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); } } }