umcg.genetica.graphics.ForestPlot Maven / Gradle / Ivy
/*
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package umcg.genetica.graphics;
import com.lowagie.text.DocumentException;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.Stroke;
import java.awt.geom.GeneralPath;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.text.DecimalFormat;
import java.util.Arrays;
import java.util.Locale;
import java.util.logging.Logger;
import javax.imageio.ImageIO;
import umcg.genetica.io.trityper.util.ChrAnnotation;
/**
*
* @author harm-jan
*/
public class ForestPlot {
private String[] geneNames;
public enum Output {
PDF, PNG
};
private static final Font LARGE_FONT = new Font("Verdana", Font.PLAIN, 14);
private static final Font LARGE_FONT_BOLD = new Font("Verdana", Font.BOLD, 14);
private static final Font SMALL_FONT = new Font("Verdana", Font.PLAIN, 10);
private static final int upMaxR = 108;
private static final int upMaxG = 189;
private static final int upMaxB = 69;
private static final int downMaxR = 0;
private static final int downMaxG = 174;
private static final int downMaxB = 239;
private static final float downMaxH = 196f/360f;
private static final float downMaxS = 1f;
private static final float downMaxBr = 0.93f;
private static final float upMaxH = 100f/360f;
private static final float upMaxS = 0.63f;
private static final float upMaxBr = 0.74f;
private static final Color red1Color = new Color(242, 101, 94, 50);
private static final Color red2Color = new Color(242, 101, 94, 25);
private static final Color gray1Color = new Color(237, 237, 237);
private static final Color gray2Color = new Color(247, 247, 247);
private static final Logger LOGGER = Logger.getLogger(Heatmap.class.getName());
private static final Stroke dashed = new BasicStroke(1, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 0, new float[]{4}, 0);
private static final Stroke line2pt = new BasicStroke(2, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND);
private static final Stroke line = new BasicStroke(1, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND);
public void drawForrestPlot(String xAxisName, String[] yAxisNames, Double[] xValues, String filename, Output output, double[] significanceThresholds, Double minX, Double maxX, int[] weights, byte[] chr, int[] chrpos, int metaRow) throws IOException, DocumentException {
Double[][] workvalues = new Double[1][xValues.length];
System.arraycopy(xValues, 0, workvalues[0], 0, xValues.length);
drawMultiForrestPlot(xAxisName, yAxisNames, workvalues, filename, output, significanceThresholds, minX, maxX, weights, chr, chrpos, metaRow);
}
public void setGeneNames(String[] geneNames) {
this.geneNames = geneNames;
}
public void drawMultiForrestPlot(String xAxisName, String[] yAxisNames, Double[][] xValues, String filename, Output output, double[] significanceThresholds, Double minX, Double maxX, int[] weights, byte[] chr, int[] chrpos, int metaRow) throws IOException, DocumentException {
if (yAxisNames.length != xValues[0].length) {
throw new IllegalArgumentException("Data length and number of row headers differ!");
}
// set locale for digit grouping
Locale defaultLocale = Locale.getDefault();
Locale.setDefault(Locale.US);
// 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;
BufferedImage bi = null;
int width = 1;
int height = 1;
bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
g2d = bi.createGraphics();
g2d.setFont(LARGE_FONT);
FontMetrics fontmetrics = g2d.getFontMetrics();
// set left margin
int leftMargin = 10;
int maxStringSize = 0;
for (String s : yAxisNames) {
maxStringSize = Math.max(maxStringSize, fontmetrics.stringWidth(s));
}
int topMargin = 10;
int plotwidth = 100;
int plotspacer = 20;
int nrPlots = xValues.length;
// width = plotwidth + max string size + 3 margins
width = (plotwidth * nrPlots) + (nrPlots * plotspacer) + maxStringSize + (leftMargin * 3);
System.out.println(width);
// height is topmargin * 2 + yAxisNames * fontsize
int textpadding = 5;
int maxBoxSize = 20;
int minBoxSize = 5;
int fontheight = fontmetrics.getHeight();
int geneNameMargin = 0;
int geneBoxHeight = 15;
if (geneNames != null) {
geneNameMargin = (leftMargin * 2) + geneBoxHeight + fontheight * 3;
}
height = (yAxisNames.length * textpadding) + (2 * textpadding) + (fontheight * yAxisNames.length) + (topMargin * 2) + geneNameMargin + fontheight + topMargin;
System.out.println(height);
// initialize plot
com.lowagie.text.pdf.PdfContentByte cb = null;
if (output == ForestPlot.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.setStroke(line);
// draw datasetnames
g2d.setColor(Color.gray);
for (int row = 0; row < yAxisNames.length; row++) {
int textStartY = topMargin + fontheight + ((row * fontheight) + (row * textpadding)) + geneNameMargin;
g2d.setFont(LARGE_FONT);
g2d.drawString(yAxisNames[row], leftMargin, textStartY);
}
g2d.setColor(Color.black);
for (int plotNr = 0; plotNr < nrPlots; plotNr++) {
// draw forrest plot
Double[] workValues = xValues[plotNr];
double min = Double.MAX_VALUE;
double max = Double.MIN_VALUE;
if (maxX != null && minX != null) {
max = maxX;
min = minX;
} else {
for (int d = 0; d < workValues.length; d++) {
if (workValues[d] != null) {
if (workValues[d] > max) {
max = workValues[d];
}
if (workValues[d] < min) {
min = workValues[d];
}
}
}
}
double origMin = min;
double origMax = max;
double absmin = 0;
boolean correctValues = false;
if (min < 0) {
absmin = Math.abs(min);
correctValues = true;
}
System.out.println("");
if (correctValues) {
min += absmin;
max += absmin;
} else {
min -= absmin;
max -= absmin;
}
Double[] correctedValues = new Double[workValues.length];
for (int i = 0; i < correctedValues.length; i++) {
// normalize to 0
if (workValues[i] != null) {
System.out.println(i + "\t" + workValues[i]);
if (correctValues) {
correctedValues[i] = workValues[i] + absmin;
} else {
correctedValues[i] = workValues[i] - absmin;
}
System.out.println(i + "\t" + correctedValues[i]);
correctedValues[i] /= max;
System.out.println(i + "\t" + correctedValues[i]);
}
}
int plotStartX = leftMargin + maxStringSize + leftMargin + (plotNr * plotspacer) + (plotNr * plotwidth);
int plotStopX = plotStartX + plotwidth;
int plotStartY = topMargin + geneNameMargin;
int plotStopY = height - 2 * topMargin - fontheight;
DecimalFormat df = new DecimalFormat("#.##");
g2d.setColor(Color.gray);
g2d.setFont(SMALL_FONT);
int strWidth = getWidth(df.format(origMin), LARGE_FONT);
g2d.drawString(df.format(origMin), plotStartX, plotStopY + 2 * leftMargin);
strWidth = getWidth(df.format(origMax), LARGE_FONT);
g2d.drawString(df.format(origMax), plotStopX - strWidth + 2, plotStopY + 2 * leftMargin);
strWidth = getWidth(df.format(0d), LARGE_FONT);
g2d.drawString(df.format(0d), plotStopX - (plotwidth / 2) - strWidth + 3, plotStopY + 2 * leftMargin);
g2d.setFont(LARGE_FONT);
if (geneNames != null) {
int geneBoxStartY = plotStartY - leftMargin * 2 - geneBoxHeight - fontheight * 3;
g2d.setColor(Color.gray);
double metaZ = workValues[metaRow];
double upperSignificance = significanceThresholds[significanceThresholds.length - 1];
int alpha = 255;
if (Math.abs(metaZ) <= Math.abs(upperSignificance)) {
alpha = 126;
}
if (metaZ > 0d) {
g2d.setColor(new Color(upMaxR, upMaxG, upMaxB, alpha));
} else {
g2d.setColor(new Color(downMaxR, downMaxG, downMaxB, alpha));
}
// get MetaZ
Color c = null;
g2d.fillRect(plotStartX, geneBoxStartY, plotwidth, geneBoxHeight);
int textStartY = geneBoxStartY + geneBoxHeight + leftMargin + leftMargin;
Rectangle2D pos = fontmetrics.getStringBounds(geneNames[plotNr], g2d);
g2d.setColor(Color.gray);
String chrStr = "Chr: " + ChrAnnotation.parseByte(chr[plotNr]);
DecimalFormat df2 = new DecimalFormat("###,###,###,###,###");
String chrPos = "Pos: " + df2.format(chrpos[plotNr]);
g2d.setFont(LARGE_FONT_BOLD);
g2d.drawString(geneNames[plotNr], plotStartX, textStartY);
g2d.setFont(SMALL_FONT);
g2d.drawString(chrStr, plotStartX, textStartY + fontheight);
g2d.drawString(chrPos, plotStartX, textStartY + fontheight * 2);
g2d.setFont(LARGE_FONT);
}
System.out.println("Min " + min + "\tmax " + max);
// draw axes
// g2d.drawLine(plotStartX, plotStartY, plotStartX, plotStopY); // y-axis 1
g2d.setColor(Color.gray);
// g2d.drawLine(plotStartX + plotwidth / 2, plotStartY, plotStartX + plotwidth / 2, plotStopY); // y-axis at 0
// g2d.drawLine(plotStartX, plotStopY, plotStopX, plotStopY); // x-axis
int plotheight = plotStopY - plotStartY;
g2d.setColor(gray1Color);
g2d.fillRect(plotStartX, plotStartY, plotwidth, plotheight);
g2d.setColor(Color.black);
System.out.println("plot height: " + plotheight);
System.out.println("plot width: " + plotwidth);
System.out.println("start " + plotStartX);
System.out.println("");
if (significanceThresholds != null) {
Color[] colors = new Color[4];
colors[0] = new Color(120, 120, 120, 128);
colors[1] = new Color(138, 138, 138, 128);
colors[2] = new Color(197, 197, 197, 128);
colors[3] = new Color(249, 249, 249, 128);
Arrays.sort(significanceThresholds);
g2d.setStroke(dashed);
for (int i = significanceThresholds.length - 1; i > -1; i--) {
double val = significanceThresholds[i];
System.out.println(i + "\t" + val);
// correct to new scale
if (correctValues) {
val += absmin;
} else {
val -= absmin;
}
System.out.println(i + "\tminmax " + val);
val /= max;
System.out.println("Perc: " + val);
int nrPixels1 = (int) Math.floor(val * plotwidth);
int nrPixels2 = plotwidth - nrPixels1;
System.out.println(i + "\tdivmax " + nrPixels1);
System.out.println(i + "\tdivmax " + nrPixels2);
// thresholds are on both sides in this plot
int startX = plotStartX + nrPixels1;
int stopX = plotStartX + nrPixels2;
int startY = plotStartY;
int stopY = plotStopY;
int boxwidth = startX - stopX;
Color selected = null;
if (i > colors.length) {
selected = colors[0];
} else {
selected = colors[i];
}
g2d.setColor(selected);
if (i > significanceThresholds.length - 2) {
g2d.setStroke(line2pt);
g2d.setColor(red1Color);
} else {
g2d.setStroke(dashed);
g2d.setColor(red2Color);
}
g2d.drawLine(startX, startY, startX, stopY);
g2d.drawLine(stopX, startY, stopX, stopY);
System.out.println(startX);
System.out.println(startY);
System.out.println(boxwidth);
System.out.println(plotheight);
}
g2d.setColor(Color.black);
}
g2d.setStroke(line);
// draw values
double[] sqrtwghts = new double[weights.length];
double maxWght = 0;
// determine the total sample
int nrTotalSamples = 0;
for (int i = 0; i < metaRow; i++) {
if (workValues[i] != null) {
nrTotalSamples += weights[i];
}
}
sqrtwghts[metaRow] = Math.sqrt(nrTotalSamples);
System.out.println("total samples: " + nrTotalSamples);
maxWght = sqrtwghts[metaRow];
for (int i = 0; i < metaRow; i++) {
sqrtwghts[i] = Math.sqrt(weights[i]);
}
// for replication studies
for (int i = metaRow+1; i < weights.length; i++) {
sqrtwghts[i] = Math.sqrt(weights[i]);
}
for (int i = 0; i < correctedValues.length; i++) {
Double val = correctedValues[i];
if (val != null) {
int posX = plotStartX + (int) Math.floor(val * plotwidth); // original threshold (right side of 0)
int posY = topMargin + fontheight + (fontheight * i) + (i * textpadding) - (textpadding / 2) + geneNameMargin;
System.out.println(i + "\t" + val + "\t" + posX + "\t" + posY);
// GeneralPath gp = new GeneralPath();
// gp.moveTo(-5,0);
// gp.lineTo(+5, 0);
// gp.
double relativeWeight = sqrtwghts[i] / maxWght;
double range = maxBoxSize - minBoxSize;
System.out.println("rel. weight: " + weights.length + "\t" + sqrtwghts[i] + "\t" + relativeWeight);
int boxSize = minBoxSize + (int) Math.ceil(range * relativeWeight);
int halfbox = boxSize / 2;
int x = posX - halfbox;
int y = posY - halfbox;
// determine fraction of max
double realZ = Math.abs(workValues[i]);
double percOfMax = realZ / origMax;
int minAlpha = 75;
int maxAlpha = 255;
int actualAlpha = minAlpha + (int) Math.ceil((maxAlpha - minAlpha) * percOfMax);
Color c = null;
float minBr = 0.5f;
if (workValues[i] >= 0) {
System.out.println(yAxisNames[i] + "\tUp color: " + realZ);
float s = (float) (upMaxS * percOfMax);
float br = minBr +(float) (upMaxBr * percOfMax);
if(br > upMaxBr){
br = upMaxBr;
}
c = Color.getHSBColor(upMaxH, s, br);
} else {
float s = (float) (downMaxS * percOfMax);
float br = minBr + (float) (downMaxBr * percOfMax);
if(br > downMaxBr){
br = downMaxBr;
}
c = Color.getHSBColor(downMaxH, s, br);
}
g2d.setColor(c);
if (i == metaRow) {
// draw diamond
g2d.fill(drawDiamond(x, y, boxSize, boxSize));
} else {
g2d.fillRect(x, y, boxSize, boxSize);
}
g2d.setColor(Color.black);
}
}
g2d.setColor(Color.gray);
g2d.setStroke(line2pt);
g2d.drawLine(plotStartX + plotwidth / 2, plotStartY, plotStartX + plotwidth / 2, plotStopY); // y-axis at 0
g2d.setStroke(line);
g2d.setColor(Color.black);
}
g2d.dispose();
if (output == ForestPlot.Output.PDF) {
g2d.dispose();
cb.restoreState();
document.close();
writer.close();
} else {
bi.flush();
ImageIO.write(bi, output.toString().toLowerCase(), new File(filename));
}
Locale.setDefault(defaultLocale);
}
public int getWidth(String text, java.awt.Font font) {
java.awt.Graphics2D g2d = (new java.awt.image.BufferedImage(1, 1, java.awt.image.BufferedImage.TYPE_INT_ARGB)).createGraphics();
java.awt.font.TextLayout tL = new java.awt.font.TextLayout(text, font, g2d.getFontRenderContext());
return (int) tL.getBounds().getWidth();
}
public GeneralPath drawDiamond(int x, int y, int width, int height) {
GeneralPath diamond = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
x += width / 2;
diamond.moveTo(x, y);
x += width / 2;
y += height / 2;
diamond.lineTo(x, y);
x -= width / 2;
y += height / 2;
diamond.lineTo(x, y);
x -= width / 2;
y -= height / 2;
diamond.lineTo(x, y);
return diamond;
}
}
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