scTDA.RootedGraph With groups=FALSE not working

[csbbcompbio]

Dear Pablo, Hope you are doing fine. I am trying to run scTDA on one of our datasets and I am facing this error: total of 616 patches required clustering this implies 1693 nodes in the mapper graph Traceback (most recent call last): File "scTDA_Tutorial.py", line 161, in c = scTDA.RootedGraph('Embryo_pca_25_0.40', 'Embryo.no_subsampling.tsv', groups=False) File "/Users/pra7mx/anaconda/lib/python2.7/site-packages/scTDA/main.py", line 1531, in init self.g3, self.dicdend = self.dendritic_graph() File "/Users/pra7mx/anaconda/lib/python2.7/site-packages/scTDA/main.py", line 1503, in dendritic_graph dil = networkx.shortest_path_length(self.gl, self.root, k) File "/Users/pra7mx/anaconda/lib/python2.7/site-packages/networkx/algorithms/shortest_paths/generic.py", line 245, in shortest_path_length p=nx.bidirectional_shortest_path(G,source,target) File "/Users/pra7mx/anaconda/lib/python2.7/site-packages/networkx/algorithms/shortest_paths/unweighted.py", line 136, in bidirectional_shortest_path results=_bidirectional_pred_succ(G,source,target) File "/Users/pra7mx/anaconda/lib/python2.7/site-packages/networkx/algorithms/shortest_paths/unweighted.py", line 186, in _bidirectional_pred_succ for w in Gsucc(v): File "/Users/pra7mx/anaconda/lib/python2.7/site-packages/networkx/classes/graph.py", line 1084, in neighbors_iter raise NetworkXError("The node %s is not in the graph." % (n,)) networkx.exception.NetworkXError: The node 0 is not in the graph.

Can you please help me with this.

Thanks,

Cheers !!

Praneet

[csbbcompbio]

I have also updated the scTDA version and tried and still error is coming up.

[pcamara]

Dear Praneet,

Thanks for pointing this out. I need more information to be able to understand what is going on. Could you please send me the input tables and the offending command so that I can reproduce the error on my side?

Thanks,

Pablo

[csbbcompbio]

Hi Pablo, Here I have attached the files I am using and also the command thats giving me the error. E8_1.txt data.txt

"c = scTDA.RootedGraph('Embryo_pca_25_0.40', 'Embryo.no_subsampling.tsv', groups=False)"

Thanks,

Cheers !! Praneet

[leungchuenyan]

Dear Pablo,

Many thanks for creating this package and the nice tutorial. I am getting a similar error as the previous post.. I wonder if there was a fix to it? I think I have the most recent scTDA by installing from https://github.com/CamaraLab/scTDA.git

Many thanks in advance !!!

Best wishes, CY

c = scTDA.RootedGraph('test_pca_25_0.40', 'test.no_subsampling.tsv', groups=False) Traceback (most recent call last): File "", line 1, in File "/Users/labuser/anaconda2/lib/python2.7/site-packages/scTDA/main.py", line 1536, in init self.g3, self.dicdend = self.dendritic_graph() File "/Users/labuser/anaconda2/lib/python2.7/site-packages/scTDA/main.py", line 1508, in dendritic_graph dil = networkx.shortest_path_length(self.gl, self.root, k) File "/Users/labuser/anaconda2/lib/python2.7/site-packages/networkx/algorithms/shortest_paths/generic.py", line 244, in shortest_path_length raise nx.NodeNotFound("Source {} not in G".format(source)) networkx.exception.NodeNotFound: Source 0 not in G