I got mad at my advisor?
She's been really nice after this, and complimenting me on small things, but I'm not sure how to go forward. 


It shows that she realized you have been stressed out, and she is willing to be helpful to make you feel better as a new student. Do not think too much. Work well. Respect her and be nice to her (really mean that. not pretend).

As time passes, the event will be forgotten and forgiven (if needed). Since you are fairly new, you will eventually get to know her more. At that time, you will be in a better position to see what went wrong and what made you lose your cool.

Also offer to proactively fix the situation. Apologies by word mean nothing. Show it in action.