sparty.pp.run_scanpy

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sparty.pp.run_scanpy#

sparty.pp.run_scanpy(sdata, resolution=0.5, layer='counts', key='leiden', table_key='table', scale=False)#

Run Scanpy normalization, dimensionality reduction, clustering, and plotting.

Parameters:

  • sdata (SpatialData) – SpatialData object (already QC-filtered).

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

  • layer (str (default: 'counts')) – Layer to use for counts.

  • key (str (default: 'leiden')) – Key to store clustering labels.

  • table_key (str (default: 'table')) – Key for table in SpatialData.

  • scale (bool (default: False)) – If True, scale data before downstream analysis.

Returns:

adata Processed AnnData object.

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