コード例 #1
0
  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);
  }
コード例 #2
0
  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);
      }
    }
  }
コード例 #3
0
  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");
    }
  }