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    <p>You can override <a href="http://www.jfree.org/jfreechart/api/javadoc/org/jfree/chart/renderer/xy/XYItemRenderer.html#getItemPaint%28int,%20int%29" rel="nofollow noreferrer"><code>getItemPaint</code></a> in the scatter plot's <code>XYLineAndShapeRenderer</code> and choose your color based on any desired combination of <code>row</code> and <code>col</code>. There's a related example <a href="https://stackoverflow.com/questions/3003373/how-to-set-different-colors-to-the-bars-in-stacked-bar-chart-in-ireport/3006785#3006785">here</a>, although it's for a different renderer.</p> <p>Addendum: The general idea appears in <code>MyRenderer</code>, which <code>extends XYLineAndShapeRenderer</code>.</p> <p><img src="https://i.stack.imgur.com/63ipp.png" alt="Scatter plot custom renderer image"></p> <pre><code>import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Paint; import java.awt.Shape; import java.util.Arrays; import javax.swing.JFrame; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.plot.DefaultDrawingSupplier; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer; import org.jfree.data.xy.DefaultXYDataset; import org.jfree.data.xy.XYDataset; public class ScatterColors extends JFrame { private static final Color centroidColor = Color.blue; private int centroidColumn; public ScatterColors(String title, final double[][] samples) { super(title); this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); DefaultXYDataset dataset = new DefaultXYDataset(); dataset.addSeries("Series", createSeries(0, samples)); JFreeChart chart = createChart(dataset); ChartPanel chartPanel = new ChartPanel(chart, false); chartPanel.setPreferredSize(new Dimension(500, 400)); this.add(chartPanel, BorderLayout.CENTER); } private double[][] createSeries(int mean, double[][] samples) { centroidColumn = samples.length; double[][] series = new double[2][samples.length + 1]; double p = 0, q = 0; for (int i = 0; i &lt; samples.length; i++) { series[0][i] = samples[i][0]; p = p + samples[i][0]; series[1][i] = samples[i][1]; q = q + samples[i][1]; } series[0][samples.length] = p / samples.length; series[1][samples.length] = q / samples.length; for (int i = 0; i &lt; series.length; i++) { System.out.println(Arrays.toString(series[i])); } return series; } private JFreeChart createChart(XYDataset dataset) { JFreeChart chart = ChartFactory.createScatterPlot( "Scatter Plot Demo", "X", "Y", dataset, PlotOrientation.VERTICAL, true, true, false); chart.setBackgroundPaint(Color.white); XYPlot plot = (XYPlot) chart.getPlot(); Shape[] cross = DefaultDrawingSupplier.createStandardSeriesShapes(); plot.setBackgroundPaint(new Color(0xffffe0)); plot.setDomainGridlinesVisible(true); plot.setDomainGridlinePaint(Color.lightGray); plot.setRangeGridlinePaint(Color.lightGray); MyRenderer renderer = new MyRenderer(false, true); plot.setRenderer(renderer); renderer.setSeriesShape(0, cross[0]); plot.setRenderer(renderer); return chart; } private class MyRenderer extends XYLineAndShapeRenderer { public MyRenderer(boolean lines, boolean shapes) { super(lines, shapes); } @Override public Paint getItemPaint(int row, int col) { if (col == centroidColumn) { return centroidColor; } else { return super.getItemPaint(row, col); } } } public static void main(String[] args) { double[][] trainingSet = { {0.428053, 0.409742,}, {0.415487, 0.401414,}, {0.404834, 0.400493,}, }; ScatterColors demo = new ScatterColors("JFreeChartDemo", trainingSet); demo.pack(); demo.setLocationRelativeTo(null); demo.setVisible(true); } } </code></pre>
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    1. CO@trashgod.I have gone through the Example you mentioned above and it has parameters as row and column but in my Example above My Centroid is Paired values(0.4161246,0.403883).which means row is 3 but Column is 0 and 1 ...How can I specify both column for a single row..Thanks
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    2. COSorry, note update about renderer. I'm not following about the data set; Can you post an [sscce](http://sscce.org/)?
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    3. CO@trashgod.I added code please go through that..see if u can help me..:
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