First ask yourself whether you really need a separate view controller. One view controller can easily hide or unhide a graph. If this graph needs its own view conroller then you could use a container view that contains the graph which refers to its own view conroller. That is what container views are made for. The "Master" view controller then would just hide and unhide the container view in response to rotation events (and layout them accordingly etc. pp.)
If you prefer to add or remove the container view from its super view (most probably self.view from the "Master" view controller's point of view) then do that instead of hiding and unhiding. That is probably most appropriate.
The upside of this appoach would be that it works regardless of the navigaiton structure you are in, regardless of whether the rotated view controller was pushed or presented modally, regardless of whether you are in a tab bar driven app or a single view app, whether you are using storyboard, works with IB as well as programmatically, etc. pp.
There is nothing wrong with fetching the window instance from the app's delegate. I just don't see the need for doing so. Seems rather complicated to me compared to the alternatives.