deconvatac.tl.rctd
==================

.. py:module:: deconvatac.tl.rctd


Functions
---------

.. autoapisummary::

   deconvatac.tl.rctd.rctd


Module Contents
---------------

.. py:function:: rctd(adata_spatial, adata_ref, labels_key, doublet_mode='full', r_lib_path=None, results_path='./rctd_results', create_rctd_kwargs={})

   Run RCTD

   Parameters 
   -----------

   adata_spatial : AnnData
       AnnData of the spatial data, filtered by highly variable features. Feature space needs to be the same as the one of adata_ref. Raw counts are expected in .X.
   adata_ref : AnnData 
       AnnData of the reference data, filtered by highly variable features. Feature space needs to be the same as the one of adata_spatial. Raw counts are expected in .X.
   labels_key : str
       Cell type key in adata_ref.obs for label information
   doublet_mode: str ["doublet", "full"]
       On which mode to run RCTD:  'doublet' (at most 1-2 cell types per pixel),
                                   'full' (no restrictions on number of cell types)
   r_lib_path : str
       Path to R library in which RCTD is installed.   
   results_path : str
       Path to save estimated cell type abundances to. 
   create_rctd_kwargs : dict 
       Parameters for create.RCTD().
       
   Returns
   --------

   - Saves estimated proportions as csv-file to results_path.