run_TSNE: Calculating t-SNE coordinates for data

In desmchoy/BinaryClust: CyTOF Analysis Pipeline Using Binary Classification Followed by Clustering

Calculating t-SNE coordinates for data

Description

This function calculates t-SNE coordinates on data. Random seed is set to 1. Returns full t-SNE object.

Usage

run_TSNE(
  data = NULL,
  scale = TRUE,
  center = FALSE,
  perplexity = 30,
  n_iter = 1000
)

Arguments

data	(Required) Data in data frame format. Expects results from load_data
scale	Default: TRUE. Option to standardise data prior to t-SNE calculations
center	Default: FALSE. Option to center data prior to PCA within the Rtsne algorithm
perplexity	Value for perplexity (Default: 30)
n_iter	Number of iterations (Default: 1000)

Examples

tsne.results <- run_TSNE(data)

t-SNE coordinates can be extracted under Y:
tsne.coordinates <- tsne.results$Y

desmchoy/BinaryClust documentation built on Sept. 14, 2024, 12:03 a.m.