annotate_hierarchy

hnoca.snapseed.annotate.annotate_hierarchy(adata, marker_hierarchy, group_name, layer=None, min_expr=0.1, **kwargs)

Annotate clusters based on a manually defined cell type and marker hierarchy.

Parameters:

Name	Type	Description	Default
adata	AnnData	AnnData object	required
marker_hierarchy	dict	dict arker genes for each celltype arranged hierarchically.	required
group_name	str	Name of the column in adata.obs that contains the cluster labels	required
layer	str | None	Layer in adata to use for expression	None
**kwargs		Additional arguments to pass to the annotation function.	{}

Returns

Dict with assignments and metrics