private void writeSelf(
String origTarget, GeneBranch currentParent, GeneBranch down, Writer writer1, Writer writer2)
throws IOException {
if (!down.isSelected()) return;
String edgeTag;
if (down.isLeaf() || travExp.getUpstream(down.gene).contains(currentParent)) {
edgeTag = SIFEnum.CONTROLS_EXPRESSION_OF.getTag();
} else edgeTag = SIFEnum.CONTROLS_STATE_CHANGE_OF.getTag();
writer1.write(currentParent.gene + "\t" + edgeTag + "\t" + down.gene + "\n");
writeWeights(origTarget, currentParent, down, edgeTag, writer2);
writeBranches(origTarget, down, writer1, writer2);
}
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);
}
}
}
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");
}
}