scirpy.util.DataHandler.get_obs

DataHandler.get_obs(columns: str) → pandas.core.series.Series

DataHandler.get_obs(columns: Sequence[str]) → pandas.core.frame.DataFrame

Get one or multiple obs columns from either MuData or AIRR AnnData

Checks if the column is available in MuData.obs. If it can’t be found or DataHandler is initalized without MuData object, AnnData.obs is tried.

The returned object always has the dimensions and index of MuData, even if only columns from AnnData are used. It is easy to subset to AnnData if required:

params.get_obs([col1, col2]).reindex(params.adata.obs_names)

Parameters

columns: one or multiple columns.

Returns

If this is a single column passed as str, a Series will be returned, otherwise a DataFrame.