tsne {M3C}R Documentation

tsne: A tsne function

Description

tsne: A tsne function

Usage

tsne(mydata, K = FALSE, labels = FALSE, perplex = 15,
  printres = FALSE, seed = FALSE, axistextsize = 18,
  legendtextsize = 18, dotsize = 5, textlabelsize = 4)

Arguments

mydata

Data frame or matrix or M3C results (list) object: if dataframe/matrix should have samples as columns and rows as features

K

Numerical value: if running on the M3C results object, which value was the optimal K? Needs manual input from user.

labels

Factor: if we want to just display gender for example, only for when running without K parameter and with a matrix or data frame

perplex

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

printres

Logical flag: whether to print the plot into current directory

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

textlabelsize

Numerical value: text inside plot label size

Value

A tsne plot object

Examples

TSNE <- tsne(mydata,perplex=15)

[Package M3C version 1.6.0 Index]