Run the t-SNE algorithm for dimensionality reduction

Run the t-SNE algorithm for dimensionality reduction

calculateTsne(norm, perplexity = 20, max.iter = 2500, seed = 12345,
  do.pca = FALSE, initial.dims = 20)

Arguments

norm	Normalized count matrix.
perplexity	Numeric vector. Determines perplexity for tsne. Default 20.
max.iter	Numeric vector. Determines iterations for tsne. Default 1000.
seed	Integer. Seed for random number generation. Defaults to 12345.
do.pca	Logical. Whether to perform dimensionality reduction with PCA before tSNE.
initial.dims	Integer. Number of dimensions from PCA to use as input in tSNE.