A plot-friendly output for the Barnes-Hut implementation of t-SNE.

Source: R/ohmytsne.R

A plot-friendly output for the Barnes-Hut implementation of t-SNE: test different perplexities and dimensions. See Rtsne::Rtsne for details on the algorithm.

ohmytsne(m, perplexity = c(15, 30, 50), ndim = ncol(m), ...)

Arguments

m

matrix; each row is an observation (eg. cell); each column is a feature (eg. gene / principal component)

perplexity

numeric vector of perplexities to use. Default: c(15, 30, 50)

ndim

numeric vector of dimensions to use. Default: ncol(m)

...

other arguments passed to Rtsne::Rtsne

Value

a dataframe with columns: id, tSNE1, tSNE2, perplexity, ndim

Details

Every combination of values for 'perplexity' and 'ndim' will be run if multiple are provided for each.

See also

Rtsne join