Compute a 2-D t-SNE embedding of genes from a distance matrix

Wraps Rtsne::Rtsne() for a distance-based t-SNE. The random seed is fixed to 233 for reproducibility.

ObtainGeneTSNE(dist, perplexity = 30)

Arguments

dist

A dist object (or symmetric matrix coercible to one) of pairwise gene distances.

perplexity

Numeric. t-SNE perplexity parameter. Default 30.

Value

A data frame with columns tSNE_1 and tSNE_2 and row names matching labels(dist).

Examples

if (FALSE) {
embedding <- ObtainGeneTSNE(as.dist(gene.dist.mat))
}