grassp.pp.aggregate_samples

aggregate_samples(data, grouping_columns, agg_func=<function median>, keep_raw=False)

Aggregate samples based on grouping columns.

Parameters:

data AnnData

The annotated data matrix with proteins as observations (rows).

grouping_columns Union[str, List[str]]

Column name(s) in data.var to group samples by.

agg_func Callable[[ndarray, Optional[int]], ndarray] (default: <function median at 0x107ebb7f0>)

Function to aggregate samples within each group. Must take an array and axis argument. Default is np.median.

keep_raw bool (default: False)

Whether to keep the unaggregated data in the .raw attribute of the returned AnnData object.

Return type:

AnnData

Returns:

AnnData New AnnData object with aggregated samples.

Notes

This function aggregates samples based on shared values in the specified grouping columns. For each group, the samples are combined using the provided aggregation function. The resulting AnnData object has one variable per unique group.