nispace.workflows.nimare_xsea

nispace.workflows.nimare_xsea(y, x='mRNA', z=None, x_collection=None, x_background=None, standardize='xz', space='MNI152NLin6Asym', data_space=None, parcellation_space=None, parcellation='Yan200', parcellation_labels=None, parcellation_hemi=['L', 'R'], y_covariates=None, colocalization_method=None, mc_method='meff', normalize_colocalizations=True, xsea_aggregation_method='mean', permute_sets=False, pooled_p=False, plot=True, binary_y=False, nimare_nulls=None, n_perm=10000, seed=None, n_proc=1, verbose=True, nispace_object=None, fetch_x_kwargs=None, init_kwargs=None, fit_kwargs=None, clean_y_kwargs=None, colocalize_kwargs=None, permute_kwargs=None, correct_p_kwargs=None, plot_kwargs=None, return_nispace_only=False)[source]

NiMARE X-set enrichment analysis (XSEA) workflow.

Convenience wrapper around xsea() for Y maps derived from NiMARE meta-analyses. Equivalent to nimare_colocalization() with XSEA enabled.

Sets background_value={"y": False} in fit_kwargs (scoped to Y only – X/Z keep normal 'auto' background handling) and routes nimare_nulls into permute_kwargs. See nimare_colocalization() for full details on NiMARE-specific parameters.

Parameters:

  • y (NIfTI image, array-like, or list) – ALE stat map or binary cluster-coverage map.

  • x (str or array-like, default="mRNA") – Reference X maps (gene-set collections for XSEA).

  • binary_y (bool, default=False) – Set True for binary or fractional cluster-coverage Y maps.

  • nimare_nulls (dict or None, default=None) – Coordinate-sampling null maps from null_maps_from_nimare(). When provided, sets maps_nulls=nimare_nulls in permute_kwargs.

Returns:

  • nsp (NiSpace) – (when return_nispace_only=True)

  • colocs, p_values, pc_values, nsp (tuple) – Deprecated. Returned when return_nispace_only=False.

Notes

All other parameters are identical to xsea().

Unlike nimare_colocalization(), this function never touches maps_which — xsea() always permutes maps_which="Y" regardless of nimare_nulls, since X is a fixed reference gene-set collection in XSEA, not something meaningfully permuted map-by-map. So nimare_nulls=None here does not fall back to X-permutation the way nimare_colocalization() does — Y is still permuted, just with freshly generated standard spatial nulls (typically Moran) instead of NiMARE coordinate-sampling nulls, which is functionally equivalent to a plain xsea() call.