ohmytsne: A plot-friendly output for the Barnes-Hut implementation of...

In jlaffy/scalop: Single Cell Analysis Operations

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

Description

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.

Usage

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

Details

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

Value

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

See Also

Rtsne join

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.