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)

Export to a SPRING project directory [Weinreb et al., 2017].

Deprecated since version 1.13.0: Use a different viewer like e.g. vitessce.

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.