monkeybread.plot.embedding_filter

monkeybread.plot.embedding_filter(adata, mask, color=None, basis='spatial', show=True, ax=None, masked_color='lightgrey', masked_alpha=1.0, masked_dot_size=None, unmasked_dot_size=None, **kwargs)

Shows a filtered embedding, allowing for examination of specific cells.

Cells in the mask will be larger and colored based on color if provided, otherwise red. Cells not in the mask will be smaller and colored gray.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • mask (Union[List[bool], List[str]]) – A mask to apply to adata.obs.index. Can be a list of cell indices or a boolean mask with the same length as the index.

  • color (Optional[str] (default: None)) – Column in adata.obs or adata.var_names used to color cells.

  • basis (Optional[str] (default: 'spatial')) – Coordinates in adata.obsm[X_{basis}] to use. Defaults to spatial.

  • show (Optional[bool] (default: True)) – Whether to show the plot or return the Axes object.

  • ax (Optional[Axes] (default: None)) – An Axes object to add the plots to.

  • kwargs – Keyword arguments that will be passed to scanpy.pl.embedding().

Return type:

Optional[Axes]

Returns:

: If show = True, returns nothing. Otherwise, returns the Axes object the plot is contained within.