I am trying to create a real time graph using nvd3.js which would be updated periodically and with the impression that the data is processed in real time.
For now I
You probably want to look at: D3 Real-Time streamgraph (Graph Data Visualization),
especially the link of the answer: http://bost.ocks.org/mike/path/
In general, I see two ways to deal with the vertical transition problem: