Error happened in computing velocity stream-- "ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (1, 4) + inhomogeneous part."

[wenhu0701]

Hi,

I used the example data to try reproducing the demo pipeline. With the adata_result generated, I used it for computing velocity stream and the error happened after running mv.velocity_graph(). Could you please help with figuring this out? Please find the details as followings. Thanks!

Best, Wen

adata_result ############################################################ AnnData object with n_obs × n_vars = 3365 × 865 obs: 'n_counts', 'celltype' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand', 'fit_alpha_c', 'fit_alpha', 'fit_beta', 'fit_gamma', 'fit_t_sw1', 'fit_t_sw2', 'fit_t_sw3', 'fit_scale_cc', 'fit_rescale_c', 'fit_rescale_u', 'fit_alignment_scaling', 'fit_model', 'fit_direction', 'fit_loss', 'fit_likelihood', 'fit_likelihood_c', 'fit_ssd_c', 'fit_var_c', 'fit_c0', 'fit_u0', 'fit_s0', 'fit_anchor_min_idx', 'fit_anchor_max_idx', 'fit_anchor_velo_min_idx', 'fit_anchor_velo_max_idx', 'velo_s_genes', 'velo_u_genes', 'velo_chrom_genes' uns: 'pca', 'neighbors', 'umap', 'celltype_colors', 'velo_s_params', 'velo_u_params', 'velo_chrom_params' obsm: 'X_pca', 'X_umap' varm: 'PCs', 'fit_anchor_c', 'fit_anchor_u', 'fit_anchor_s', 'fit_anchor_c_sw', 'fit_anchor_u_sw', 'fit_anchor_s_sw', 'fit_anchor_c_velo', 'fit_anchor_u_velo', 'fit_anchor_s_velo' layers: 'ambiguous', 'matrix', 'spliced', 'unspliced', 'Ms', 'Mu', 'ATAC', 'fit_t', 'fit_state', 'velo_s', 'velo_u', 'velo_chrom' obsp: 'distances', 'connectivities', '_RNA_conn', '_ATAC_conn'

Computing velocity stream and latent time

mv.velocity_graph(adata_result)

computing velocity graph (using 1/16 cores) /Users/apple/Wen/anaconda/anaconda3/envs/rstudio/lib/python3.8/site-packages/ipywidgets/widgets/widget.py:503: DeprecationWarning: The ipykernel.comm.Comm class has been deprecated. Please use the comm module instead.For creating comms, use the function from comm import create_comm. self.comm = Comm(**args) 100% 3365/3365 [00:05<00:00, 624.22cells/s]

ValueError Traceback (most recent call last) Cell In[211], line 2 1 #Computing velocity stream and latent time ----> 2 mv.velocity_graph(adata_result)

File ~/Wen/anaconda/anaconda3/envs/rstudio/lib/python3.8/site-packages/multivelo/dynamical_chrom_func.py:3504, in velocity_graph(adata, vkey, xkey, kwargs) 3502 if vkey+'_norm_genes' not in adata.var.columns: 3503 adata.var[vkey+'_norm_genes'] = adata.var[vkey+'_genes'] -> 3504 scv.tl.velocity_graph(adata, vkey=vkey+'_norm', xkey=xkey, kwargs)

File ~/Wen/anaconda/anaconda3/envs/rstudio/lib/python3.8/site-packages/scvelo/tools/velocity_graph.py:363, in velocity_graph(data, vkey, xkey, tkey, basis, n_neighbors, n_recurse_neighbors, random_neighbors_at_max, sqrt_transform, variance_stabilization, gene_subset, compute_uncertainties, approx, mode_neighbors, copy, n_jobs, backend) 359 n_jobs = get_n_jobs(n_jobs=n_jobs) 360 logg.info( 361 f"computing velocity graph (using {n_jobs}/{os.cpu_count()} cores)", r=True 362 ) --> 363 vgraph.compute_cosines(n_jobs=n_jobs, backend=backend) 365 adata.uns[f"{vkey}_graph"] = vgraph.graph 366 adata.uns[f"{vkey}_graph_neg"] = vgraph.graph_neg

File ~/Wen/anaconda/anaconda3/envs/rstudio/lib/python3.8/site-packages/scvelo/tools/velocity_graph.py:175, in VelocityGraph.compute_cosines(self, n_jobs, backend) 172 n_obs = self.X.shape[0] 174 # TODO: Use batches and vectorize calculation of dX in self._calculate_cosines --> 175 res = parallelize( 176 self._compute_cosines, 177 range(self.X.shape[0]), 178 n_jobs=n_jobs, 179 unit="cells", 180 backend=backend, 181 )() 182 uncertainties, vals, rows, cols = map(_flatten, zip(*res)) 184 vals = np.hstack(vals)

File ~/Wen/anaconda/anaconda3/envs/rstudio/lib/python3.8/site-packages/scvelo/core/_parallelize.py:138, in parallelize..wrapper(*args, *kwargs) 126 pbar, queue, thread = None, None, None 128 res = Parallel(n_jobs=n_jobs, backend=backend)( 129 delayed(callback)( 130 ((i, cs) if use_ixs else (cs,)), (...) 135 for i, cs in enumerate(collections) 136 ) --> 138 res = np.array(res) if as_array else res 139 if thread is not None: 140 thread.join()

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (1, 4) + inhomogeneous part.

[jacobrepucci]

Hey there,

So that I can best replicate the issue on my end, could I ask what versions of the required packages you're using?

[wenhu0701]

Hi! Thanks for the reply, please find the packages as followings: python 3.8.2 multivelo = 0.1.3, pandas = 2.0.3, numpy = 1.24.4, scvelo =0.2.5, scanpy = 1.9.5, scipy = 1.10.1, matplotlib = 3.7.3

[jacobrepucci]

This is an issue originating with scvelo. However, as you can see in the links below, changing the python and package versions you use appears to fix the error!

https://github.com/theislab/scvelo/issues/1109

https://github.com/theislab/scvelo/issues/1121

Alternatively, you could edit the local scvelo code so that the line res = np.array(res) if as_array else res in scvelo/core/_parallelize.py is instead res = np.array(res, dtype=object) if as_array else res

[jacobrepucci]

Good news: this issue was fixed in the most recent release of scvelo!

I'm going to go ahead and close this issue.