/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.survival.kaplanmeier.figure;
import org.biojava.nbio.survival.cox.*;
import javax.imageio.ImageIO;
import javax.swing.*;
import java.awt.*;
import java.awt.geom.AffineTransform;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileWriter;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashMap;
/**
*
* @author Scooter Willis <willishf at gmail dot com>
*/
public class KaplanMeierFigure extends JPanel {
private static final long serialVersionUID = 1L;
ArrayList<String> title = new ArrayList<String>();
/**
*
*/
private int top;
/**
*
*/
private int bottom;
/**
*
*/
private int left;
private int yaxisLabel = 20;
/**
*
*/
private int right;
int titleHeight;
int xAxisLabelHeight;
int labelWidth;
double minTime = 0.0;
double maxTime = 10.0;
double minPercentage = 0.0;
double maxPercentage = 1.0;
FontMetrics fm;
KMFigureInfo kmfi = new KMFigureInfo();
LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<String, ArrayList<CensorStatus>>();
ArrayList<String> lineInfoList = new ArrayList<String>();
SurvFitInfo sfi = new SurvFitInfo();
private String fileName = "";
private ArrayList<Double> xAxisTimeValues = new ArrayList<Double>();
private ArrayList<Integer> xAxisTimeCoordinates = new ArrayList<Integer>();
/**
*
*/
public KaplanMeierFigure() {
super();
setSize(500, 400);
setBackground(Color.WHITE);
}
/**
* Get the name of the groups that are being plotted in the figure
*
* @return
*/
public ArrayList<String> getGroups() {
return new ArrayList<String>(survivalData.keySet());
}
/**
* To get the median percentile for a particular group pass the value of
* .50.
*
* @param group
* @param percentile
* @return
*/
public Double getSurvivalTimePercentile(String group, double percentile) {
StrataInfo si = sfi.getStrataInfoHashMap().get(group);
ArrayList<Double> percentage = si.getSurv();
Integer percentileIndex = null;
for (int i = 0; i < percentage.size(); i++) {
if (percentage.get(i) == percentile) {
if (i + 1 < percentage.size()) {
percentileIndex = i + 1;
}
break;
} else if (percentage.get(i) < percentile) {
percentileIndex = i;
break;
}
}
if (percentileIndex != null) {
return si.getTime().get(percentileIndex);
} else {
return null;
}
}
/**
*
* @param kmfi
*/
public void setKMFigureInfo(KMFigureInfo kmfi) {
this.kmfi = kmfi;
if (kmfi.width != null && kmfi.height != null) {
this.setSize(kmfi.width, kmfi.height);
}
}
public KMFigureInfo getKMFigureInfo() {
return kmfi;
}
/**
*
* @param lineInfoList
*/
public void setFigureLineInfo(ArrayList<String> lineInfoList) {
this.lineInfoList = lineInfoList;
this.repaint();
}
/**
*
* @param title Title of figures
* @param ci
* @param strataVariable The column that based on value will do a figure
* line
* @param legendMap Map the value in the column to something readable
* @param useWeighted
* @throws Exception
*/
public void setCoxInfo(ArrayList<String> title, CoxInfo ci, String strataVariable, LinkedHashMap<String, String> legendMap, Boolean useWeighted) throws Exception {
LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<String, ArrayList<CensorStatus>>();
ArrayList<SurvivalInfo> siList = ci.getSurvivalInfoList();
int n = 0;
int event = 0;
for (SurvivalInfo si : siList) {
String strata = si.getOriginalMetaData(strataVariable);
String legend = legendMap.get(strata);
if (legend == null) {
legend = strata;
}
ArrayList<CensorStatus> censorStatusList = survivalData.get(legend);
if (censorStatusList == null) {
censorStatusList = new ArrayList<CensorStatus>();
survivalData.put(legend, censorStatusList);
}
CensorStatus cs = new CensorStatus(strata, si.getTime(), si.getStatus() + "");
cs.weight = si.getWeight();
censorStatusList.add(cs);
n++;
if (si.getStatus() == 1) {
event++;
}
}
setSurvivalData(title, survivalData, useWeighted);
CoxCoefficient cc = ci.getCoefficient(strataVariable);
//DecimalFormat df = new DecimalFormat("#.##");
String line1 = "HR=" + fmt(cc.getHazardRatio(), 2, 0) + " (CI:" + fmt(cc.getHazardRatioLoCI(), 2, 0) + "-" + fmt(cc.getHazardRatioHiCI(), 2, 0) + ")";
String line2 = "p=" + fmt(cc.getPvalue(), 3, 0);
// String line2 = "logrank P=" + fmt(ci.getScoreLogrankTestpvalue(), 3, 0);
String line3 = "n=" + n + " events=" + event;
// System.out.println("setCoxInfo=" + cc.pvalue + " " + title);
ArrayList<String> lines = new ArrayList<String>();
lines.add(line1);
lines.add(line2);
lines.add(line3);
setFigureLineInfo(lines);
}
/**
*
* @param d
* @param precision
* @param pad
* @return
*/
public static String fmt(Double d, int precision, int pad) {
String value = "";
DecimalFormat dfe = new DecimalFormat("0.00E0");
String dpad = "0.";
double p = 1.0;
for (int i = 0; i < (precision); i++) {
dpad = dpad + "0";
p = p / 10.0;
}
DecimalFormat df = new DecimalFormat(dpad);
if (Math.abs(d) >= p) {
value = df.format(d);
} else {
value = dfe.format(d);
}
int length = value.length();
int extra = pad - length;
if (extra > 0) {
for (int i = 0; i < extra; i++) {
value = " " + value;
}
}
return value;
}
/**
*
* @return
*/
public SurvFitInfo getSurvivalFitInfo() {
return sfi;
}
/**
* Allow setting of points in the figure where weighted correction has been
* done and percentage has already been calculated.
*
* @param title
* @param sfi
* @param userSetMaxTime
*/
public void setSurvivalData(ArrayList<String> title, SurvFitInfo sfi, Double userSetMaxTime) {
this.title = title;
LinkedHashMap<String, StrataInfo> strataInfoHashMap = sfi.getStrataInfoHashMap();
Double mTime = null;
for (StrataInfo si : strataInfoHashMap.values()) {
for (double t : si.getTime()) {
if (mTime == null || t > mTime) {
mTime = t;
}
}
}
int evenCheck = Math.round(mTime.floatValue());
if (evenCheck % 2 == 1) {
evenCheck = evenCheck + 1;
}
this.maxTime = evenCheck;
if (userSetMaxTime != null && userSetMaxTime > maxTime) {
this.maxTime = userSetMaxTime;
}
this.sfi = sfi;
if (sfi.getStrataInfoHashMap().size() == 1) {
return;
}
this.repaint();
}
/**
* The data will set the max time which will result in off time points for
* tick marks
*
* @param title
* @param survivalData
* @param useWeighted
* @throws Exception
*/
public void setSurvivalData(ArrayList<String> title, LinkedHashMap<String, ArrayList<CensorStatus>> survivalData, Boolean useWeighted) throws Exception {
this.setSurvivalData(title, survivalData, null, useWeighted);
}
/**
*
* @param title
* @param survivalData
* @param userSetMaxTime
* @param useWeighted
* @throws Exception
*/
public void setSurvivalData(ArrayList<String> title, LinkedHashMap<String, ArrayList<CensorStatus>> survivalData, Double userSetMaxTime, Boolean useWeighted) throws Exception {
this.title = title;
this.survivalData = survivalData;
Double mTime = null;
ArrayList<String> labels = new ArrayList<String>(survivalData.keySet());
Collections.sort(labels);
for (String legend : labels) {
ArrayList<CensorStatus> censorStatusList = survivalData.get(legend);
for (CensorStatus cs : censorStatusList) {
if (mTime == null || cs.time > mTime) {
mTime = cs.time;
}
}
}
int evenCheck = Math.round(mTime.floatValue());
if (evenCheck % 2 == 1) {
evenCheck = evenCheck + 1;
}
this.maxTime = evenCheck;
if (userSetMaxTime != null && userSetMaxTime > maxTime) {
this.maxTime = userSetMaxTime;
}
//calculate percentages
SurvFitKM survFitKM = new SurvFitKM();
sfi = survFitKM.process(survivalData, useWeighted);
this.repaint();
}
/**
* Save data from survival curve to text file
*
* @param fileName
* @throws Exception
*/
public void saveSurvivalData(String fileName) throws Exception {
FileWriter fw = new FileWriter(fileName);
fw.write("index\tTIME\tSTATUS\tGROUP\r\n");
int index = 0;
for (String group : survivalData.keySet()) {
ArrayList<CensorStatus> sd = survivalData.get(group);
for (CensorStatus cs : sd) {
String line = index + "\t" + cs.time + "\t" + cs.censored + "\t" + cs.group + "\r\n";
index++;
fw.write(line);
}
}
fw.close();
}
DecimalFormat df = new DecimalFormat("#.#");
@Override
public void paintComponent(Graphics g) // draw graphics in the panel
{
int width = getWidth(); // width of window in pixels
int height = getHeight(); // height of window in pixels
setFigureDimensions();
g.setColor(Color.white);
g.clearRect(0, 0, width, height);
super.paintComponent(g); // call superclass to make panel display correctly
drawLegend(g);
drawSurvivalCurves(g);
drawFigureLineInfo(g);
// Drawing code goes here
}
private void drawFigureLineInfo(Graphics g) {
Graphics2D g2 = (Graphics2D) g;
setRenderingHints(g2);
g2.setColor(Color.BLACK);
fm = getFontMetrics(getFont());
int yoffset = fm.getHeight() * lineInfoList.size();
int x = getTimeX(kmfi.figureLineInfoLowerPercentX * maxTime);
int y = getPercentageY(kmfi.figureLineInfoLowerPercentY) - yoffset;
for (String line : lineInfoList) {
g2.drawString(line, x, y);
y = y + fm.getHeight();
}
}
private void drawSurvivalCurves(Graphics g) {
Graphics2D g2 = (Graphics2D) g;
setRenderingHints(g2);
g2.setStroke(kmfi.kmStroke);
int colorIndex = 0;
ArrayList<String> labels = new ArrayList<String>(sfi.getStrataInfoHashMap().keySet());
Collections.sort(labels);
LinkedHashMap<String, StrataInfo> strataInfoHashMap = sfi.getStrataInfoHashMap();
for (String legend : labels) {
StrataInfo si = strataInfoHashMap.get(legend);
g2.setColor(kmfi.legendColor[colorIndex]);
colorIndex++;
for (int i = 0; i < si.getSurv().size() - 1; i++) {
double p0time = si.getTime().get(i);
double p1time = si.getTime().get(i + 1);
double p0percentage = si.getSurv().get(i);
double p1percentage = si.getSurv().get(i + 1);
if (i == 0) {
g2.drawLine(getTimeX(0), getPercentageY(1), getTimeX(p0time), getPercentageY(1));
g2.drawLine(getTimeX(p0time), getPercentageY(1), getTimeX(p0time), getPercentageY(p0percentage));
}
g2.drawLine(getTimeX(p0time), getPercentageY(p0percentage), getTimeX(p1time), getPercentageY(p0percentage));
g2.drawLine(getTimeX(p1time), getPercentageY(p0percentage), getTimeX(p1time), getPercentageY(p1percentage));
// if (si.getStatus().get(i) == 0) {
if (i > 0 && si.getNcens().get(i) > 0) {
g2.drawLine(getTimeX(p0time), getPercentageY(p0percentage) - 4, getTimeX(p0time), getPercentageY(p0percentage) + 4);
g2.drawLine(getTimeX(p0time) - 4, getPercentageY(p0percentage), getTimeX(p0time) + 4, getPercentageY(p0percentage));
}
}
}
String maxString = "";
for (String legend : labels) {
if (legend.length() > maxString.length()) {
maxString = legend;
}
}
int offset = fm.stringWidth(maxString);
int x = getTimeX(kmfi.legendUpperPercentX * maxTime) - offset;
int y = getPercentageY(kmfi.legendUpperPercentY);
colorIndex = 0;
for (String legend : labels) {
g2.setColor(kmfi.legendColor[colorIndex]);
colorIndex++;
g2.drawLine(x - 20, y - (fm.getHeight() / 3), x - 5, y - (fm.getHeight() / 3));
g2.drawString(legend, x, y);
y = y + fm.getHeight();
}
}
/**
* Get the X coordinate based on a time value
*
* @param value
* @return
*/
private int getTimeX(double value) {
double d = left + (((right - left) * value) / (maxTime - minTime));
return (int) d;
}
/**
* Get the Y coordinate based on percent value 0.0-1.0
*
* @param value
* @return
*/
private int getPercentageY(double value) {
value = 1.0 - value;
double d = top + (((bottom - top) * value) / (maxPercentage - minPercentage));
return (int) d;
}
/**
* @return the fileName
*/
public String getFileName() {
return fileName;
}
/**
* @return the top
*/
public int getTop() {
return top;
}
/**
* @return the bottom
*/
public int getBottom() {
return bottom;
}
/**
* @return the left
*/
public int getLeft() {
return left;
}
/**
* @return the right
*/
public int getRight() {
return right;
}
/**
* @return the xAxisTimeValues
*/
public ArrayList<Double> getxAxisTimeValues() {
return xAxisTimeValues;
}
/**
* @return the xAxisTimeValues
*/
public ArrayList<Integer> getxAxisTimeCoordinates() {
return xAxisTimeCoordinates;
}
class PlotInfo {
double time;
double atRisk;
double censored;
double events;
double percentage;
@Override
public String toString() {
return time + "\t" + atRisk + "\t" + censored + "\t" + events + "\t" + (atRisk - events) + "\t" + percentage;
}
}
/**
* Do higher quality rendering options
*
* @param g
*/
private void setRenderingHints(Graphics2D g) {
RenderingHints rh = new RenderingHints(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
rh.put(RenderingHints.KEY_DITHERING, RenderingHints.VALUE_DITHER_ENABLE);
rh.put(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_GASP);
rh.put(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
g.setRenderingHints(rh);
}
/**
* Setup the axis, labels etc
*
* @param g
*/
private void drawLegend(Graphics g) {
Graphics2D g2 = (Graphics2D) g;
setRenderingHints(g2);
g2.setColor(Color.BLACK);
Font font = g2.getFont();
Font f = new Font(font.getFontName(), Font.BOLD, font.getSize());
g2.setFont(f);
fm = getFontMetrics(f);
int fontHeight = fm.getHeight();
for (int i = 0; i < title.size(); i++) {
if (fm.stringWidth(title.get(i)) > .8 * this.getWidth()) {
f = new Font(font.getFontName(), Font.BOLD, 10);
g2.setFont(f);
fm = getFontMetrics(f);
}
g2.drawString(title.get(i), (getSize().width - fm.stringWidth(title.get(i))) / 2, ((i + 1) * fontHeight));
// g2.setFont(font);
}
// draw the maxPercentage and minPercentage values
String label = df.format(minPercentage);
g2.drawString(label, left - 5 - (fm.stringWidth(label)), bottom + titleHeight / 6);
g2.drawLine(left - 5, bottom, left, bottom);
double d = minPercentage + kmfi.yaxisPercentIncrement;
//double graphHeight = top - bottom;
while (d < maxPercentage) {
int yvalue = bottom - (int) (d * (bottom - top));
label = df.format(d * 100);
g2.drawString(label, left - 5 - (fm.stringWidth(label)), yvalue + titleHeight / 6); //
g2.drawLine(left - 5, yvalue, left, yvalue);
d = d + kmfi.yaxisPercentIncrement;
}
label = df.format(maxPercentage * 100);
g2.drawString(label, left - 5 - (fm.stringWidth(label)), top + (titleHeight) / 6);
g2.drawLine(left - 5, top, left, top);
// Create a rotation transformation for the font.
AffineTransform fontAT = new AffineTransform();
// Derive a new font using a rotatation transform
fontAT.rotate(270 * java.lang.Math.PI / 180);
Font theDerivedFont = f.deriveFont(fontAT);
// set the derived font in the Graphics2D context
g2.setFont(theDerivedFont);
// Render a string using the derived font
int yaxisHeight = fm.stringWidth(kmfi.yAxisLegend);
g2.drawString(kmfi.yAxisLegend, yaxisLabel, (bottom - (int) (.5 * (bottom - top))) + yaxisHeight / 2);
// put the original font back
g2.setFont(f);
double timeDistance = maxTime - minTime;
double timeIncrement = timeDistance * kmfi.xaxisPercentIncrement;
double timeInt = (int) Math.floor(timeIncrement);
if (timeInt < 1.0) {
timeInt = 1.0;
}
adjustedPercentIncrement = timeInt / timeDistance;
d = adjustedPercentIncrement; //kmfi.xaxisPercentIncrement;
xAxisTimeValues.clear();
xAxisTimeCoordinates.clear();
//if we don't have time values then use percentage to set time. Not perfect but allows different tics
if (kmfi.xAxisLabels.isEmpty()) {
xAxisTimeValues.add(minTime);
xAxisTimeCoordinates.add(left);
while (d <= 1.0) {
double xaxisTime = ((minTime * kmfi.timeScale) + d * ((maxTime - minTime) * kmfi.timeScale)); //
xAxisTimeValues.add(xaxisTime);
Integer coordinate = left + (int) (d * (right - left));
xAxisTimeCoordinates.add(coordinate);
// System.out.println(d + " " + left + " " + right + " " + coordinate + " " + minTime + " " + maxTime);
d = d + adjustedPercentIncrement; //kmfi.xaxisPercentIncrement;
}
} else {
minTime = kmfi.xAxisLabels.get(0);
maxTime = kmfi.xAxisLabels.get(kmfi.xAxisLabels.size() - 1);
for (Double xaxisTime : kmfi.xAxisLabels) {
xAxisTimeValues.add(xaxisTime);
d = (xaxisTime - minTime) / (maxTime - minTime);
Integer coordinate = left + (int) (d * (right - left));
xAxisTimeCoordinates.add(coordinate);
}
}
for (int i = 0; i < xAxisTimeValues.size(); i++) {
Double xaxisTime = xAxisTimeValues.get(i);
Integer xCoordinate = xAxisTimeCoordinates.get(i);
label = df.format(xaxisTime);
if (i == xAxisTimeValues.size() - 1) {
g2.drawString(label, xCoordinate - (fm.stringWidth(label)), bottom + fm.getHeight() + 5);
} else {
g2.drawString(label, xCoordinate - (fm.stringWidth(label) / 2), bottom + fm.getHeight() + 5);
}
g2.drawLine(xCoordinate, bottom, xCoordinate, bottom + 5);
}
// draw the vertical and horizontal lines
g2.setStroke(kmfi.axisStroke);
g2.drawLine(left, top, left, bottom);
g2.drawLine(left, bottom, right, bottom);
// draw xAxis legend
g2.drawString(kmfi.xAxisLegend, getSize().width / 2 - (fm.stringWidth(kmfi.xAxisLegend) / 2), bottom + 2 * fm.getHeight() + 10);
}
Double adjustedPercentIncrement = 0.0;
/**
* Get the percentage increment for the time axis
*
* @return
*/
public Double getTimeAxisIncrementPercentage() {
return adjustedPercentIncrement;
}
/**
* Reset the various bounds used to draw graph
*/
private void setFigureDimensions() {
fm = getFontMetrics(getFont());
titleHeight = kmfi.titleHeight;//fm.getHeight();
xAxisLabelHeight = titleHeight;
labelWidth = Math.max(fm.stringWidth(df.format(minPercentage)),
fm.stringWidth(df.format(maxPercentage))) + 5;
top = kmfi.padding + titleHeight;
bottom = this.getHeight() - kmfi.padding - xAxisLabelHeight;
left = kmfi.padding + labelWidth + yaxisLabel;
right = this.getWidth() - kmfi.padding;
}
/**
* Combine the KM and Num risk into one image
*
* @param fileName
*/
public void savePNGKMNumRisk(String fileName) {
if (fileName.startsWith("null") || fileName.startsWith("Null") || fileName.startsWith("NULL")) {
return;
}
this.fileName = fileName;
NumbersAtRiskPanel numbersAtRiskPanel = new NumbersAtRiskPanel();
numbersAtRiskPanel.setKaplanMeierFigure(this);
numbersAtRiskPanel.setSize(this.getWidth(), numbersAtRiskPanel.getHeight());
BufferedImage imageKM = new BufferedImage(this.getWidth(), this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2D = imageKM.createGraphics();
this.paint(graphics2D);
BufferedImage imageNumRisk = new BufferedImage(numbersAtRiskPanel.getWidth(), numbersAtRiskPanel.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2DNumRisk = imageNumRisk.createGraphics();
numbersAtRiskPanel.paint(graphics2DNumRisk);
BufferedImage image = new BufferedImage(numbersAtRiskPanel.getWidth(), numbersAtRiskPanel.getHeight() + this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D g = image.createGraphics();
g.drawImage(imageKM, 0, 0, null);
g.drawImage(imageNumRisk, 0, this.getHeight(), null);
try {
ImageIO.write(image, "png", new File(fileName));
} catch (Exception ex) {
ex.printStackTrace();
}
}
/**
*
* @param fileName
*/
public void savePNG(String fileName) {
if (fileName.startsWith("null") || fileName.startsWith("Null") || fileName.startsWith("NULL")) {
return;
}
this.fileName = fileName;
BufferedImage image = new BufferedImage(this.getWidth(), this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2D = image.createGraphics();
this.paint(graphics2D);
try {
ImageIO.write(image, "png", new File(fileName));
} catch (Exception ex) {
ex.printStackTrace();
}
}
/**
* @param args the command line arguments
*/
public static void main(String[] args) {
// TODO code application logic here
try {
KaplanMeierFigure kaplanMeierFigure = new KaplanMeierFigure();
LinkedHashMap<String, ArrayList<CensorStatus>> survivalDataHashMap = new LinkedHashMap<String, ArrayList<CensorStatus>>();
// if (false) { //http://sph.bu.edu/otlt/MPH-Modules/BS/BS704_Survival/
// ArrayList<CensorStatus> graph1 = new ArrayList<CensorStatus>();
// graph1.add(new CensorStatus("A", 24.0, "0"));
// graph1.add(new CensorStatus("A", 3.0, "1"));
// graph1.add(new CensorStatus("A", 11.0, "0"));
// graph1.add(new CensorStatus("A", 19.0, "0"));
// graph1.add(new CensorStatus("A", 24.0, "0"));
// graph1.add(new CensorStatus("A", 13.0, "0"));
//
// graph1.add(new CensorStatus("A", 14.0, "1"));
// graph1.add(new CensorStatus("A", 2.0, "0"));
// graph1.add(new CensorStatus("A", 18.0, "0"));
// graph1.add(new CensorStatus("A", 17.0, "0"));
// graph1.add(new CensorStatus("A", 24.0, "0"));
// graph1.add(new CensorStatus("A", 21.0, "0"));
// graph1.add(new CensorStatus("A", 12.0, "0"));
//
// graph1.add(new CensorStatus("A", 1.0, "1"));
// graph1.add(new CensorStatus("A", 10.0, "0"));
// graph1.add(new CensorStatus("A", 23.0, "1"));
// graph1.add(new CensorStatus("A", 6.0, "0"));
// graph1.add(new CensorStatus("A", 5.0, "1"));
// graph1.add(new CensorStatus("A", 9.0, "0"));
// graph1.add(new CensorStatus("A", 17.0, "1"));
//
// survivalDataHashMap.put("Label 1", graph1);
//
//
//
// }
if (true) {
ArrayList<CensorStatus> graph1 = new ArrayList<CensorStatus>();
graph1.add(new CensorStatus("A", 1.0, "1"));
graph1.add(new CensorStatus("A", 1.0, "1"));
graph1.add(new CensorStatus("A", 1.0, "1"));
graph1.add(new CensorStatus("A", 2.0, "1"));
graph1.add(new CensorStatus("A", 2.0, "1"));
graph1.add(new CensorStatus("A", 3.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "1"));
graph1.add(new CensorStatus("A", 4.0, "0"));
graph1.add(new CensorStatus("A", 5.0, "1"));
graph1.add(new CensorStatus("A", 5.0, "1"));
graph1.add(new CensorStatus("A", 8.0, "0"));
graph1.add(new CensorStatus("A", 8.0, "0"));
graph1.add(new CensorStatus("A", 8.0, "0"));
graph1.add(new CensorStatus("A", 8.0, "0"));
graph1.add(new CensorStatus("A", 8.0, "0"));
graph1.add(new CensorStatus("A", 8.0, "0"));
graph1.add(new CensorStatus("A", 8.0, "1"));
graph1.add(new CensorStatus("A", 9.0, "1"));
graph1.add(new CensorStatus("A", 9.0, "1"));
graph1.add(new CensorStatus("A", 9.0, "1"));
graph1.add(new CensorStatus("A", 9.0, "1"));
graph1.add(new CensorStatus("A", 9.0, "1"));
graph1.add(new CensorStatus("A", 13.0, "0"));
graph1.add(new CensorStatus("A", 13.0, "0"));
graph1.add(new CensorStatus("A", 13.0, "1"));
survivalDataHashMap.put("Label 1", graph1);
ArrayList<CensorStatus> graph2 = new ArrayList<CensorStatus>();
graph2.add(new CensorStatus("A", 1.0, "1"));
graph2.add(new CensorStatus("A", 1.0, "1"));
graph2.add(new CensorStatus("A", 1.0, "0"));
graph2.add(new CensorStatus("A", 3.0, "0"));
graph2.add(new CensorStatus("A", 3.0, "1"));
graph2.add(new CensorStatus("A", 4.0, "1"));
graph2.add(new CensorStatus("A", 4.0, "1"));
graph2.add(new CensorStatus("A", 4.0, "1"));
graph2.add(new CensorStatus("A", 4.0, "1"));
graph2.add(new CensorStatus("A", 5.0, "1"));
graph2.add(new CensorStatus("A", 5.0, "0"));
graph2.add(new CensorStatus("A", 5.0, "0"));
graph2.add(new CensorStatus("A", 5.0, "0"));
graph2.add(new CensorStatus("A", 6.0, "1"));
graph2.add(new CensorStatus("A", 6.0, "0"));
graph2.add(new CensorStatus("A", 7.0, "0"));
graph2.add(new CensorStatus("A", 7.0, "0"));
graph2.add(new CensorStatus("A", 7.0, "0"));
graph2.add(new CensorStatus("A", 7.0, "0"));
graph2.add(new CensorStatus("A", 8.0, "1"));
graph2.add(new CensorStatus("A", 8.0, "1"));
graph2.add(new CensorStatus("A", 8.0, "1"));
graph2.add(new CensorStatus("A", 8.0, "1"));
graph2.add(new CensorStatus("A", 8.0, "1"));
graph2.add(new CensorStatus("A", 8.0, "0"));
graph2.add(new CensorStatus("A", 9.0, "0"));
graph2.add(new CensorStatus("A", 9.0, "1"));
graph2.add(new CensorStatus("A", 10.0, "0"));
graph2.add(new CensorStatus("A", 10.0, "0"));
graph2.add(new CensorStatus("A", 10.0, "0"));
survivalDataHashMap.put("Label 2", graph2);
}
ArrayList<String> figureInfo = new ArrayList<String>();
//DecimalFormat dfe = new DecimalFormat("0.00E0");
//DecimalFormat df = new DecimalFormat("0.00");
JFrame application = new JFrame();
application.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
application.add(kaplanMeierFigure);
kaplanMeierFigure.setSize(500, 400);
application.setSize(500, 400); // window is 500 pixels wide, 400 high
application.setVisible(true);
ArrayList<String> titles = new ArrayList<String>();
titles.add("Line 1");
titles.add("line 2");
kaplanMeierFigure.setSurvivalData(titles, survivalDataHashMap, true);
// figureInfo.add("HR=2.1 95% CI(1.8-2.5)");
// figureInfo.add("p-value=.001");
kaplanMeierFigure.setFigureLineInfo(figureInfo);
kaplanMeierFigure.savePNGKMNumRisk("/Users/Scooter/Downloads/test.png");
} catch (Exception e) {
e.printStackTrace();
}
}
}