Hello,
I accidentally provided the name of a reduction that didn't exist in my Seurat object to SCimplify_for_Seurat(). Strangely, the function ran for hours, used far more memory than when the correct reduction name was provided, and ultimately failed with a cryptic error. Basically, I think I simple internal check that the reductions exist in the object would be helpful.
I ran this exact code to reproduce the issue (where everything is a legitimate input except the RNA reduction):
seur_meta = SCimplify_for_Seurat(
seur, assay = c("RNA", "ATAC"),
reduction = list("does_not_exist", "integrated.lsi.harmony"),
dims = list(1:30, 2:30), gamma = 75,
label = "mid_cluster"
)
And this was the eventual error:
Error in igraph::cluster_walktrap(graph) :
At vendor/cigraph/src/community/walktrap/walktrap_graph.cpp:207 : Vertex with zero strength found: all vertices must have positive strength for walktrap. Invalid value
Calls: SCimplify_for_Seurat -> <Anonymous>
Execution halted
Thanks!
Best,
-Nick
Hello,
I accidentally provided the name of a reduction that didn't exist in my Seurat object to
SCimplify_for_Seurat(). Strangely, the function ran for hours, used far more memory than when the correct reduction name was provided, and ultimately failed with a cryptic error. Basically, I think I simple internal check that the reductions exist in the object would be helpful.I ran this exact code to reproduce the issue (where everything is a legitimate input except the RNA reduction):
And this was the eventual error:
Thanks!
Best,
-Nick