nispace.workflows.simple_colocalization

nispace.workflows.simple_colocalization#

nispace.workflows.simple_colocalization(y, x='PET', z=None, x_collection=None, standardize='xz', parcellation='Schaefer200', parcellation_labels=None, y_covariates=None, colocalization_method='spearman', p_from_average_y=False, plot=True, combat=False, n_perm=10000, seed=None, n_proc=1, verbose=True, nispace_object=None, fetch_x_kwargs={}, init_kwargs={}, clean_y_kwargs={}, colocalize_kwargs={}, permute_kwargs={}, correct_p_kwargs={}, plot_kwargs={})[source]#

Simple colocalization workflow.

Parameters:

  • y (array-like or pandas DataFrame or list) – Input Y data to colocalize with X. Can be a numpy array, pandas DataFrame, (list of) path(s) to a file(s) or list of image objects.

  • x (str or array-like, default="PET") – Input X data. Can be a string indicating a reference dataset (“PET”, “mRNA”, …), or inputs types as listed for y.

  • z (array-like or None, default=None) – Optional confound data to regress out. Can be “gm”, or input types as listed for y.

  • x_collection (str or None, default=None) – If x is a string reference dataset, specifies which collection to use.

  • standardize (str, default="xz") – Which data to standardize. Can contain “x”, “y”, and/or “z”.

  • parcellation (str or int, default=_PARC_DEFAULT) – Brain parcellation to use. Can be a string name or integer ID.

  • parcellation_labels (array-like or None, default=None) – Optional labels for the parcellation regions.

  • y_covariates (array-like or None, default=None) – Optional covariates to regress from Y data.

  • colocalization_method (str or list, default="spearman") – Method(s) to use for colocalization. Can be “spearman”, “pearson”, etc.

  • p_from_average_y (bool, default=False) – Whether to compute p-values from averaged Y values.

  • plot (bool, default=True) – Whether to generate visualization plots.

  • combat (bool, default=False) – Whether to apply ComBat harmonization.

  • n_perm (int, default=10000) – Number of permutations for null distribution.

  • seed (int or None, default=None) – Random seed for reproducibility.

  • n_proc (int, default=-1) – Number of processes for parallel computation. -1 uses all CPUs.

  • verbose (bool, default=True) – Whether to print progress messages.

  • nispace_object (NiSpace or None, default=None) – Optional pre-initialized NiSpace object to use.

  • fetch_x_kwargs (dict, default={}) – Additional arguments for fetching X data.

  • init_kwargs (dict, default={}) – Additional arguments for NiSpace initialization.

  • clean_y_kwargs (dict, default={}) – Additional arguments for Y data cleaning.

  • colocalize_kwargs (dict, default={}) – Additional arguments for colocalization.

  • permute_kwargs (dict, default={}) – Additional arguments for permutation testing.

  • correct_p_kwargs (dict, default={}) – Additional arguments for p-value correction.

  • plot_kwargs (dict, default={}) – Additional arguments for plotting.

Returns:

  • colocs (dict or array) – Colocalization values for each method.

  • p_values (dict or array) – Uncorrected p-values for each method.

  • p_fdr_values (dict or array) – FDR-corrected p-values for each method.

  • nsp (NiSpace) – The NiSpace object containing all results.

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