omicverse.pl.embedding_adjust

omicverse.pl.embedding_adjust(adata, groupby, exclude=(), basis='X_umap', ax=None, adjust_kwargs=None, text_kwargs=None)[source]

Get locations of cluster median and adjust text labels accordingly.

Borrowed from scanpy github forum.

Parameters:

  • adata – AnnData object

  • groupby – str Key in adata.obs for grouping

  • exclude (default: ()) – tuple, optional (default=()) Groups to exclude from labeling

  • basis (default: 'X_umap') – str, optional (default=’X_umap’) Embedding basis key in adata.obsm

  • ax (default: None) – matplotlib.axes.Axes, optional (default=None) Axes object to plot on

  • adjust_kwargs (default: None) – dict, optional (default=None) Arguments for adjust_text function

  • text_kwargs (default: None) – dict, optional (default=None) Arguments for text annotation

Returns:

dict

Dictionary of median positions for each group

Return type:

medians