tiledbsoma.ExperimentAxisQuery.to_spatialdata

ExperimentAxisQuery.to_spatialdata(X_name: str, *, column_names: AxisColumnNames | None = None, X_layers: Sequence[str] = (), obsm_layers: Sequence[str] = (), obsp_layers: Sequence[str] = (), varm_layers: Sequence[str] = (), varp_layers: Sequence[str] = (), drop_levels: bool = False, scene_presence_mode: str = 'obs')

Returns a SpatialData object containing the query results

This is a low-level routine intended to be used by loaders for other in-core formats, such as AnnData, which can be created from the resulting objects.

Parameters:

• X_name – The X layer to read and return in the X slot.

• column_names – The columns in the var and obs dataframes to read.

• X_layers – Additional X layers to read and return in the layers slot.

• obsm_layers – Additional obsm layers to read and return in the obsm slot.

• obsp_layers – Additional obsp layers to read and return in the obsp slot.

• varm_layers – Additional varm layers to read and return in the varm slot.

• varp_layers – Additional varp layers to read and return in the varp slot.

• drop_levels – If True remove unused categories from the AnnData table with the measurement data.

• scene_presence_mode – Method for determining what scenes to return data from. Valid options are obs (use obs_spatial_presence dataframe) and var (use var_spatial_presence dataframe). Defaults to obs.