Hi,
Hope anyone can help me. My UMAP looks weird. I can see from the annotation, that the same cell type is found at the edges of a large radial/star-shaped “cluster”. Here, the different colors are different immune cell types in a PBMC sample. Do anyone have an idea why this happens, or which parameters I need to adjust to improve it?
This is before batch correction, but I would expect my dataset to not really have any batches. They have all been processed in one go.
Thank you!