iS-CellR
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t-SNE problem
Hi again, I have a problem when I run iS-CellR:
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 977
Number of edges: 27340
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8657
Number of communities: 7
Elapsed time: 0 seconds
Warning: The following arguments are not used: pca, reduction.use, dims.use
Suggested parameter: reduction instead of reduction.use; dims instead of dims.use
Warning in normalizePath(path = fast_tsne_path) :
path[1]="FIt-SNE-master/bin/fast_tsne": No such file or directory
Warning: Error in fftRtsne: fast_tsne_path 'FIt-SNE-master/bin/fast_tsne' does not exist or is not executable
87: stop
86: fftRtsne
85: RunTSNE.matrix
82: RunTSNE.DimReduc
80: RunTSNE.Seurat
74: observeEventHandler [/tmp/Rtmpi0mx5t/shinyapp59342312516d/iS-CellR-master/server.R#824]
3: runApp
2: runUrl
1: shiny::runGitHub
I check, I have only the .gitignore in FIt-SNE-master/bin/ and it is the same in their github: https://github.com/KlugerLab/FIt-SNE/tree/master/bin
Also, it's a shame that you don't present the UMAP representation while you are calculating it.