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JinmiaoChenLab / Rphenograph

Rphenograph: R implementation of the PhenoGraph algorithm
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Weird error when working with a lot of cells #15

Open jgarces02 opened 4 years ago

jgarces02 commented 4 years ago

Hi there,

Thanks for this useful package. I'm running it with a total of 1,5 millions of cells considering only 10 features and I'm getting this weird error, together with a (also very weird) PCA:

Run Rphenograph starts:
  -Input data of 1500000 rows and 10 columns
  -k is set to 15
  Finding nearest neighbors...DONE ~ 1236.863 s
  Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 110.193 s
  Build undirected graph from the weighted links...DONE ~ 110.629 s
  Run louvain clustering on the graph ...DONE ~ 135.736 s
Run Rphenograph DONE, totally takes 1593.421s.
  Return a community class
  -Modularity value: 0.8961815
  -Number of clusters: 31Warning messages:
1: In recycleSingleBracketReplacementValue(value, x, i) :
  number of values supplied is not a sub-multiple of the number of values to be replaced

image

I tried to repeat the clustering with less cells (a total of 15.000) and none warning is appearing and the PCA is correctly colored (apparently)...

image

...maybe this could be a bug when working with so much cells? Thanks a lot for your help!