private Set<String> getDownstream(String mut) {
Set<String> tfs = new HashSet<String>();
tfs.add(mut);
if (depth > 1) tfs.addAll(travSt.getDownstream(tfs, depth - 1));
return travExp.getDownstream(tfs);
}
private void writeWeights(
String orig, GeneBranch from, GeneBranch to, String edgeType, Writer writer)
throws IOException {
Set<String> dwstr = to.getAllGenes();
dwstr.retainAll(downstream.get(orig));
assert !dwstr.isEmpty();
double cumPval = calcPVal(orig, dwstr);
boolean upreg = calcChangeDirection(orig, to.gene);
String key = from.gene + " " + edgeType + " " + to.gene;
writer.write("edge\t" + key + "\tcolor\t" + val2Color(cumPval, 0) + "\n");
writer.write("edge\t" + key + "\twidth\t2\n");
if (affectedDw.get(orig).contains(to.gene)) {
double pval = calcPVal(orig, Collections.singleton(to.gene));
writer.write("node\t" + to.gene + "\tcolor\t" + val2Color(pval, upreg ? 1 : -1) + "\n");
} else {
writer.write("node\t" + to.gene + "\tcolor\t255 255 255\n");
}
}
private boolean[] getMutated(Set<String> genes) {
boolean[] b = new boolean[portalAcc.getAlterations(genes.iterator().next()).getSize()];
for (String gene : genes) {
AlterationPack alts = portalAcc.getAlterations(gene);
Change[] ch = alts.get(Alteration.MUTATION);
for (int i = 0; i < ch.length; i++) {
if (ch[i].isAltered()) b[i] = true;
}
}
return b;
}
private Map<String, Double> getExpressionPvals(
Set<String> targets, boolean[] set1, boolean[] set2) {
Map<String, Double> map = new HashMap<String, Double>();
Histogram2D h = new Histogram2D(0.2);
System.out.println("targets = " + targets.size());
Progress prg = new Progress(targets.size());
for (String sym : targets) {
prg.tick();
if (expMan.getNonZeroRatio(sym) == 0) continue;
double pval = calcDiffPval(sym, set1, set2, true);
if (Double.isNaN(pval)) continue;
if (pval == 0) pval = 1E-11;
double pPerm = calcDiffPval(sym, set1, set2, false);
if (pPerm == 0) pPerm = 1E-5;
h.count(-Math.log(pval), -Math.log(pPerm));
// pval = 0 is not real and it is not compatible with fisher's combined probability.
// below is a better approximation.
// if (pval == 0)
// {
// pval = 1E-11;
// }
map.put(sym, pval);
}
Histogram2DPlot p = new Histogram2DPlot(h);
p.setLines(Arrays.asList(new double[] {1, 0}));
p.setVisible(true);
return map;
}