spatialtis.NMD_marker

class spatialtis.NMD_marker(data, pval=0.01, importance_cutoff=0.5, layer_key=None, tree_kwargs=None, **kwargs)[source]

Identify neighbor markers dependent marker

The neighborhood is treated as a single cell.

Parameters

  • data (anndata._core.anndata.AnnData) – AnnData object to perform analysis

  • exp_std_cutoff – Standard deviation, threshold to filter out markers that are not variant enough

  • pval (float) – The p-value threshold to determine significance

  • selected_markers – Select your interested markers

  • layers_key – {layers_key}

  • tree_kwargs (Optional[Dict]) – The keyword arguments that pass to the boosting tree class, (Default: n_jobs=-1, random_state=0)

  • **kwargs – Pass to spatialtis.abc.AnalysisBase

  • importance_cutoff (Union[int, float]) –

  • layer_key (Optional[str]) –

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