First of all give id to HTML tag where you have added ng-controller directive.
<div ng-controller="MyController" id="myControllerDiv">
var element = document.getElementById("myControllerDiv");
This will give us that element, we will find it's corresponding angular element.
var angularElement = angular.element(element);
Now we will get it's scope and using that scope, we can all any function of MyController
This will call myFunction defined in MyController.
Hope this helps you.