visionpy.api.start_vision#

visionpy.api.start_vision(adata, name, norm_data_key=None, compute_neighbors_on_key=None, signature_varm_key=None, signature_names_uns_key=None, port=None, debug=False)[source]#

Wrapper function to start VISION server.

Parameters:

  • adata (Union[str, AnnData]) – AnnData object

  • name (str) – Name for the VISION session

  • norm_data_key (Union[Literal['use_raw'], str, None] (default: None)) – Key for layer with log library size normalized data. If None (default), uses adata.X

  • compute_neighbors_on_key (Optional[str] (default: None)) – Key in adata.obsm to use for computing neighbors. If None, use neighbors stored in adata. If no neighbors have been previously computed an error will be raised.

  • signature_varm_key (Optional[str] (default: None)) – Key in adata.varm for signatures. If None (default), no signatures. Matrix should encode positive genes with 1, negative genes with -1, and all other genes with 0

  • signature_names_uns_key (Optional[str] (default: None)) – Key in adata.uns for signature names. If None, attempts to read columns if signature_varm_key is a pandas DataFrame. Otherwise, uses Signature_1, Signature_2, etc.

  • port (Optional[int] (default: None)) – The port of the webserver. Defaults to 5000.