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

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.