Working example is here.
Basically, there is code for initial load, where all circles, tooltips, etc. are created and positioned in initial places. As well, the layout (pack) is created.
Than, on each button press, new data is loaded into pack, and the pack is recalculated. That crucial code is here:
Here you bind (load) now data into pack layout: (in my example its random data, of course you'll have your data from json or code or similar):
pack.value(function(d) { return 1 +
Math.floor(Math.random()*501); });
Here the new layout is calculated:
pack.nodes(data);
After that, elements are transitioned to new positions, and its attributes are changed as you determine.
I just want to stress that I don't use enter/update/exit pattern or transformations (that you might see in others solutions), since I believe this introduces unnecessary complexity for examples like this.
Here are some pics with transition in action:
Start:
Transition:
End: