spatialtis.spatial_enrichment¶
- class spatialtis.spatial_enrichment(data, threshold=None, layer_key=None, selected_markers=None, resample=500, pval=0.01, order=False, **kwargs)[source]¶
Profiling markers spatial enrichment using permutation test
Similar to neighborhood analysis which tells you the relationship between different type of cells. This analysis tells you the spatial relationship between markers.
- Parameters
data (anndata._core.anndata.AnnData) – AnnData object to perform analysis
threshold (Optional[float]) – The expression level to determine whether a marker is positive
layer_key (Optional[str]) – The layer in AnnData to perform analysis
selected_markers (Optional[Union[List, Tuple, pandas.core.series.Series, numpy.ndarray]]) – Select your interested markers
resample (int) – Number of times to perform resample
pval (float) – The p-value threshold to determine significance
order (bool) – If False, (Cell_A, Cell_B) and (Cell_B, Cell_A) are the same interaction (Default: False)
**kwargs – Pass to
spatialtis.abc.AnalysisBase
See also