Evaluation;
import weka.classifiers.evaluation.ThresholdCurve;
import weka.core.Instances;
/**
*
* @author Administrator
*/
public class rocCurveGraphs {
public static void createRocCurvesWithConfidence(ArrayList<Object> alFoldsROCs, boolean classification, String outfile, String extension) {
TreeMap<String, RocObject> tmFoldsROCs = new TreeMap<>();
// retreive roc data of each class
for (Object ROC : alFoldsROCs) {
Evaluation eval;
Instances data;
if (classification) {
Weka_module.ClassificationResultsObject cr = (Weka_module.ClassificationResultsObject) ROC;
eval = cr.evaluation;
data = cr.dataset;
} else {
Weka_module.RegressionResultsObject rr = (Weka_module.RegressionResultsObject) ROC;
eval = rr.evaluation;
data = rr.dataset;
}
boolean hasMoreClasses = true;
int classIndex = 0;
// for each class
for (int i = 0; i < data.numClasses(); i++) {
try {
//get class name
String className = data.classAttribute().value(classIndex);
//get roc object (or create it if first time)
RocObject ro;
if (tmFoldsROCs.containsKey(className)) {
ro = tmFoldsROCs.get(className);
} else {
ro = new RocObject();
}
//get roc values
Instances rocCurve = new ThresholdCurve().getCurve(eval.predictions(), classIndex);
//iterate through roc values and store them into Roc objects
ArrayList<Double> alTPR = new ArrayList<>();
ArrayList<Double> alFPR = new ArrayList<>();
for (String s : rocCurve.toString().split("\n")) {
if (!s.startsWith("@") && !s.trim().isEmpty()) {
alTPR.add(Double.parseDouble(s.split(",")[rocCurve.attribute("True Positive Rate").index()]));
alFPR.add(Double.parseDouble(s.split(",")[rocCurve.attribute("False Positive Rate").index()]));
}
}
ro.TPRvalues.add(alTPR);
ro.FPRvalues.add(alFPR);
tmFoldsROCs.put(className, ro);
} catch (Exception e) {
e.printStackTrace();
hasMoreClasses = false;
}
classIndex++;
}
}
//create picture
XYDataset data = createRocDataset(tmFoldsROCs);
String title = outfile.replace(Main.project + ".", "").replace(Main.wd, "");
JFreeChart chart = createChart(data, title);
exportChartToPNG(chart, outfile + extension);
}
public static XYDataset createRocDataset(TreeMap<String, RocObject> tm) {
XYSeriesCollection dataset = new XYSeriesCollection();
//for each fold
for (String classe : tm.keySet()) {
XYSeries serie = new XYSeries(classe, false);
RocObject ro = tm.get(classe);
for (int i = 0; i < ro.FPRvalues.size(); i++) {
//XYSeries serie = new XYSeries(classe + "_fold" + i,false);
for (int j = 0; j < ro.FPRvalues.get(i).size(); j++) {
serie.add(ro.FPRvalues.get(i).get(j), ro.TPRvalues.get(i).get(j));
}
//dataset.addSeries(serie);
}
dataset.addSeries(serie);
}
return dataset;
}
public static void exportChartToPNG(JFreeChart chart, String outfile) {
try {
ChartUtilities.saveChartAsPNG(new File(outfile), chart, 1024, 768);
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Creates a chart.
*
* @param dataset the data for the chart.
* @return a chart.
*/
private static JFreeChart createChart(XYDataset dataset, String title) {
// create the chart...
JFreeChart chart = ChartFactory.createXYLineChart(
title, // chart title
"False positive rate (1 - specificity)", // x axis label
"True positive rate (sensitivity)", // y axis label
dataset, // data
PlotOrientation.VERTICAL,
true, // include legend
true, // tooltips
false // urls
);
chart.setBackgroundPaint(Color.white);
LegendTitle legend = chart.getLegend();
legend.setPosition(RectangleEdge.RIGHT);
// get a reference to the plot for further customisation...
XYPlot plot = (XYPlot) chart.getPlot();
plot.setBackgroundPaint(Color.white);
plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
plot.setDomainGridlinePaint(Color.black);
plot.setRangeGridlinePaint(Color.black);
//deviation renderer
//color codes: http://htmlcolorcodes.com/
DeviationRenderer renderer = new DeviationRenderer(true, false);
// renderer.setSeriesStroke(0, new BasicStroke(3.0f, BasicStroke.CAP_ROUND,
// BasicStroke.JOIN_ROUND));
// renderer.setSeriesStroke(0, new BasicStroke(3.0f));
// renderer.setSeriesStroke(1, new BasicStroke(3.0f));
// renderer.setSeriesFillPaint(0, new Color(255, 118, 118)); //light red
// renderer.setSeriesFillPaint(1, new Color(118, 180, 255)); //light blue
plot.setRenderer(renderer);
// //smooth line renderer
// XYSplineRenderer rend = new XYSplineRenderer();
// rend.setPrecision(2);
// plot.setRenderer(rend);
//Axis modifications
NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
yAxis.setRange(-0.01, 1.01);
NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
xAxis.setRange(-0.01, 1.01);
return chart;
}
private static class RocObject {
public String classe;
public ArrayList<ArrayList<Double>> TPRvalues;
public ArrayList<ArrayList<Double>> FPRvalues;
public RocObject() {
TPRvalues = new ArrayList<>();
FPRvalues = new ArrayList<>();
}
}
}
Datasets
Models
