public AllMultilevelCoefs(CoefArgs args) throws IOException {
this.args = args;
files = new Vector<File>();
keys = new Vector<String>();
coefs = new Vector<MultilevelCoefs>();
File dir = args.dir();
for (int i = 0; i < args.keys.length; i++) {
keys.add(args.keys[i]);
File f = CoefArgs.coefFile(dir, args.keys[i]);
files.add(f);
coefs.add(new MultilevelCoefs(f));
System.out.println(String.format("Loaded: %s", args.keys[i]));
}
}
public static void main(String[] argarray) {
CoefArgs args = CoefArgs.parse(argarray);
try {
AllMultilevelCoefs coefs = new AllMultilevelCoefs(args);
Matrix matrix = coefs.matrix(true);
Matrix covar = matrix.transpose().times(matrix);
SingularValueDecomposition svd = covar.svd();
Matrix U = svd.getU();
double[] d1 = normalize(column(U, 1));
double[] d2 = normalize(column(U, 2));
String[] genes = coefs.genes();
DataFrame<MultilevelCoefs.XYPoint> points =
new DataFrame<MultilevelCoefs.XYPoint>(MultilevelCoefs.XYPoint.class);
for (int i = 0; i < genes.length; i++) {
double[] gr = row(matrix, i);
double x = inner(gr, d1), y = inner(gr, d2);
MultilevelCoefs.XYPoint point = new MultilevelCoefs.XYPoint(x, y, genes[i]);
points.addObject(point);
System.out.println(point.toString());
}
System.out.println("U: ");
println(U, System.out);
ModelScatter scatter = new ModelScatter();
scatter.addModels(points.iterator());
scatter.setProperty(ModelScatter.colorKey, Coloring.clearer(Color.red));
coefs.save(
new File(
String.format(
"C:\\Documents and Settings\\tdanford\\Desktop\\sigma_%s.txt", args.compare)));
new ModelScatter.InteractiveFrame(scatter, "PCA");
} catch (IOException e) {
e.printStackTrace();
}
}