error in tl.paga: Invalid vertex ID

[sokratiag]

Hello,

I have encountered the following error in scv.tl.paga:

adata.uns['neighbors']['distances'] = adata.obsp['distances']
adata.uns['neighbors']['connectivities'] = adata.obsp['connectivities']

scv.tl.paga(adata, groups='Clusters_new')
df = scv.get_df(adata, 'paga/transitions_confidence', precision=2).T
df.style.background_gradient(cmap='Blues').format('{:.2g}')

versions: scvelo 0.3.2 (python 3.8.3) igraph 0.11.6

Error:

~/.local/lib/python3.8/site-packages/igraph/clustering.py in cluster_graph(self, combine_vertices, combine_edges)
334 """
335 result = self.graph.copy()
--> 336 result.contract_vertices(self.membership, combine_vertices)
337 if combine_edges is not False:
338 result.simplify(combine_edges=combine_edges)

InternalError: Error at src/constructors/basic_constructors.c:75: Invalid (negative or too large) vertex ID. -- Invalid vertex ID

Any ideas on how to solve it? Thanks!

[lcxlcx]

I have encountered the same problem, do you have a solution？

[mailmrcai]

this bug was caused by cluster name. I fixed this by:

adata = adata[~adata.obs['clusters'].isin([None,np.nan])].copy() #cluster / louvain

filter adata before the first step

[ugur0sahin]

That worked for me thanks !