I am recently having some weird plotting when I compute PAGA graphs, and to test if it was a problem with my dataset I decided to run the full notebook from the Trajectory inference for hematopoiesis tutorial (scanpy-tutorials/paga-paul15.ipynb at master · scverse/scanpy-tutorials · GitHub).
However, I get the same weird loking graphs when I run the pl.paga function. As an example:
sc.pl.paga(adata, color=[‘louvain’, ‘Hba-a2’, ‘Elane’, ‘Irf8’])
What could be happening here? Before they were looking just like in the tutorial.
I updated scanpy and other packages to to the latest version, but the problem persists.