I just adopted a puppy on saturday - a female who we named Percy. She is a Shepherd/Spaniel/Retriever mix and is about 9 weeks old. For the most part, Percy is very loving and enjoys being held and given affection. She loves giving kisses and having her belly rubbed. But yesterday all of a sudden she started barking and growling for no apparent reason and then today she put herself under the couch and barked ferociously at me when I tried to coax her out. I'm not sure how to handle this. I want a gentle and loving pet. I don't want to have to be afraid of her.

are you going to enrol at obedience? a good school may be able to help with combating future agresiveness.
I would suggest to play it a bit by ear at the moment given that she is very new to your home. I am not suggesting to ignore the behaviour, but do keep in mind that dogs can show aggression due to fear, and it would be scary from a pups perspective to end up,all of a sudden with unfarmiliar smells, environment and ppl around her. Hiding under the couch may be indicating she is trying to flight to a place that she feels protected and safe and you aproaching her when she feels that way, could be confronting and intimidating to her.
Did you accidently hurt her? step on a tail or something too, could have frightened her a bit and made her upset?
Has she calmed down since you first posted this question? Has she done it again since?
Crate training may be a bit of help to you, it will at least give pup a safe place of her own that she can go to for refuge when feeling scared, intimidated or just needs time out.

First, I hope you are not isolating the pup away from you when home, especially at night. Should let her sleep in the same room with you, and have initially one preson as her main trainer, for learning to go outside , feeding, treats, rewarding her. I have had only three dogs in my life, and every dog is unique, but most all will fall into a pattern, because they are dogs. At one point the pup will challenge you, it could be very subtle, but it needs to be addressed on the spot or each time it slides by it will take more work to let all know who the boss dog is!! Out of three dogs, one never challenged, the other two did! One male as a pup, growled when I put his food dish down to eat, and I wanted to slide the dish in a little out of traffic, I immediately put my hand over the food dish so he had the option to bite my hand or give in to me and he was a doberman so I took a cool chance, and like a good dog he moved back hopeing I will give him his food back which I did. After that never a challenge again! Now the female was very young and qualified as a puppy did not want to come into the house, so when I went to get her she would run away but when I got her she would squirm around trying to escape and growling. On about the third occasion, I had to catch her and she bit me very deep with her puppy teeth and I was really bleeding and I just commly rowed her over on her belly and as my blood dripped on her she tryed to get loose but I held her until she stopped and when she did, she not only can into the house but followed me. I never hurt her just immobilized until she settled down. Each situation will be different just do not inflict pain it is not necessary! So far your pup has really done nothing yet to require more then love and reassurance!