I’ve been following along with the PBMC 3k preprocessing and clustering tutorial, both the with 3k dataset and my dataset. I get identical results up to the UMAP step. During this step, my UMAP plot is nothing like the one produced by the tutorial (and the exact same thing is seen when using my own data set). Changing the UMAP plot with PAGA produces strange results as well…
I was wondering if this would be because for some reason that I have UMAP incorrectly installed, or that I am just missing some argument somewhere. I’d like to get this figured out and think it’s probably just some simple solution that I’m missing, but I’m not sure as I am very new to Scanpy and Python in general (I am currently transitioning from R/Seurat to Python/Scanpy).
Any help would be appreciated!