cycombinepy.detect_batch_effect_express

cycombinepy.detect_batch_effect_express(adata, markers=None, batch_key='batch', sample_key='sample', downsample=None, out_dir=None, seed=472)

Quick 3-panel batch-effect summary (EMD heatmap, density, MDS).

Returns a dict of matplotlib figures keyed by "emd", "density" and "mds". If out_dir is given, the figures are saved as PNGs and the dict is still returned for further inspection.

Matches detect_batch_effect_express in R/detect_batch_effect.R.

Return type:

dict

Parameters:

• adata (AnnData)

• markers (Iterable[str] | None)

• batch_key (str)

• sample_key (str | None)

• downsample (int | None)

• out_dir (str | PathLike | None)

• seed (int)