spatialtis.spatial_coexp

class spatialtis.spatial_coexp(data, method='spearman', use_cell_type=False, layer_key=None, corr_thresh=0.5, **kwargs)[source]

Identifying spatial co-expression markers using correlation

The correlation is calculated within pairs of neighbor cells

Parameters

  • data (anndata._core.anndata.AnnData) – AnnData object to perform analysis

  • method (Optional[str]) – “spearman” or “pearson” (Default: “spearman”)

  • use_cel_type – Whether to use cell type information

  • selected_markers – Select your interested markers

  • layer_key (Optional[str]) – The layer in AnnData to perform analysis

  • corr_thresh (Union[int, float]) – The minimum correlation value to store the result,

  • **kwargs – Pass to spatialtis.abc.AnalysisBase

  • use_cell_type (bool) –

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