spatialtis.NMD_marker#
- spatialtis.NMD_marker(data, pval=0.01, selected_markers=None, importance_cutoff=0.5, layer_key=None, tree_kwargs=None, export_key='nmd_marker', **kwargs)[source]#
Identify neighbor markers dependent marker
The neighborhood is treated as a single cell.
- Parameters
- dataAnnData
The AnnData to work with.
- importance_cutofffloat
Standard deviation, threshold to filter out markers that are not variant enough.
- pvalfloat
The p-value threshold to determine significance.
- selected_markerslist of str
Select your interested markers.
- layer_key{layers_key}
- tree_kwargsdict
The keyword arguments that pass to the boosting tree class, (Default: n_jobs=-1, random_state=0).
- export_keystr
The key used to store result.
- **kwargs
Config for the analysis, for details check
spatialtis.abc.AnalysisBase.