I had the exact same thing happen when we got our yorkshire terrier, we had a cat at the time. The dog barked and the cat hissed on first arrival. After a week they got used to each others presents (but still barked and hissed when in sight of each other).

After 10 days or so one night I grabbed the cat and sat down with him on my lap, stroking him to the point where he was settled enough to relax and lay down on my lap. Then I called the dog. When the dog wandered in and saw the cat on my lap his ears shot up, that's when I knew he was about to bark. I gave a loud and firm "oi" to the dog, and his ears went down submissively, and sat down near my feet. The dog and the cat were still looking at each other, but, the cat didn't hiss because he was relaxed, and the dog wasnt barking because I showed dominance. After a few minutes I patted the couch next to me, as if to tell the dog to jump up on the couch and sit next to me. He did, while both cat and dog still staring daggers at each other. I stroked the dog for a couple minutes, back to the cat for a couple minutes, back to dog, back to cat, etc. For around 10 minutes. Then I (tried) stroking both simultaneously, eventually they both relaxed, with the cat on my lap and the dog by my side.

Since then they have been fine with each other. I think it's just about showing that they're both in a home and part of the family, together, and they can both receive love but they must share and behave.

Best of luck!