More than 3 dimensions in runTSNE
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@a9c5eb20
Last seen 4 months ago
United States

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( )

dimensions scater runTSNE • 586 views
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Entering edit mode

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.

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Thanks for the explanation!

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