dynamo.pl.cell_cycle_scores

dynamo.pl.cell_cycle_scores(adata, cells=None, save_show_or_return='show', save_kwargs={})[source]

Plot a heatmap of cells ordered by cell cycle position.

Parameters:
  • adata (AnnData) – an AnnData object.

  • cells (Optional[list]) – a list of cell ids used to subset the AnnData object. If None, all cells would be used. Defaults to None.

  • save_show_or_return (Literal['save', 'show', 'return']) – whether to save, show, or return the figure. Available flags are “save”, “show”, and “return”. Defaults to “show”.

  • save_kwargs (Dict[str, Any]) – a dictionary that will be passed to the save_show_ret function. By default, it is an empty dictionary and the save_show_ret function will use the {“path”: None, “prefix”: ‘scatter’, “dpi”: None, “ext”: ‘pdf’, “transparent”: True, “close”: True, “verbose”: True} as its parameters. Otherwise you can provide a dictionary that properly modify those keys according to your needs. Defaults to {}.

Raises:

NotImplementedError – unavailable save_show_or_return

Return type:

Optional[Axes]

Returns:

Axes of the plotted figure if save_show_or_return is set to “return”; otherwise, return None.