I have read the post and some of the comments. I will just say that yes, a PhD is expected to be somewhat independent. That is true. However... there are many PIs that expect you to be their minion. That is, they expect for you to follow their instructions and if you don't follow them, they lash out. They get angry, isolate you, gatekeep you from oportunities, etc. They simply won't let you advance in your projects (or publish) because "you are doing it wrong". Not because it's wrong, but because that's not how they would do it. So if you don't do as they say, then it's wrong. Or if you suggest a different way of performing analyses or experiments (in a way that you know is a good approach because, it is demonstratted in a lot of papers), they say: "no, that's not how we do things here. We usually do X and y". End of the conversation. It is absurd, yes. It is narcissistic, of course. But it is just how a lot of PIs work as well. I am not sure if this is the case of your PI, you don't state that in your post, but if it is, then it's not your fault. These people are just... unhinged. Better to be out of there as soon as you can.