scanpy.external.exporting.spring_project

scanpy.external.exporting.spring_project(adata, project_dir, embedding_method, subplot_name=None, cell_groupings=None, custom_color_tracks=None, total_counts_key='n_counts', neighbors_key=None, overwrite=False)

Exports to a SPRING project directory [Weinreb17].

Visualize annotation present in adata. By default, export all gene expression data from adata.raw and categorical and continuous annotations present in adata.obs.

See SPRING or [Weinreb17] for details.

Parameters:

adata : AnnData

Annotated data matrix: adata.uns['neighbors'] needs to be present.

project_dir : Union[Path, str]

Path to directory for exported SPRING files.

embedding_method : str

Name of a 2-D embedding in adata.obsm

subplot_name : Optional[str] (default: None)

Name of subplot folder to be created at project_dir+"/"+subplot_name

cell_groupings : Union[str, Iterable[str], None] (default: None)

Instead of importing all categorical annotations when None, pass a list of keys for adata.obs.

custom_color_tracks : Union[str, Iterable[str], None] (default: None)

Specify specific adata.obs keys for continuous coloring.

total_counts_key : str (default: 'n_counts')

Name of key for total transcript counts in adata.obs.

overwrite : bool (default: False)

When True, existing counts matrices in project_dir are overwritten.

Examples

See this tutorial.