spatialtis.spatial_enrichment#
- spatialtis.spatial_enrichment(data, threshold=None, layer_key=None, selected_markers=None, resample=500, pval=0.01, export_key='spatial_enrichment', **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
- dataAnnData
The AnnData to work with.
- thresholdfloat
The expression level to determine whether a marker is positive
- layer_keystr
The layer in AnnData to perform analysis.
- selected_markerslist of str
Select your interested markers.
- resampleint, default: 500
Number of times to perform resample
- pvalfloat
The p-value threshold to determine significance.
- export_keystr
The key used to store result.
- **kwargs
Config for the analysis, for details check
spatialtis.abc.AnalysisBase.
See also