SOAPy_st.tl.domain_from_local_moran
- SOAPy_st.tl.domain_from_local_moran(adata: AnnData, score_key: str, moran_label_key: str = 'hotspot', k: int = 6, pvalue_filter: float = 0.05, attribute_filter: float | None = None, spatial_lag_filter: float | None = None, zscore: bool = True, fdr: bool = True, scale: str | float = 'hires', spatial_in_obsm: str = 'spatial', inplace: bool = True) AnnData
Using the local moran method generate the spatial domain.
Parameters
- adataanndata.AnnData
An AnnData object containing spatial omics data and spatial information.
- score_keystr
The key for the Moran index need to be computed. It could be gene name ,key in adata.obs_index or AUCell name.
- moran_label_keystr
The key for storing Moran labels in adata.obs.
- kint, optional
Number of nearest neighbors in KNN.
- pvalue_filterfloat, optional
Threshold for determining hotspot regions based on the p-value of the local Moran’s I statistic. A smaller value indicates higher statistical significance, typically set to 0.05 or another significance level. For a detailed explanation, see https://pysal.org/esda/generated/esda.Moran_Local.html#esda.Moran_Local
- attribute_filterfloat, optional
Threshold for attribute filtering (AUCell score). If provided, it affects how observations are labeled as “Hotspot” or “Not” based on whether the attribute value is greater than or equal to this threshold. For a detailed explanation, see https://pysal.org/esda/generated/esda.Moran_Local.html#esda.Moran_Local
- spatial_lag_filterfloat, optional
Threshold for the average attribute of neighboring spots. If provided, it affects how observations are labeled as “Hotspot” or “Not” based on whether the spatial lag value of the local Moran’s I statistic is greater than or equal to this threshold.
- zscorebool, optional
If True, calculate the z-score of the attribute.
- fdrbool, optional
If True, the p-values were corrected for FDR.
- scaleUnion[str, float], optional
scale used in subsequent analyses. If it’s Visium data it can also be HE image labels (hires or lower). Most of the time you don’t need to change this.
- spatial_in_obsmstr, optional
The key of spatial coordinates in adata.obsm.
- inplacebool, optional
If True, Modify directly in the original adata.
Returns
anndata.AnnData.uns['SOAPy']['local_moran']- Local Moran information for each spot