umcg.genetica.graphics.Heatmap Maven / Gradle / Ivy
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package umcg.genetica.graphics;
import JSci.maths.ArrayMath;
import com.lowagie.text.DocumentException;
import com.lowagie.text.Rectangle;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.GradientPaint;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.util.logging.Logger;
import javax.imageio.ImageIO;
/**
*
* @author juha
*/
public class Heatmap {
private static final Font ROW_FONT = new Font("Verdana", Font.PLAIN, 14);
private static final Font COL_FONT = new Font("Verdana", Font.PLAIN, 10);
private static final Font LEGEND_FONT = new Font("Verdana", Font.PLAIN, 14);
// private static final int LEGEND_X = 10;
private static final int LEGEND_Y = 10;
private static final int LEGEND_WIDTH = 200;
private static final int LEGEND_HEIGHT = 100;
private static final Logger LOGGER = Logger.getLogger(Heatmap.class.getName());
public enum Output {
PDF, PNG
};
/**
* Original heatmap implementation Juha
*
* @param values
* @param rowHeaders
* @param colHeaders
* @param width
* @param height
* @param filename
* @param output
* @throws IOException
* @throws DocumentException
*/
public static void drawHeatmap(double[][] values, String[] rowHeaders, String[] colHeaders, int width, int height, String filename, Output output) throws IOException, DocumentException {
if (values.length != rowHeaders.length) {
throw new IllegalArgumentException("Data length and number of row headers differ!");
}
if (values[0].length != colHeaders.length) {
throw new IllegalArgumentException("Data length and number of column headers differ!");
}
// set up Graphics2D depending on required format using iText in case PDF
Graphics2D g2d = null;
com.lowagie.text.Document document = null;
com.lowagie.text.pdf.PdfWriter writer = null;
com.lowagie.text.pdf.PdfContentByte cb = null;
BufferedImage bi = null;
if (output == Output.PDF) {
Rectangle rectangle = new Rectangle(width, height);
document = new com.lowagie.text.Document(rectangle);
writer = com.lowagie.text.pdf.PdfWriter.getInstance(document, new java.io.FileOutputStream(filename));
document.open();
cb = writer.getDirectContent();
//com.lowagie.text.pdf.DefaultFontMapper fontMap = new com.lowagie.text.pdf.DefaultFontMapper();
cb.saveState();
g2d = cb.createGraphics(width, height);
} else {
bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
g2d = bi.createGraphics();
}
g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g2d.setColor(Color.white);
g2d.fillRect(0, 0, width, height);
g2d.setFont(ROW_FONT);
FontMetrics fontmetrics = g2d.getFontMetrics();
int leftMargin = 0;
for (String s : rowHeaders) {
leftMargin = Math.max(leftMargin, fontmetrics.stringWidth(s));
}
leftMargin += 10;
g2d.setFont(COL_FONT);
fontmetrics = g2d.getFontMetrics();
int topMargin = 0;
for (String s : colHeaders) {
topMargin = Math.max(topMargin, fontmetrics.stringWidth(s));
}
topMargin += 10;
topMargin += 200;
int plotWidth = width - leftMargin;
int plotHeight = height - topMargin;
int tileW = (int) (double) plotWidth / values[0].length; // tile width in pixels
int tileH = (int) (double) plotHeight / values.length; // tile height in pixels
if (tileW < 3) {
throw new IllegalArgumentException("Map tiles would become less than 3 pixels wide. Output a wider image or use less columns.");
}
if (tileH < 3) {
throw new IllegalArgumentException("Map tiles would become less than 3 pixels tall. Output a wider image or use less rows.");
}
// draw row headers
g2d.setFont(ROW_FONT);
g2d.setColor(Color.black);
for (int row = 0; row < values.length; row++) {
g2d.drawString(rowHeaders[row], 0, topMargin + row * tileH + tileH / 2 + 5);
}
// draw col headers
g2d.setFont(COL_FONT);
g2d.setColor(Color.black);
for (int col = 0; col < values[0].length; col++) {
g2d.rotate(-Math.PI / 2.0);
// g2d.drawString(colHeaders[col], leftMargin + col * tileW + tileW / 2, 20);
g2d.drawString(colHeaders[col], -topMargin + 10, leftMargin + col * tileW + tileW / 2);
g2d.rotate(Math.PI / 2.0);
}
// draw heatmap
double min = ArrayMath.min(values);
double max = ArrayMath.max(values);
normalize(values);
for (int row = 0; row < values.length; row++) {
for (int col = 0; col < values[0].length; col++) {
// g2d.setColor(getColor(values[row][col]));
g2d.setColor(getRGB(values[row][col]));
g2d.fillRect(leftMargin + col * tileW, topMargin + row * tileH, tileW, tileH);
}
}
// draw scale legend
int legendX = width - LEGEND_WIDTH - 20;
GradientPaint gp = new GradientPaint(
legendX, LEGEND_Y, Color.blue,
legendX + LEGEND_WIDTH / 2, LEGEND_Y, Color.white);
g2d.setPaint(gp);
g2d.fillRect(legendX, LEGEND_Y, LEGEND_WIDTH / 2, LEGEND_HEIGHT);
gp = new GradientPaint(
legendX + LEGEND_WIDTH / 2, LEGEND_Y, Color.white,
legendX + LEGEND_WIDTH, LEGEND_Y, Color.red);
g2d.setPaint(gp);
g2d.fillRect(legendX + LEGEND_WIDTH / 2, LEGEND_Y, LEGEND_WIDTH / 2, LEGEND_HEIGHT);
g2d.setColor(Color.black);
g2d.setFont(LEGEND_FONT);
String minStr = Math.round(min) + "";
int stringWidth = fontmetrics.stringWidth(minStr);
g2d.drawString(minStr, legendX - stringWidth / 2, LEGEND_Y + LEGEND_HEIGHT + 20);
String avgStr = Math.round((max - min) / 2) + "";
stringWidth = fontmetrics.stringWidth(avgStr);
g2d.drawString(avgStr, legendX + LEGEND_WIDTH / 2 - stringWidth / 2, LEGEND_Y + LEGEND_HEIGHT + 20);
String maxStr = Math.round(max) + "";
stringWidth = fontmetrics.stringWidth(maxStr);
g2d.drawString(maxStr, legendX + LEGEND_WIDTH - stringWidth / 2, LEGEND_Y + LEGEND_HEIGHT + 20);
g2d.dispose();
if (output == Output.PDF) {
cb.restoreState();
document.close();
writer.close();
} else {
bi.flush();
ImageIO.write(bi, output.toString().toLowerCase(), new File(filename));
}
}
/**
* Correlation heatmap implementation Marc Jan Always use minimal value:-1
* and maximum value: 1
*
* @param values
* @param rowHeaders
* @param colHeaders
* @param width
* @param height
* @param filename
* @param output
* @throws IOException
* @throws DocumentException
*/
public static void drawCorrelationHeatmap(double[][] values, String[] rowHeaders, String[] colHeaders, int width, int height, String filename, Output output) throws IOException, DocumentException {
if (values.length != rowHeaders.length) {
throw new IllegalArgumentException("Data length and number of row headers differ!");
}
if (values[0].length != colHeaders.length) {
throw new IllegalArgumentException("Data length and number of column headers differ!");
}
// set up Graphics2D depending on required format using iText in case PDF
Graphics2D g2d = null;
com.lowagie.text.Document document = null;
com.lowagie.text.pdf.PdfWriter writer = null;
com.lowagie.text.pdf.PdfContentByte cb = null;
BufferedImage bi = null;
if (output == Output.PDF) {
com.lowagie.text.Rectangle rectangle = new com.lowagie.text.Rectangle(width, height);
document = new com.lowagie.text.Document(rectangle);
writer = com.lowagie.text.pdf.PdfWriter.getInstance(document, new java.io.FileOutputStream(filename));
document.open();
cb = writer.getDirectContent();
cb.saveState();
//com.lowagie.text.pdf.DefaultFontMapper fontMap = new com.lowagie.text.pdf.DefaultFontMapper();
g2d = cb.createGraphics(width, height);
} else {
bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
g2d = bi.createGraphics();
}
g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g2d.setColor(Color.white);
g2d.fillRect(0, 0, width, height);
g2d.setFont(ROW_FONT);
FontMetrics fontmetrics = g2d.getFontMetrics();
int leftMargin = 0;
for (String s : rowHeaders) {
leftMargin = Math.max(leftMargin, fontmetrics.stringWidth(s));
}
leftMargin += 10;
g2d.setFont(COL_FONT);
fontmetrics = g2d.getFontMetrics();
int topMargin = 0;
for (String s : colHeaders) {
topMargin = Math.max(topMargin, fontmetrics.stringWidth(s));
}
topMargin += 10;
topMargin += 200;
int plotWidth = width - leftMargin;
int plotHeight = height - topMargin;
int tileW = (int) (double) plotWidth / values[0].length; // tile width in pixels
int tileH = (int) (double) plotHeight / values.length; // tile height in pixels
if (tileW < 3) {
throw new IllegalArgumentException("Map tiles would become less than 3 pixels wide (" + plotWidth + "/" + values[0].length + " = " + ((double) plotWidth / values[0].length) + "). Output a wider image or use less columns.");
}
if (tileH < 3) {
throw new IllegalArgumentException("Map tiles would become less than 3 pixels tall (" + plotHeight + "/" + values.length + " = " + ((double) plotHeight / values.length) + "). Output a wider image or use less rows.");
}
// draw row headers
g2d.setFont(ROW_FONT);
g2d.setColor(Color.black);
for (int row = 0; row < values.length; row++) {
g2d.drawString(rowHeaders[row], 0, topMargin + row * tileH + tileH / 2 + 5);
}
// draw col headers
g2d.setFont(COL_FONT);
g2d.setColor(Color.black);
for (int col = 0; col < values[0].length; col++) {
g2d.rotate(-Math.PI / 2.0);
// g2d.drawString(colHeaders[col], leftMargin + col * tileW + tileW / 2, 20);
g2d.drawString(colHeaders[col], -topMargin + 10, leftMargin + col * tileW + tileW / 2);
g2d.rotate(Math.PI / 2.0);
}
// draw heatmap
double min = -1;
double max = 1;
normalizeCorrelations(values);
for (int row = 0; row < values.length; row++) {
for (int col = 0; col < values[0].length; col++) {
// g2d.setColor(getColor(values[row][col]));
g2d.setColor(getRGB(values[row][col]));
g2d.fillRect(leftMargin + col * tileW, topMargin + row * tileH, tileW, tileH);
}
}
// draw scale legend
int legendX = width - LEGEND_WIDTH - 20;
GradientPaint gp = new GradientPaint(
legendX, LEGEND_Y, Color.blue,
legendX + LEGEND_WIDTH / 2, LEGEND_Y, Color.white);
g2d.setPaint(gp);
g2d.fillRect(legendX, LEGEND_Y, LEGEND_WIDTH / 2, LEGEND_HEIGHT);
gp = new GradientPaint(
legendX + LEGEND_WIDTH / 2, LEGEND_Y, Color.white,
legendX + LEGEND_WIDTH, LEGEND_Y, Color.red);
g2d.setPaint(gp);
g2d.fillRect(legendX + LEGEND_WIDTH / 2, LEGEND_Y, LEGEND_WIDTH / 2, LEGEND_HEIGHT);
g2d.setColor(Color.black);
g2d.setFont(LEGEND_FONT);
String minStr = Math.round(min) + "";
int stringWidth = fontmetrics.stringWidth(minStr);
g2d.drawString(minStr, legendX - stringWidth / 2, LEGEND_Y + LEGEND_HEIGHT + 20);
String avgStr = "0";
stringWidth = fontmetrics.stringWidth(avgStr);
g2d.drawString(avgStr, legendX + LEGEND_WIDTH / 2 - stringWidth / 2, LEGEND_Y + LEGEND_HEIGHT + 20);
String maxStr = Math.round(max) + "";
stringWidth = fontmetrics.stringWidth(maxStr);
g2d.drawString(maxStr, legendX + LEGEND_WIDTH - stringWidth / 2, LEGEND_Y + LEGEND_HEIGHT + 20);
g2d.dispose();
if (output == Output.PDF) {
cb.restoreState();
document.close();
writer.close();
} else {
bi.flush();
ImageIO.write(bi, output.toString().toLowerCase(), new File(filename));
}
}
/**
* Converts the given array to 0...1 scale linearly.
*
* @param values
*/
private static void normalize(double[][] values) {
double min = ArrayMath.min(values);
double max = ArrayMath.max(values) + min;
System.out.println("Range: " + min + " -- " + max);
for (int row = 0; row < values.length; row++) {
for (int col = 0; col < values[0].length; col++) {
values[row][col] += min;
values[row][col] /= max;
System.out.println(values[row][col]);
}
}
System.out.println("min " + ArrayMath.min(values));
System.out.println("max " + ArrayMath.max(values));
}
/**
* Converts the given correlation (-1 to 1) array to 0...1 scale linearly.
* Add 1 and divide by 2.
*
* @param values
*/
private static void normalizeCorrelations(double[][] values) {
for (int row = 0; row < values.length; row++) {
for (int col = 0; col < values[0].length; col++) {
values[row][col] = (values[row][col] + 1) / 2;
}
}
}
private Rectangle getScaleGradient(int width, int height) {
com.lowagie.text.Rectangle r = new com.lowagie.text.Rectangle(width, height);
return r;
}
private static Color getRGB(double power) {
if (power < 0.5) {
power *= 2;
return new Color((float) power, (float) power, 1f); // blue to white, 0 -> 1: (0, 0, 1) -> (1, 1, 1)
} else {
power -= 0.5;
power *= 2;
return new Color(1f, (float) (1 - power), (float) (1 - power)); // white to red, 0 -> 1: (1, 1, 1) -> (1, 0, 0)
}
// return new Color(0f, 0f, (float) (1 - power)); // blue to black
// return new Color(1f, 1f, (float) (1 - power)); // white to yellow
// return new Color(1f, 1f, (float) power); // yellow to white
}
private static Color getColor(double power) {
float h = (float) (power * 0.3); // Hue
// float h = (float) (240d / 360d); // Blue Hue
float s = (float) 0.9; // Saturation
float b = (float) 0.9; // Brightness
return Color.getHSBColor(h, s, b);
}
}
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