API
===

Spacemake class
---------------

Accessing spacemake objects from python

.. autoclass:: spacemake.smk.Spacemake
    :members:

H&E integration module
----------------------

.. autofunction:: spacemake.spatial.he_integration.align_he_spot_img

.. autofunction:: spacemake.spatial.he_integration.align_he_aggregated_img

.. autofunction:: spacemake.spatial.he_integration.attach_he_adata

novosparc integration module
----------------------------

.. autofunction:: spacemake.spatial.novosparc_integration.novosparc_denovo

.. autofunction:: spacemake.spatial.novosparc_integration.save_novosparc_res

.. autofunction:: spacemake.spatial.novosparc_integration.novosparc_mapping

.. autofunction:: spacemake.spatial.novosparc_integration.quantify_clusters_spatially