ehrapy.tools.add_medcat_annotation_to_obs¶
- ehrapy.tools.add_medcat_annotation_to_obs(adata, name, use_key='medcat_annotations', added_colname=None, copy=False)[source]¶
Add info extracted from free text as a binary column to obs.
Indicates whether the specific entity to color by has been found in that row or not.
- Parameters:
adata (
AnnData
) – AnnData object that holds the data to annotate.name (
Iterable
[str
] |str
) – Name of the entity to add as a column to obs.use_key (
str
, default:'medcat_annotations'
) – Key to use for the annotated results.added_colname (
Iterable
[str
] |str
|None
, default:None
) – Name of the column to add to obs. If None, name will be used.copy (
bool
, default:False
) – Whether to copy adata or not.
- Return type:
- Returns:
Returns None if copy=False, else returns an AnnData object. Sets the following fields;
- adata.obs[name | added_coname]
pandas.DataFrame
Added column(s) to adata.obs, indicating whether the specific entity to color by has been found in that row or not.
- adata.obs[name | added_coname]