anndict.simplify_obs_column

anndict.simplify_obs_column(adata, column, new_column_name, simplification_level='')

Simplifies labels in the specified column of the AnnData object and stores the result in a new column using map_cell_type_labels_to_simplified_set().

Parameters:

adata AnnData

The AnnData object containing the data.

column str

The column in adata.obs containing the cell type labels to simplify.

new_column_name str

The name of the new column to store the simplified labels.

simplification_level str (default: '')

A qualitative description of how much you want the labels to be simplified. Could be anything, like 'extremely', 'barely', or 'compartment-level'.

Return type:

dict

Returns:

A dict mapping the original labels to the simplified set of labels.

Notes

Modifies adata by adding adata.obs[new_column_name] (i.e. the new labels) in-place.

Example

import anndict as adt

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

label_mapping = adt.simplify_obs_column(adata,
                        'cell_subtype',
                        new_column_name = 'cell_type',
                        simplification_level = 'cell type level'
                        )

print(adata.obs) # New column added
>     cell_subtype               cell_type_level
> 0   cd8+ t cell                t cell
> 1   cd4+ t cell                t cell
> 2   venous endothelial cell    endothelial cell
> 3   arterial endothelial cell  endothelial cell