Try running your drawing actions after jframe creation, i.e.
// create a new window to hold the visualization
JFrame frame = new JFrame("prefuse example");
// ensure application exits when window is closed
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.add(d);
frame.pack(); // layout components in window
frame.setVisible(true); // show the window
vis.run("draw");
vis.run("layout");
Or, if that doesn't work, calling frame.repaint(). You need to force drawing of the visualization somehow, I'm thinking.