scSLAT.model.preprocess.scanpy_workflow

scSLAT.model.preprocess.scanpy_workflow(adata, filter_cell=False, min_gene=200, min_cell=30, call_hvg=True, n_top_genes=2500, batch_key=None, n_comps=50, viz=False, resolution=0.8)

Scanpy workflow using Seurat HVG

Parameters:

• adata (anndata._core.anndata.AnnData) – adata

• filter_cell (typing.Optional[bool]) – whether to filter cells and genes

• min_gene (typing.Optional[int]) – min number of genes per cell

• min_cell (typing.Optional[int]) – min number of cells per gene

• call_hvg (typing.Optional[bool]) – whether to call highly variable genes (only support seurat_v3 method)

• n_top_genes (typing.Union[int, typing.List, None]) – n top genes or gene list

• n_comps (typing.Optional[int]) – n PCA components

• viz (typing.Optional[bool]) – whether to run visualize steps

• resolution (typing.Optional[float]) – resolution for leiden clustering (used when viz=True)

Return type:

anndata._core.anndata.AnnData

Returns:

anndata object