public void generateInfluenceGraphs(List<String> result) {
DownstreamTree tree =
new DownstreamTree(
travSt,
travExp,
new BranchDataProvider() {
@Override
public Color getColor(String gene, String root) {
double pval = calcPVal(root, Collections.singleton(gene));
String colS = val2Color(pval, calcChangeDirection(root, gene) ? 1 : -1);
String[] c = colS.split(" ");
return new Color(
Integer.parseInt(c[0]), Integer.parseInt(c[1]), Integer.parseInt(c[2]));
}
@Override
public double getThickness(GeneBranch branch, String root) {
Set<String> dwstr = branch.getAllGenes();
double cumPval = calcPVal(root, dwstr);
return Math.min(-Math.log(cumPval), 5);
}
});
String dir = this.dir + dataset.name() + "/";
File d = new File(dir);
if (!d.exists()) d.mkdirs();
assert d.isDirectory();
for (String mut : result) {
GeneBranch g = tree.getTree(mut, downstream.get(mut), depth);
g.trimToMajorPaths(downstream.get(mut));
if (g.selectLeaves(affectedDw.get(mut))) {
if (!affectedDw.get(mut).isEmpty() && affectedDw.get(mut).size() < 6)
RadialInfluenceTree.write(g.copy(true), false, dir + mut + ".svg");
writeTree(g, dir);
}
}
}
