scmorph.pp.aggregate

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scmorph.pp.aggregate#

scmorph.pp.aggregate(adata, well_key='infer', group_keys=None, method='median', progress=True)#

Aggregate single-cell measurements into well-level profiles

Parameters:

  • adata (AnnData) – Annotated data matrix

  • well_key (str (default: 'infer')) – Name of column in metadata used to define wells.

  • group_keys (Union[str, list[str], None] (default: None)) – Other column names to group by, e.g. plate names

  • method (str (default: 'median')) – Which aggregation to perform. Must be one of ‘mean’, ‘median’, ‘std’, ‘var’, ‘sem’, ‘mad’, and ‘mad_scaled’ (i.e. median/mad)

  • progress (bool (default: True)) – Whether to show a progress bar

Note

If this function produces warnings about dividing by zero, this means that at least one group had a median absolute deviation of 0 for a feature. This means that this feature is constant in that group. However, this will produce missing values. Before proceeding, you should therefore use drop_na() with feature_threshold=1 and cell_threshold=0 to remove features with missing values.

Return type:

AnnData

Returns:

dists Aggregated annotated data matrix

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