scispy.pp.run_scanpy

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scispy.pp.run_scanpy#

scispy.pp.run_scanpy(sdata, min_counts=20, resolution=0.5, positive_coord_only=True, key='leiden', scale=True)#

Filter and run scanpy analysis.

Parameters:

  • sdata (SpatialData) – SpatialData object.

  • min_counts (int (default: 20)) – minimum transcript count to keep cell.

  • resolution (float (default: 0.5)) – resolution for clustering.

  • key (str (default: 'leiden')) – key to add for clusters.

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