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 [Weinreb et al., 2017].

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 Weinreb et al. [2017] for details.

Parameters:

adata AnnData

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

project_dir Path | str

Path to directory for exported SPRING files.

embedding_method str

Name of a 2-D embedding in adata.obsm

subplot_name str | None (default: None)

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

cell_groupings 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 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.

Return type:

None

Examples

See this tutorial.