mmc.umap_interrogate_level()

mmochi.utils.umap_interrogate_level(adata, level, batch_key=None, key_added='lin', umap_basis='X_umap', cmap=None, **kwargs)

Plots UMAPs showing events selected by high-confidence thresholding and used for training and breaks down annotation confusion onto the UMAP. X_umap must be generated before running this function.

Parameters:

  • adata (AnnData) – AnnData object to use for plotting

  • level (str) – Level of the classifier to interrogate

  • batch_key (str (default: None)) – Name of batch in adata to use for UMAP, uses batch_iterator to find key

  • key_added (str (default: 'lin')) – Key in the adata.obsm that contains the classification results

  • umap_basis (str (default: 'X_umap')) – Passed to scanpy.pl.embedding as basis

  • cmap (Optional[List[str]] (default: None)) – Color map information used to color

  • kwargs – Sent to scanpy.pl.embedding