It definitely sounds as though your puppy is extremely anxious around you, and is afraid. Puppies with a gentle, non-dominant nature react by becoming fearful and anxious, in extreme cases this anxiety can become a fear-based aggression. Is your puppy young? If so, if you treat this problem correctly you should be able to help her to 'forget' your harsh treatment of her (dogs are amazingly forgiving) and feel less anxious around you. Crouch down beside her whenever possible, you will seem less threatening that way. I would recommend that you slowly start to spend 'fun time' with her. Once (s)he is feeling more comfortable around you again, you should become the 'fun guy' for a while. It took time for your puppy to learn to be scared of you, and it will take time for her to learn to trust you again. You need to be patient, and loving, and give her a chance to learn about you all over again.
