public static String readableFileSize(long size) {
if (size <= 0) return "0";
final String[] units = new String[] {"B", "KB", "MB", "GB", "TB"};
int digitGroups = (int) (Math.log10(size) / Math.log10(1024));
return new DecimalFormat("#,##0.#").format(size / Math.pow(1024, digitGroups))
+ " "
+ units[digitGroups];
}
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);
}
private long normalizeMax(long l) {
int exp = (int) Math.log10((double) l);
long multiple = (long) Math.pow(10.0, exp);
int i = (int) (l / multiple);
l = (i + 1) * multiple;
return l;
}
/**
* Returns the number of digits in x.
*
* @param x a whole number.
* @return 1 if x is 0, otherwise the number of digits.
*/
public static int numDigits(int x) {
if (x == 0) return 1;
return (int) (Math.log10(x)) + 1; // 250 -> log250 = 2.something -> 2+1 -> 3
}
@Override
protected void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
int width = getWidth() - Border.left - Border.right;
int height = getHeight() - Border.top - Border.bottom;
g2.translate(Border.left, Border.top);
// create x and y axes
g2.setColor(Color.black);
g2.drawLine(0, height, width, height);
g2.drawLine(0, 0, 0, height);
g2.setFont(g2.getFont().deriveFont(10.0f));
FontMetrics fm = g2.getFontMetrics();
if (xValues.length == 0 || target == null || xValues[xValues.length - 1] <= 0) {
return;
}
double factor;
String yText;
Application app = Application.getInstance();
Shaking.Type t = app.getSpectrumParameter();
if (t == Shaking.Type.PSA) {
factor = Application.EarthAcceleration1;
yText = t.toString().toUpperCase() + ", g";
} else if (t == Shaking.Type.DRS) {
factor = 100;
yText = t.toString().toUpperCase() + ", cm";
} else {
LOG.warn("unsupported spectrum parameter: " + t.toString());
return;
}
synchronized (target) {
// determine min/max of x and y axis
double xMin;
double xMax;
double dx = 0;
if (logScale) {
xMin = Math.log10(xValues[0]);
xMax = Math.log10(xValues[xValues.length - 1]);
} else {
xMin = 0.0;
xMax = xValues[xValues.length - 1];
}
if (xMax > xMin) {
dx = (double) width / (xMax - xMin);
}
double yMin = 0;
double yMax = 0;
double dy = 0;
boolean first = true;
for (double v : reference1) {
if (first) {
first = false;
/*yMin =*/ yMax = v;
}
/*yMin = Math.min(yMin, v);*/
yMax = Math.max(yMax, v);
}
for (double v : reference2) {
if (first) {
first = false;
/*yMin =*/ yMax = v;
}
/*yMin = Math.min(yMin, v);*/
yMax = Math.max(yMax, v);
}
for (Shaking s : target.spectralValues) {
if (first) {
first = false;
/*yMin =*/ yMax = s.expectedSI * factor;
} else {
/*yMin = Math.min(yMin, s.expectedSI * factor);*/
yMax = Math.max(yMax, s.expectedSI * factor);
}
/*
yMin = Math.min(yMin, s.expectedSI * factor);
yMin = Math.min(yMin, s.percentile84 * factor);
yMin = Math.min(yMin, s.percentile16 * factor);
*/
yMax = Math.max(yMax, s.expectedSI * factor);
yMax = Math.max(yMax, s.percentile84 * factor);
yMax = Math.max(yMax, s.percentile16 * factor);
}
if (yMax > yMin) {
dy = (double) height / (yMax - yMin);
}
List<Point> expectedPoints = new ArrayList();
List<Point> percentile84Points = new ArrayList();
List<Point> percentile16Points = new ArrayList();
List<Point> ref1Points = new ArrayList();
List<Point> ref2Points = new ArrayList();
int x, y, iV;
boolean isFreq = app.isUseFrequencies();
for (int i = 0; i < xValues.length; i++) {
if (logScale) {
x = (int) ((Math.log10(xValues[i]) - xMin) / (xMax - xMin) * width);
} else {
x = (int) ((xValues[i] - xMin) / (xMax - xMin) * width);
}
iV = isFreq ? xValues.length - i - 1 : i;
if (iV < target.spectralValues.size()) {
Shaking s = target.spectralValues.get(iV);
y = (int) ((yMax - s.expectedSI * factor) * dy);
expectedPoints.add(new Point(x, y));
y = (int) ((yMax - s.percentile84 * factor) * dy);
percentile84Points.add(new Point(x, y));
y = (int) ((yMax - s.percentile16 * factor) * dy);
percentile16Points.add(new Point(x, y));
}
if (iV < reference1.size()) {
y = (int) ((yMax - reference1.get(iV)) * dy);
ref1Points.add(new Point(x, y));
}
if (iV < reference2.size()) {
y = (int) ((yMax - reference2.get(iV)) * dy);
ref2Points.add(new Point(x, y));
}
}
// Y-axis
String text;
int halfAscent = fm.getAscent() / 2 - 1;
double q = Math.log10(2 * (yMax - yMin) * 2 * fm.getHeight() / height);
double rx = q - Math.floor(q);
int d = rx < 0.3 ? 1 : rx > 0.7 ? 5 : 2;
double tickStep = d * Math.pow(10, Math.floor(q - rx));
for (double v = 0; v < yMax; v += tickStep) {
y = height - (int) (v * dy) - 1;
g2.drawLine(0, y, -TickLength, y);
text = Double.toString(((int) (v * 1000.0 + 0.5)) / 1000.0);
int w = (int) fm.getStringBounds(text, null).getWidth();
g2.drawString(text, -TickLength - 3 - w, y + halfAscent);
}
// X-axis
q = Math.log10(2 * (xMax - xMin) * 50 / width);
rx = q - Math.floor(q);
d = rx < 0.3 ? 1 : rx > 0.7 ? 5 : 2;
tickStep = d * Math.pow(10, Math.floor(q - rx));
for (double v = xMin; v < xMax; v += tickStep) {
x = (int) ((v - xMin) * dx);
g2.drawLine(x, height, x, height + TickLength);
text = String.format("%.2f", logScale ? Math.pow(10, v) : v);
// String text = Double.toString(logScale ? Math.pow(10, v) : v);//((int) (v * 1000.0 +
// 0.5)) / 1000.0);
int w = (int) fm.getStringBounds(text, null).getWidth();
g2.drawString(text, x - w / 2, height + TickLength + 3 + fm.getAscent());
}
// axis label
g2.setFont(g2.getFont().deriveFont(14.0f));
AffineTransform orig = g2.getTransform();
int w = (int) ((height + fm.getStringBounds(yText, null).getWidth()) / 2);
g2.translate(-Border.left + fm.getAscent() + 7, w);
g2.rotate(-Math.PI / 2);
g2.drawString(yText, 0, 0);
g2.setTransform(orig);
text = "vibration " + (isFreq ? "frequency, Hz" : "period, s");
g2.drawString(
text,
(int) ((width - fm.getStringBounds(text, null).getWidth()) / 2),
height + TickLength + 3 + 2 * fm.getHeight());
g2.setClip(0, 0, width, height);
g2.setStroke(DefaultStroke);
g2.setColor(Ref1Color);
drawGraph(g2, ref1Points);
g2.setColor(Ref2Color);
drawGraph(g2, ref2Points);
g2.setStroke(PercentileStroke);
g2.setColor(ShakingColor);
drawGraph(g2, percentile16Points);
drawGraph(g2, percentile84Points);
g2.setStroke(DefaultStroke);
drawGraph(g2, expectedPoints);
}
}
