SOAPy_st.tl.cal_spark

SOAPy_st.tl.cal_spark(adata: AnnData, gene_name: list | str | None = None, method: Literal['gaussian', 'poisson'] = 'gaussian', num_core: int = 5, spatial_in_obsm: str = 'spatial') → DataFrame

Perform SPARK analysis on spatial omics data. Doi: 10.1038/s41592-019-0701-7 Github: https://github.com/xzhoulab/SPARK

Parameters

adataanndata.AnnData

An AnnData object containing spatial omics data and spatial information.

gene_nameUnion[list, str, None], optional

List of genes of interest or a single gene name to focus the analysis on. If None, the analysis will consider all genes in the dataset.

methodLiteral[‘gaussian’, ‘poisson’], optional

The statistical method to be used for the analysis. Must be one of ‘gaussian’ or ‘poisson’.

num_coreint

The number of CPU core.

spatial_in_obsmstr

The key of spatial coordinates in adata.obsm

Returns

pd.DataFrame

A Pandas DataFrame containing the results of the SPARK analysis.