dynamo.pl.show_landscape

dynamo.pl.show_landscape(adata, Xgrid, Ygrid, Zgrid, basis='umap', save_show_or_return='show', save_kwargs={})

Plot the quasi-potential landscape.

Parameters

• adata (AnnData) – AnnData object that contains Xgrid, Ygrid and Zgrid data for visualizing potential landscape.

• Xgrid (numpy.ndarray) – x-coordinates of the Grid produced from the meshgrid function.

• Ygrid (numpy.ndarray) – y-coordinates of the Grid produced from the meshgrid function.

• Zgrid (numpy.ndarray) – z-coordinates or potential at each of the x/y coordinate.

• basis (str (default: umap)) – The method of dimension reduction. By default it is trimap. Currently it is not checked with Xgrid and Ygrid.

• save_show_or_return ({‘show’, ‘save’, ‘return’} (default: show)) – Whether to save, show or return the figure.

• save_kwargs (dict (default: {})) – A dictionary that will passed to the save_fig function. By default it is an empty dictionary and the save_fig function will use the {“path”: None, “prefix”: ‘show_landscape’, “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.

Returns

Return type

A 3D plot showing the quasi-potential of each cell state.