Apologies for the delayed response. The results you are looking at is from the optical spectrum analyzer, so it corresponds to the spectrum at optical frequencies, and it won't be able to show the modulation of the signal that is at much lower frequencies.
In our WDM example, we use a demultiplexer to isolate the signal of each band and plot their eye diagram. I think a similar approach should be used.
Let us know if you have any question.