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 Annodata object.basis (str (default: trimap)) – The reduced dimension embedding of cells to visualize.
layer (str or None (default: None)) – Which layer of the data will be used for vector field function reconstruction. This will be used in conjunction with X.
X ('np.ndarray' (dimension: n_obs x n_features)) – Original data. Not used
dims (list or None (default: None)) – The dimensions that will be used for vector field reconstruction.
n (int (default: 10)) – Number of samples for calculating the fixed points.
VecFld (dictionary or None (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 fixed point identification.
- Returns
adata – 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.
- Return type