dynamo.vf.topography
- dynamo.vf.topography(adata, basis='umap', layer=None, X=None, dims=None, n=25, VecFld=None, **kwargs)[source]
Map the topography of the single cell vector field in (first) two dimensions.
- Parameters:
adata (
AnnData
) – an AnnData object.basis (
Optional
[str
]) – The reduced dimension embedding of cells to visualize.layer (
Optional
[str
]) – Which layer of the data will be used for vector field function reconstruction. This will be used in conjunction with X.dims (
Optional
[list
]) – The dimensions that will be used for vector field reconstruction.n (
Optional
[int
]) – Number of samples for calculating the fixed points.VecFld (
Optional
[VecFldDict
]) – 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:
- 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.