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Is there a way to make the graph plots offset from each other so that each plot can be seen separately, but can still be compared to the others. For example, when designing digital logic circuits it is hard to tell what each of the individual inputs are doing compared to the output. If the plots were offset from each other and all visible separately you would be able to see exactly when each input is high or low and compare that to your output.

Yep, this is a problem. What you can do is add a little fudge factor, like 0.05 volts to the second trace, 0.1 volts to the next, or whatever voltage will give you just a little trace separation.

Or you can add a lot, like twice the signal level, to end up with multiple separated but synchronized traces.