deconvatac.tl.rctd

deconvatac.tl.rctd#

Functions#

rctd(adata_spatial, adata_ref, labels_key[, ...])

Run RCTD

Module Contents#

deconvatac.tl.rctd.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_spatialAnnData

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_refAnnData

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_keystr

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_pathstr

Path to R library in which RCTD is installed.

results_pathstr

Path to save estimated cell type abundances to.

create_rctd_kwargsdict

Parameters for create.RCTD().

Returns#

  • Saves estimated proportions as csv-file to results_path.

Contents