Hello,
I turned to scanpy to analyze metacells datasets and I am intrigued by the draw_graph to show data toppology, potentially with PAGA or MST. For one of my datasets it worked beautifully with the metacell clusters aligning and not being too sparse, for all the other datasets the graph becomes sort of a cloud with no clear “directionality” or axes.
I guess it is an issue of neighbours/biology or settings in calling scanpy.tl.draw_graph and scanpy.pl.draw_graph?
Thank you very much in advance for the support.
Best