tiledbsoma.io.to_anndata

tiledbsoma.io.to_anndata(experiment: Experiment, measurement_name: str, *, X_layer_name: str | None = 'data', extra_X_layer_names: Sequence[str] | KeysView[str] | None = None, obs_id_name: str | None = None, var_id_name: str | None = None, obsm_varm_width_hints: Dict[str, Dict[str, int]] | None = None, uns_keys: Sequence[str] | None = None) → AnnData

Converts the experiment group to AnnData format. Choice of matrix formats is following what we often see in input .h5ad files:

  • X as scipy.sparse.csr_matrix

  • obs,``var`` as pandas.dataframe

  • obsm,``varm`` arrays as numpy.ndarray

  • obsp,``varp`` arrays as scipy.sparse.csr_matrix

The X_layer_name is the name of the TileDB-SOMA measurement’s X collection which will be outgested to the resulting AnnData object’s adata.X. If this is None, then the return value’s adata.X will be None, and adata.layers will be unpopulated. If this is not None, then adata.X will be taken from this layer name within the input measurement.

The extra_X_layer_names are used to specify how the output adata object’s adata.layers is populated. The default behavior – extra_X_layer_names being None – means that adata.layers will be empty. If extra_X_layer_names is a provided list these will be used for populating adata.layers. If you want all the layers to be outgested, without having to name them individually, you can use extra_X_layer_names=experiment.ms[measurement_name].X.keys(). To make this low-friction for you, we introduce one more feature: we’ll ignore X_layer_name when populating adata.layers. For example, if X keys are "a", "b", "c", "d", and you say X_layer_name="b" and extra_X_layer_names=experiment.ms[measurement_name].X.keys(), we’ll not write "b" to adata.layers.

The obs_id_name and var_id_name are columns within the TileDB-SOMA experiment which will become index names within the resulting AnnData object’s obs/var dataframes. If not specified as arguments, the TileDB-SOMA’s dataframes will be checked for an original-index-name key. When that also is unavailable, these default to "obs_id" and "var_id", respectively.

The obsm_varm_width_hints is optional. If provided, it should be of the form {"obsm":{"X_tSNE":2}} to aid with export errors.

If uns_keys is provided, only the specified top-level uns keys are extracted. The default is to extract them all. Use uns_keys=[] to not ingest any uns keys.

Lifecycle

Maturing.