Description Usage Arguments Value Examples
Calculates a spectral tSNE representation of the data, based either on PCA or diffusion map reductions.
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object |
An URD object |
dim.use |
(Character) Whether to calculate the tSNE projection from PCs ( |
which.dims |
(Numeric vector) Which PCs (or diffusion components) to use. Defaults to the significant PCs. (We don't estimate the significant diffusion components, so if using diffusion map reduction, probably should explicitly specify this.) |
theta |
(Numeric) Speed/accuracy trade-off for Barnes-Hut approximation of tSNE (0-1, 0 is exact tSNE, higher is less accurate, default is 0.5) |
max_iter |
(Numeric) Number of iterations to perform |
verbose |
(Logical) Should Rtsne print progress updates? |
perlexity |
(Numeric) Perplexity parameter for the tSNE |
An URD object with tSNE coordinates stored in the @tsne.y
slot.
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