My significant other (SO) and I are in five years of relationship. We met working in a lab and she already earned her PhD at that time. I was a graduate student. She was the main person I went after my adviser if I had logical questions about my project and helped me the process throughout. We now have two publications together. We worked professionally together for almost three years. She knows my potential both personally and professionally.
I am wondering if it is okay to use a letter of recommendation from her to apply for a PhD program. Updated: I edited the word "supervisor" as suggested by a commenter. She wasn't an official supervisor but, provided tremendous help with analytical issues. We also stay collaborating on other research projects until today even after we both were out of the lab.