SOAPy_st.tl.gene_cluster
- SOAPy_st.tl.gene_cluster(adata: AnnData, k: int, norm: bool = True, method: Literal['poly', 'loess'] = 'poly', pvalue: float | None = None, fdr: bool = False, range_min: float | None = None, correlation: float | None = None, best_k_sdbw: bool = True, num_spots: int = 50, inplace: bool = True) AnnData
The regression curves of multiple genes are clustered, and the curves can be screened by adjusting a variety of indicators
Parameters
- adataanndata.AnnData
An AnnData object containing spatial omics data and spatial information.
- kint
The number of cluster
- normbool, optional
If true, data normalization
- methodLiteral[‘poly’, ‘loess’], optional
Polynomial regression(poly) and Lowess regression(loess).
- pvaluefloat, optional
Threshold for the p-value in Polynomial regression.
- fdrbool, optional
If True, the p-values were corrected for FDR.
- range_minfloat, optional
Genes whose expression range is less than this value are discarded.
- correlationfloat, optional
Threshold for the correlation
- best_k_sdbwbool, optional
Automated cluster number screening using sdbw.
- num_spotsint, optional
The number of sampling points in curves clustering.
- inplacebool, optional
Whether to change the original adata.
Returns
anndata.AnnData.uns['SOAPy']['poly']['df_param_poly'] or ['SOAPy']['loess']['df_param_loess']- Storeadditional params for curves