/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.charts;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.renderer.ContinuousColorScale;
import org.broad.igv.track.TrackType;
import org.broad.igv.ui.color.ColorUtilities;
import org.broad.igv.ui.color.PaletteColorTable;
import java.awt.*;
import java.awt.geom.Path2D;
import java.util.*;
import java.util.List;
/**
* Renders a scatterplot
*
* @author Jim Robinson
* @date 10/25/11
*/
public class ScatterPlot {
public static final Color VERY_LIGHT_GRAY = new Color(250, 250, 250);
PaletteColorTable colorTable;
ScatterPlotData spData;
Axis xAxis = new Axis(Axis.Orientation.HORIZONTAL);
Axis yAxis = new Axis(Axis.Orientation.VERTICAL);
private XYDataModel dataModel;
Set<XYDataPoint> selectedPoints;
Rectangle pointShape = new Rectangle(7, 7);
int offsetX = pointShape.getBounds().width / 2;
int offsetY = pointShape.getBounds().height / 2;
HashSet<String> filteredSeries = new HashSet<String>();
public static boolean isDataCategory(String selectedCategory) {
return selectedCategory.equals(TrackType.COPY_NUMBER.toString()) ||
selectedCategory.equals(TrackType.GENE_EXPRESSION.toString()) ||
selectedCategory.equals(TrackType.DNA_METHYLATION.toString());
}
public ScatterPlot(ScatterPlotData spData) {
this.spData = spData;
}
public synchronized void setModel(XYDataModel dataModel) {
this.dataModel = dataModel;
colorTable = new PaletteColorTable(ColorUtilities.getPalette("Set 1"));
double minX = Double.MAX_VALUE;
double maxX = -minX;
double minY = minX;
double maxY = maxX;
for (String sn : dataModel.getSeriesNames()) {
List<XYDataPoint> dataPoints = dataModel.getDataPoints(sn);
for (XYDataPoint dataPoint : dataPoints) {
double x = dataPoint.getX();
double y = dataPoint.getY();
if (!Double.isNaN(x) && !Double.isNaN(y)) {
minX = Math.min(minX, x);
maxX = Math.max(maxX, x);
minY = Math.min(minY, y);
maxY = Math.max(maxY, y);
}
}
}
xAxis.setRange(minX, maxX);
yAxis.setRange(minY, maxY);
xAxis.setLabel(dataModel.getXLabel());
yAxis.setLabel(dataModel.getYLabel());
}
public void draw(Graphics2D graphics, Rectangle bounds, Rectangle clipRect) {
if (dataModel == null) return;
// graphics.setColor(Color.white);
// X ticks
Color c = graphics.getColor();
Stroke s = graphics.getStroke();
drawGrid(graphics, bounds, clipRect);
graphics.setColor(c);
graphics.setStroke(s);
String categoryName = dataModel.getCategoryName();
for (String sn : dataModel.getSeriesNames()) {
if (filteredSeries.contains(sn)) continue;
Color color = null;
double[] categoryValues = null;
if (isDataCategory(categoryName)) {
categoryValues = spData.getDataValues(categoryName);
} else {
color = getColor(categoryName, sn);
graphics.setColor(color);
}
List<XYDataPoint> dataPoints = dataModel.getDataPoints(sn);
for (XYDataPoint dataPoint : dataPoints) {
double x = dataPoint.getX();
double y = dataPoint.getY();
if (!Double.isNaN(x) && !Double.isNaN(y)) {
int px = xAxis.getPixelForValue(x);
int pY = yAxis.getPixelForValue(y);
if (clipRect.contains(px, pY)) {
if (isDataCategory(categoryName)) {
color = getDataColor(categoryName, categoryValues[dataPoint.getIdx()]);
graphics.setColor(color);
}
graphics.fillOval(px - offsetX, pY - offsetY, pointShape.width, pointShape.height);
}
}
}
// Mutations
Stroke stroke = graphics.getStroke();
BasicStroke thickLine = new BasicStroke(2);
graphics.setStroke(thickLine);
graphics.setColor(Color.black);
for (XYDataPoint dataPoint : dataPoints) {
double x = dataPoint.getX();
double y = dataPoint.getY();
if (!Double.isNaN(x) && !Double.isNaN(y)) {
int px = xAxis.getPixelForValue(x);
int pY = yAxis.getPixelForValue(y);
if (clipRect.contains(px, pY) && dataPoint.getMutationCount() > 0) {
graphics.drawOval(px - offsetX - 1, pY - offsetY - 1, pointShape.width + 1, pointShape.height + 1);
}
}
}
graphics.setStroke(stroke);
// Outline selected points. this is done here, inside the "series" loop, so that series filtering is
// respected. I would be more effecient to do it outside
if (selectedPoints != null) {
graphics.setColor(Color.ORANGE);
for (XYDataPoint dataPoint : dataPoints) {
if (selectedPoints.contains(dataPoint)) {
double x = dataPoint.getX();
double y = dataPoint.getY();
if (!Double.isNaN(x) && !Double.isNaN(y)) {
int px = xAxis.getPixelForValue(x);
int pY = yAxis.getPixelForValue(y);
if (clipRect.contains(px, pY)) {
graphics.drawRect(px - offsetX, pY - offsetY, pointShape.width, pointShape.height);
}
}
}
}
}
}
// Outline selected points
// graphics.setColor(Color.ORANGE);
// if (selectedPoints != null) {
// for (XYDataPoint dataPoint : selectedPoints) {
// double x = dataPoint.getX();
// double y = dataPoint.getY();
// if (!Double.isNaN(x) && !Double.isNaN(y)) {
// int px = xAxis.getPixelForValue(x);
// int pY = yAxis.getPixelForValue(y);
// if (clipRect.contains(px, pY)) {
// graphics.drawRect(px - offsetX - 1, pY - offsetY - 1, pointShape.width + 2, pointShape.height + 2);
// }
// }
//
// }
// }
}
Map<TrackType, ContinuousColorScale> colorScales = new HashMap<TrackType, ContinuousColorScale>();
private Color getDataColor(String categoryName, double categoryValue) {
TrackType tt = TrackType.valueOf(categoryName);
ContinuousColorScale scale = colorScales.get(tt);
if (scale == null) {
scale = PreferencesManager.getPreferences().getColorScale(tt);// IGV.getInstance().getSession().getColorScale(tt);
}
return scale.getColor((float) categoryValue);
}
public XYDataPoint getDataPointAtPixel(int px, int py) {
double x = xAxis.getDataValueForPixel(px);
double y = yAxis.getDataValueForPixel(py);
double toleranceX = ((pointShape.width + 1) / xAxis.getScale()) / 2;
double toleranceY = ((pointShape.height + 1) / yAxis.getScale()) / 2;
return dataModel.getDataPointAtPixel(x, y, toleranceX, toleranceY);
}
public Color getColor(String categoryName, String sn) {
return colorTable.get(sn);
// Color color;
// if (categoryName == null || categoryName.equals("")) {
// color = Color.blue;
// } else if (categoryName.equals("Mut Count")) {
// if (sn == null || sn.equals("") || sn.equals("Unknown")) {
// color = Color.darkGray;
// } else if (sn.equals("0")) {
// color = Color.green.darker();
// } else if (sn.equals("1")) {
// color = Color.blue;
// } else if (sn.equals("2")) {
// color = Color.orange;
// } else {
// color = Color.red;
// }
// } else {
// color = AttributeManager.getInstance().getColor(categoryName, sn);
// }
//
// // White is the "no-value" color in the attribute panel, but it doesn't work well on the plot. Switch to black
// if (color == Color.white) color = Color.darkGray;
// return color;
}
private void drawGrid(Graphics2D graphics, Rectangle bounds, Rectangle clipRect) {
graphics.setColor(new Color(161, 196, 214));
graphics.setStroke(ChartPanel.DOT1);
double[] xticks = xAxis.ticks;
double xtick = xticks[0];
int px = 0;
while (px < bounds.x + bounds.width) {
px = xAxis.getPixelForValue(xtick);
if (px > bounds.x && px < bounds.x + bounds.width) {
graphics.drawLine(px, bounds.y, px, bounds.y + bounds.height);
}
xtick += xticks[1];
}
double[] yticks = yAxis.ticks;
double ytick = yticks[0];
int py = bounds.y + bounds.height;
while (py > bounds.y) {
py = yAxis.getPixelForValue(ytick);
if (py > bounds.y && py < bounds.y + bounds.height) {
graphics.drawLine(bounds.x, py, bounds.x + bounds.width, py);
}
ytick += yticks[1];
}
// Emphasize zero
graphics.setColor(Color.blue.darker());
graphics.setStroke(ChartPanel.DOT2);
px = xAxis.getPixelForValue(0);
if (px > clipRect.x && px < clipRect.x + clipRect.width) {
graphics.drawLine(px, clipRect.y, px, clipRect.y + clipRect.height);
}
py = yAxis.getPixelForValue(0);
if (py > clipRect.y && py < clipRect.y + clipRect.height) {
graphics.drawLine(clipRect.x, py, clipRect.x + clipRect.width, py);
}
}
public void selectPointsInPath(Path2D path) {
if (dataModel != null) {
selectedPoints = dataModel.getDataPointsIn(path);
}
}
public void clearSelections() {
selectedPoints = null;
}
public void addSeriesFilter(String sn) {
filteredSeries.add(sn);
}
public void removeSeriesFilter(String sn) {
filteredSeries.remove(sn);
}
public XYDataModel getDataModel() {
return dataModel;
}
}