dynamo.pl.fate

dynamo.pl.fate(adata, x=0, y=1, basis='pca', color='ntr', ax=None, save_show_or_return='show', save_kwargs={}, **kwargs)[source]

Draw the predicted integration paths on the low-dimensional embedding.

Parameters:

adata (AnnData) – an Annodata object.
x (int) – the column index of the low dimensional embedding for the x-axis. Defaults to 0.
y (int) – the column index of the low dimensional embedding for the y-axis. Defaults to 1.
basis (str) – the basis used for dimension reduction. Defaults to “pca”.
color (str) – any column names or gene expression, etc. that will be used for coloring cells. Defaults to “ntr”.
ax (Optional[Axes]) – the matplotlib axes object where new plots will be added to. Only applicable to drawing a single component. If None, new axis would be created. Defaults to None.
save_show_or_return (Literal['save', 'show', 'return']) – whether to save, show or return the figure. Defaults to “show”.
save_kwargs (Dict[str, Any]) –
a dictionary that will be passed to the save_fig function. By default, it is an empty dictionary and the save_fig function will use the

{
“path”: None, “prefix”: ‘phase_portraits’, “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 – any other kwargs to be passed to dynamo.pl.scatters.

Return type:

Optional[Axes]

Returns:

None would be returned by default. If save_show_or_return is set to be return, the matplotlib axis of the plot would be returned.