iFlyChat JavaScript SDK has a function named 'minimiseChat' which can be used to minimise chat window of a specific user room. You may use the function in the following manner:
iflychat.minimiseChat({id: '1', /* id of the user or room */name: 'admin' /*name of the user or room */​});
This function takes a JS object as parameter which should have following properties:
id
name