runTSNE-SCD-method: Perform t-distributed stochastic neighbour embedding

In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description

Retrieve diffusion map object

Usage

## S4 method for signature 'SCD'
runTSNE(object, ndims = 3, perplexity = 30, theta = 0.5,
  pca = FALSE, seed = NULL, verbose = FALSE, use_dist = FALSE,
  dist_fun = NULL, distmat = NULL, ...)

Arguments

object	Single Cell Data Set object
ndims	Number of dimensions for new embedding
perplexity	Perplecity parameter
theta	Theta parameter
pca	Logical, Perform initial PCA reduction
seed	Set random seed
verbose	To show output
use_dist	Default FALSE. Calculate a distance metric on the data and use this in the Rtsne function.
dist_fun	Default NULL. If NULL will use (1 - spearman_correlation(data)) / 2. Otherwise provide a function to use on the data matrix.
distmat	Deafult NULL. Optionally give the distance matrix to use to speed up analysis.
...	Additional parameters to pass to Rtsne()

Details

Retrieve diffusion map object

Value

Returns an upadate Single Cell Dataset object

Author(s)

Wajid Jawaid

wjawaid/bglab documentation built on May 4, 2019, 6:33 a.m.