Creating heatmaps using SWT XY Graph

I just discovered a brilliant library SWT XYGraph to create heatmaps. The following image is an example of a chromatogram heatmap. Mass spectrometric chromatograms are three-dimensional data sets containing scans (Y), mass fragments (X) and intensities (Z).

This is a short example of how to use the SWT XYGraph library. Get the libraries and include them in your project:

org.csstudio.swt.widgets_2.0.1.201207141617.jar
org.csstudio.swt.xygraph_2.0.1.201207141617.jar

The libraries are published under the EPL v1.0 license.

This is the code I’ve used to create a chromatogram heatmap:

LightweightSystem lightweightSystem = new LightweightSystem(canvas);
lightweightSystem.getRootFigure().setBackgroundColor(display.getSystemColor(SWT.COLOR_WHITE));
IntensityGraphFigure intensityGraphFigure = new IntensityGraphFigure();
intensityGraphFigure.setForegroundColor(display.getSystemColor(SWT.COLOR_BLACK));
intensityGraphFigure.getXAxis().setTitle("m/z");
intensityGraphFigure.getYAxis().setTitle("scan");
...
int dataHeight = stopScan - startScan + 1; // y -> scans
int dataWidth = stopIon - startIon + 1; // x -> m/z values
/**
 * Parse the data
 */
float maxIntensity = 0;
float[] heatmapData = new float[dataWidth * dataHeight * 2];
/**
 * Y-Axis: Scans
 */
for(int scan = startScan; scan <= stopScan; scan++) {
	int xScan = scan - startScan; // xScan is zero based, scan maybe not
	IExtractedIonSignal extractedIonSignal;
	try {
		extractedIonSignal = extractedIonSignals.getExtractedIonSignal(scan);
		for(int ion = startIon; ion <= stopIon; ion++) {
			/**
			 * X-Axis: m/z intensities
			 */
			int xIon = ion - startIon; // xIon is zero based, ion maybe not
			float abundance = extractedIonSignal.getAbundance(ion);
			if(abundance > maxIntensity) {
				maxIntensity = abundance;
			}
			heatmapData[xScan * dataWidth + xIon] = abundance;
		}
	} catch(NoExtractedIonSignalStoredException e) {
		logger.warn(e);
	}
}
/**
 * Set the ranges and min/max values.
 */
intensityGraphFigure.getXAxis().setRange(new Range(startIon, stopIon));
intensityGraphFigure.getYAxis().setRange(new Range(stopScan, startScan));
intensityGraphFigure.setMin(0); // Intensity
intensityGraphFigure.setMax(maxIntensity / 1000.0d); // Intensity
intensityGraphFigure.setDataHeight(dataHeight);
intensityGraphFigure.setDataWidth(dataWidth);
intensityGraphFigure.setColorMap(new ColorMap(PredefinedColorMap.JET, true, true));
/**
 * Set the heatmap data
 */
lightweightSystem.setContents(intensityGraphFigure);
intensityGraphFigure.setDataArray(heatmapData);

The chromatogram heatmap feature will be available in the next OpenChrom release, version 0.7.0 “Nernst”, scheduled for end of October 2012.

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