Are you using the website, or generating your own plots using Python (or R)? If you're using the website, the skeleton viewer does allow you to show and hide the synapses from particular input/output connections.
If you're using Python, it would be helpful to see the code you're using so far. Then we might be able to suggest some modifications to achieve what you're looking for. I think the answer will involve fetch_synapse_connections:
You can respond here, or you can continue the discussion on this related GitHub thread of yours, if you think that's appropriate:
Best,
Stuart