mesa.ecospatial.calculate_MDI
- mesa.ecospatial.calculate_MDI(spatial_data, scales, library_key, library_id, spatial_key, cluster_key, selecting_scale=False, random_patch=False, plotfigs=False, savefigs=False, patch_kwargs={}, other_kwargs={})
Calculate the multiscale diversity index (MDI) for spatial data.
- Parameters:
spatial_data (Union[
ad.AnnData,pd.DataFrame]) – The spatial data to be used for calculating the diversity indices.scales (Union[tuple, list]) – The scales at which the diversity index is to be calculated.
library_key (str) – The key to access the library data within spatial_data.
library_id (Union[tuple, list]) – The identifiers of the libraries involved in the analysis.
spatial_key (Union[str, List[str]]) – Key(s) used to access the spatial data from spatial_data.
cluster_key (str) – The key to access the cluster data which categorizes the spatial entities.
selecting_scale (bool, optional) – Specifies whether to run GDI at each scale to help decide the finest scale.
random_patch (bool, optional) – Specifies whether patches should be generated in a random manner. Default is False.
plotfigs (bool, optional) – Whether to plot figures during the analysis. Default is False.
savefigs (bool, optional) – Whether to save the generated figures to disk. Default is False.
patch_kwargs (dict, optional) – Additional keyword arguments used for patch generation. Defaults to an empty dictionary.
other_kwargs (dict, optional) – Other keyword arguments that may influence the analysis. Defaults to an empty dictionary.
- Returns:
A DataFrame containing the diversity value at each scale and the overall multiscale diversity index (MDI).
- Return type: