Closed namsaraeva closed 3 months ago
import pertpy as pt import scanpy as sc adata = pt.dt.bhattacherjee() milo = pt.tl.Milo() mdata = milo.load(adata) sc.pp.neighbors(mdata["rna"]) milo.make_nhoods(mdata["rna"]) mdata = milo.count_nhoods(mdata, sample_col="orig.ident") milo.da_nhoods(mdata, design="~label") milo.annotate_nhoods(mdata, anno_col='cell_type') milo.plot_da_beeswarm(mdata)
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