dynamo.pl.lap_min_time

dynamo.pl.lap_min_time(adata, basis='pca', show_paths=False, show_elbow=True, show_elbow_func=False, color='ntr', figsize=(6, 4), n_col=3, save_show_or_return='show', save_kwargs={}, **kwargs)[source]

Plot minimum time of the least action paths.

Parameters:

  • adata (AnnData) – an AnnData object.

  • basis (str) – the basis used for dimension reduction. Defaults to “pca”.

  • show_paths (bool) – whether to plot the path together with the time. Defaults to False.

  • show_elbow (bool) – whether to mark the elbow point on time-action curve. Defaults to True.

  • show_elbow_func (bool) – whether to show the time-action curve that elbow is on. Defaults to False.

  • color (str) – any column names or gene expression, etc. that will be used for coloring cells. Defaults to “ntr”.

  • figsize (Tuple[float, float]) – the size of the figure. Defaults to (6, 4).

  • n_col (int) – the number of subplot columns. Defaults to 3.

  • save_show_or_return (Literal['save', 'show', 'both', 'all']) – whether to save or show the figure. Can be one of “save”, “show”, “both” or “all”. “both” and “all” have the same effect. The axis of the plot cannot be returned here. 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 {}.

  • **kwargs – not used here.

Raises:

NotImplementedError – unsupported method to find the elbow.

Return type:

None