Spectrum (version 0.2)

tsne: tsne: A tsne function for similarity matrices or ordinary data

Description

tsne: A tsne function for similarity matrices or ordinary data

Usage

tsne(mydata, labels = FALSE, perplex = 15, seed = FALSE,
  axistextsize = 18, legendtextsize = 18, dotsize = 3,
  similarity = TRUE)

Arguments

mydata

Data frame or matrix: kernel matrix or data frame with samples as columns, features as rows

labels

Factor: to label the plot with colours

perplex

Numerical value: this is the perplexity parameter for tsne, it usually requires adjusting for each dataset

seed

Numerical value: to repeat the results exactly, setting seed is required

axistextsize

Numerical value: axis text size

legendtextsize

Numerical value: legend text size

dotsize

Numerical value: dot size

similarity

Logical flag: whether input is similarity matrix or not

Value

A tsne plot object

Examples

# NOT RUN {
ex_tsne <- tsne(blobs[,1:50],perplex=15,similarity=FALSE)
# }