dynamo.vf.topography

dynamo.vf.topography(adata, basis='umap', layer=None, X=None, dims=None, n=25, VecFld=None, show_progress=False, **kwargs)[source]

Map the topography of the single cell vector field in (first) two or three dimensions.

Parameters:

  • adata (AnnData) – an AnnData object.

  • basis (Optional[str] (default: 'umap')) – The reduced dimension embedding of cells to visualize.

  • layer (Optional[str] (default: None)) – Which layer of the data will be used for vector field function reconstruction. This will be used in conjunction with X.

  • X (Optional[ndarray] (default: None)) – Original data. Not used

  • dims (Optional[list] (default: None)) – The dimensions that will be used for vector field reconstruction.

  • n (Optional[int] (default: 25)) – Number of samples for calculating the fixed points.

  • VecFld (Optional[VecFldDict] (default: None)) – The reconstructed vector field function.

  • kwargs – Key word arguments passed to the find_fixed_point function of the vector field class for high dimension

  • identification. (fixed point)

Return type:

AnnData

Returns:

AnnData object that is updated with the VecFld or ‘VecFld_’ + basis dictionary in the uns attribute. The VecFld2D key stores an instance of the VectorField2D class which presumably has fixed points, nullcline,

separatrix, computed and stored.