Entering edit mode
Hello,
How to obtain more than 3 dimensions in runTSNE? The following code will raise an error.
library(scater)
example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce <- runTSNE(example_sce, ncomponents=5)
sessionInfo( )
This is actually an Rtsne specification not scater. I don't think TSNE with >2 dimensions makes sense, given the nature of the embedding. It's a qualitative stochastic representation of the data meant for visualisation. Adding extra dimensions over 2 just makes it difficult to visualise again.
If you really want an embedding with 5 dims, then just use runUMAP. I still think it's a bad idea, but this will at least run.
Thanks for the explanation!