Ignition comes with some events that you might need.
afterIgnEvents
This is an event you can use if you want your code to run after all the Ignition javascript stuff loads. This is good if you want to make sure jquery, scrollmagic and all click events have been loaded.
To use:
document.addEventListener('afterIgnEvents', function () {
//your code
});
After Toggled Event
If your using the data-toggle ability on an element, you can have more javascript run afterwards. See here to learn more.