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) – Key to use for the annotated results.added_colname (
Iterable[str] |str|None) – Name of the column to add to obs. If None, name will be used.copy (
bool) – 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]