troubleshooting scanpy pseudotime error

[yulianatan]

following steps on this tutorial error on line 10,

AttributeError Traceback (most recent call last)
in
1 #denoising graph
----> 2 sc.tl.diffmap(myeloid_cluster)
3 sc.pp.neighbors(harmonized, n_neighbors=20, n_pcs=18, metric="correlation", method='umap')
4 sc.tl.draw_graph(myeloid_cluster)

/opt/conda/lib/python3.7/site-packages/scanpy/tools/_diffmap.py in diffmap(adata, n_comps, copy)
47 raise ValueError('Provide any value greater than 2 for n_comps. ')
48 adata = adata.copy() if copy else adata
---> 49 _diffmap(adata, n_comps=n_comps)
50 return adata if copy else None

/opt/conda/lib/python3.7/site-packages/scanpy/tools/_dpt.py in _diffmap(adata, n_comps)
14 start = logg.info(f'computing Diffusion Maps using n_comps={n_comps}(=n_dcs)')
15 dpt = DPT(adata)
---> 16 dpt.compute_transitions()
17 dpt.compute_eigen(n_comps=n_comps)
18 adata.obsm['X_diffmap'] = dpt.eigen_basis

/opt/conda/lib/python3.7/site-packages/scanpy/neighbors/init.py in compute_transitions(self, density_normalize)
807 # q[i] is an estimate for the sampling density at point i
808 # it's also the degree of the underlying graph
--> 809 q = np.asarray(W.sum(axis=0))
810 if not issparse(W):
811 Q = np.diag(1.0/q)

AttributeError: 'NoneType' object has no attribute 'sum'