ehrapy.tools.get_medcat_annotation_overview¶
- ehrapy.tools.get_medcat_annotation_overview(adata, status='Affirmed', use_key='medcat_annotations')[source]¶
Provide an overview for the annotation results. An overview will look like the following:
cui (the CUI), nsubjects (from how many rows this one got extracted), type_ids (TUIs), name(name of the entitiy), perc_subjects (how many rows relative to absolute number of rows)
- Parameters:
medcat_obj – The current MedCAT object which holds all infos on NLP analysis with MedCAT and ehrapy.
n – Basically the parameter for head() of pandas Dataframe. How many of the most common entities should be shown?
status (
str) – One of “Affirmed” (default), “Other” or “Both”. Displays stats for either only affirmed entities, negated ones or both.use_key (
str) – Key to use for the annotated results.
- Return type:
- Returns:
A Pandas DataFrame with the overview stats.