/**
* Takes a matrix of values and creates a new data source that stores the values in (x, y, value)
* format.
*
* @param data Original data source with values in each cell.
* @return New data source with (x, y, value) columns
*/
@SuppressWarnings("unchecked")
public static DataSource createRasterData(DataSource data) {
if (data == null) {
throw new NullPointerException("Cannot convert null data source.");
}
DataTable coordsValueData = new DataTable(Double.class, Double.class, Double.class);
// Generate pixel data with (x, y, value)
Statistics stats = data.getStatistics();
double min = stats.get(Statistics.MIN);
double max = stats.get(Statistics.MAX);
double range = max - min;
int i = 0;
for (Comparable<?> cell : data) {
int x = i % data.getColumnCount();
int y = -i / data.getColumnCount();
double v = Double.NaN;
if (cell instanceof Number) {
Number numericCell = (Number) cell;
v = (numericCell.doubleValue() - min) / range;
}
coordsValueData.add((double) x, (double) y, v);
i++;
}
return coordsValueData;
}
@SuppressWarnings("unchecked")
public SimplePiePlot() {
// Create data
DataTable data = new DataTable(Integer.class);
for (int i = 0; i < SAMPLE_COUNT; i++) {
int val = random.nextInt(8) + 2;
data.add((random.nextDouble() <= 0.15) ? -val : val);
}
// Create new pie plot
PiePlot plot = new PiePlot(data);
// Format plot
plot.getTitle().setText(getDescription());
// Change relative size of pie
plot.setRadius(0.9);
// Display a legend
plot.setLegendVisible(true);
// Add some margin to the plot area
plot.setInsets(new Insets2D.Double(20.0, 40.0, 40.0, 40.0));
PieSliceRenderer pointRenderer = (PieSliceRenderer) plot.getPointRenderer(data);
// Change relative size of inner region
pointRenderer.setInnerRadius(0.4);
// Change the width of gaps between segments
pointRenderer.setGap(0.2);
// Change the colors
LinearGradient colors = new LinearGradient(COLOR1, COLOR2);
pointRenderer.setColor(colors);
// Show labels
pointRenderer.setValueVisible(true);
pointRenderer.setValueColor(Color.WHITE);
pointRenderer.setValueFont(Font.decode(null).deriveFont(Font.BOLD));
// Add plot to Swing component
add(new InteractivePanel(plot), BorderLayout.CENTER);
}
public LinePlotTest() {
super(new BorderLayout());
setPreferredSize(new Dimension(800, 600));
setBackground(Color.WHITE);
// load data from file ----------------------------------------------
// basemean, log2foldchange
DataTable nonSigData = new DataTable(Double.class, Double.class);
DataTable sigData = new DataTable(Double.class, Double.class);
try (CSVReader reader = new CSVReader(new FileReader("rnaSeqExample.csv"))) {
String[] nextLine;
int row = 0;
while ((nextLine = reader.readNext()) != null) {
if (row != 0) {
// needs to have a p-value
if (nextLine[2].equals("NA")) continue;
double baseMean = Double.parseDouble(nextLine[1]);
double log2Change = Double.parseDouble(nextLine[2]);
if (nextLine[6].equals("NA") || Double.parseDouble(nextLine[6]) > 0.05) {
nonSigData.add(Math.log10(baseMean), log2Change);
} else {
sigData.add(Math.log10(baseMean), log2Change);
}
}
row++;
}
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("Non-significant: " + nonSigData.getRowCount());
System.out.println("Significant: " + sigData.getRowCount());
XYPlot plot = new XYPlot(nonSigData, sigData);
// set point renderer for data
PointRenderer points = new DefaultPointRenderer2D();
points.setShape(new Ellipse2D.Double(-2.0, -2.0, 4.0, 4.0));
points.setColor(NONSIG_COLOR);
plot.setPointRenderer(nonSigData, points);
PointRenderer pointsRed = new DefaultPointRenderer2D();
pointsRed.setShape(new Ellipse2D.Double(-2.0, -2.0, 4.0, 4.0));
pointsRed.setColor(SIG_COLOR);
plot.setPointRenderer(sigData, pointsRed);
// Display on screen
add(new InteractivePanel(plot), BorderLayout.CENTER);
}
