voyagerpy.spatial.get_spot_coords#

voyagerpy.spatial.get_spot_coords(adata: AnnData, subset: None | Series | slice = None, as_tuple: bool = True, as_df: bool = False, res: str | None = None) → ndarray | Tuple[ndarray, ndarray] | DataFrame#

Get the spot coordinates in the image.

Parameters:

  • adata (AnnData) – Annontated data matrix.

  • subset (Union[None, pd.Series, slice], optional) – Subset of observations to get the spot coordinates from, by default None.

  • as_tuple (bool, optional) – If True, return the coordinates as a tuple of arrays (x, y), by default True

  • as_df (bool, optional) – If True, return the the coordinates as a dataframe, by default False.

  • res (Optional[str], optional) – The resolution to scale the coordinates for. If None, this is determined automatically , by default None.

Returns:

The coordinates of the selected spots, as a tuple, dataframe, or Nx2 array.

Return type:

Union[np.ndarray, Tuple[np.ndarray, np.ndarray], pd.DataFrame]