Mix FXML with "pure javafx" code

I have an application, where the UI is built with FXML for the most part. But I am trying to add a menubar, and I used "pure java" without using FXML. I got no errors but the menubar is not visible. What did I do wrong?

Here is the code:

Parent root = FXMLLoader.load(getClass().getResource("FXMLDocument.fxml"));


    Scene scene = new Scene(root);

    stage.setScene(scene);
    stage.show();

     MenuBar menubar = new MenuBar ();
    Menu file = new Menu ("File");
    Menu options = new Menu ("options");
    Menu help = new Menu ("help");

    MenuItem save = new MenuItem ("save");
    MenuItem close = new MenuItem ("close");
    MenuItem open = new MenuItem ("open");
    MenuItem exit = new MenuItem ("exit");

    file.getItems().addAll(save, close, open, new SeparatorMenuItem(),exit);


    Menu color = new Menu ("Colors");
    Menu prefs = new Menu ("Preferences");

    options.getItems().addAll(color, prefs);

    MenuItem red = new MenuItem ("red");
    color.getItems().add(red);

    MenuItem setExample = new MenuItem ("SetExample");
    prefs.getItems().add(setExample);


    //root.getChildren().add(menubar);
    menubar.getMenus().addAll(file, options, help);
    BorderPane root2 = new BorderPane();
    root2.setTop(menubar);