ehrapy.anndata.get_obs_df¶

ehrapy.anndata.get_obs_df(adata, keys=(), obsm_keys=(), *, layer=None, features=None)[source]¶

Return values for observations in adata.

Parameters:

adata (AnnData) – AnnData object to get values from.
keys (Iterable[str]) – Keys from either .var_names, .var[gene_symbols], or .obs.columns.
obsm_keys (Iterable[tuple[str, int]]) – Tuple of (key from obsm, column index of obsm[key]).
layer (str) – Layer of adata.
features (str) – Column of adata.var to search for keys in.

Returns:

A dataframe with adata.obs_names as index, and values specified by keys and obsm_keys.

Examples

>>> import ehrapy as ep
>>> adata = ep.dt.mimic_2(encoded=True)
>>> ages = ep.ad.get_obs_df(adata, keys=["age"])