anndict.wrappers.create_label_hierarchy_adata_dict

anndict.wrappers.create_label_hierarchy_adata_dict(adata, col, simplification_levels)

Create a hierarchy of simplified labels based on a given column in AnnData.

This function generates multiple levels of simplified labels from a single column in adata.obs. Each successive level of simplification is created using the specified simplification level.

Parameters:

adata AnnData

Annotated data matrix containing the column to be simplified.

col str

Name of the column in adata.obs to be simplified.

simplification_levels list[str]

List of simplification levels to apply. Each level should be a value that can be used by the simplify_obs_column function.

Return type:

dict

Returns:

A dict mapping new column names to their corresponding simplified label mappings. The keys are the names of the new columns created for each simplification level, and the values are the mappings returned by simplify_obs_column() for each level.

Example

import anndict as adt

print(adata.obs)
>     subtype
> 0   cd8+ t cell
> 1   cd4+ t cell
> 2   venous endothelial cell
> 3   arterial endothelial cell

label_mapping = adt.create_label_hierarchy(adata,
                        'subtype',
                        ['cell type level', 'cell class level', 'compartment level'])

print(adata.obs) # New columns added
>     subtype                    subtype_cell_type_level     subtype_cell_class_level    subtype_compartment_level
> 0   cd8+ t cell                t cell                      lymphocyte                  immune
> 1   cd4+ t cell                t cell                      lymphocyte                  immune
> 2   venous endothelial cell    endothelial cell            endothelial cell            stromal
> 3   arterial endothelial cell  endothelial cell            endothelial cell            stromal