omicverse.space.CellMap

omicverse.space.CellMap#

class omicverse.space.CellMap(adata_sc, adata_sp, use_rep_sc='X_pca', use_rep_sp='X_pca')[source]#

SpatRio CellMap class for mapping single cells to spatial coordinates.

This class implements optimal transport-based mapping of single cells to spatial coordinates using expression similarity and spatial awareness. It provides methods for both mapping and coordinate assignment.

Parameters:

  • adata_sc (anndata.AnnData) – Single-cell reference AnnData.

  • adata_sp (anndata.AnnData) – Spatial AnnData to receive mapped cells.

  • use_rep_sc (str, default="X_pca") – Representation key in adata_sc.obsm used for transport.

  • use_rep_sp (str, default="X_pca") – Representation key in adata_sp.obsm used for transport.

  • Attributes –

    adata_sc: AnnData

    Single-cell RNA sequencing data.

    adata_sp: AnnData

    Spatial transcriptomics data.

    use_rep_sc: str

    Representation key for single-cell data.

    use_rep_sp: str

    Representation key for spatial data.

    spatrio_decon: pandas.DataFrame

    Deconvolution results after mapping.

    spatrio_map: pandas.DataFrame

    Coordinate assignment results.

  • Examples – 

    >>> import scanpy as sc
>>> import omicverse as ov
>>> # Load data
>>> adata_sc = sc.read_h5ad('single_cell.h5ad')
>>> adata_sp = sc.read_h5ad('spatial.h5ad')
>>> # Initialize CellMap
>>> cm = ov.space.CellMap(
...     adata_sc=adata_sc,
...     adata_sp=adata_sp,
...     use_rep_sc='X_pca'
... )

__init__(adata_sc, adata_sp, use_rep_sc='X_pca', use_rep_sp='X_pca')[source]#

Initialize CellMap with single-cell and spatial references.

Parameters:

  • adata_sc (anndata.AnnData) – Single-cell reference object to be projected into spatial coordinates.

  • adata_sp (anndata.AnnData) – Spatial transcriptomics object providing spot locations.

  • use_rep_sc (str, default="X_pca") – Embedding key in adata_sc.obsm used for alignment.

  • use_rep_sp (str, default="X_pca") – Embedding key in adata_sp.obsm used for alignment.

Methods

__init__(adata_sc, adata_sp[, use_rep_sc, ...])

Initialize CellMap with single-cell and spatial references.

assign_coord(**kwargs)

Assign concrete spatial coordinates to mapped single cells.

map([sc_type, sp_type, alpha, aware_power, ...])

Map single cells to spatial spots by optimal transport.
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