T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation

An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten (see < https://github.com/lvdmaaten/bhtsne/> for more information on the original implementation).


CRANversion Travis-CI BuildStatus codecov.io CRAN mirrordownloads

Installation

To install from CRAN:

install.packages("Rtsne") # Install Rtsne package from CRAN

To install the latest version from the github repository, use:

if(!require(devtools)) install.packages("devtools") # If not already installed
devtools::install_github("jkrijthe/Rtsne")

Usage

After installing the package, use the following code to run a simple example (to install, see below).

library(Rtsne) # Load package
iris_unique <- unique(iris) # Remove duplicates
set.seed(42) # Sets seed for reproducibility
tsne_out <- Rtsne(as.matrix(iris_unique[,1:4])) # Run TSNE
plot(tsne_out$Y,col=iris_unique$Species,asp=1) # Plot the result

Details

This R package offers a wrapper around the Barnes-Hut TSNE C++ implementation of [2] [3]. Changes were made to the original code to allow it to function as an R package and to add additional functionality and speed improvements.

References

[1] L.J.P. van der Maaten and G.E. Hinton. Visualizing High-Dimensional Data Using t-SNE. Journal of Machine Learning Research 9(Nov):2579-2605, 2008.

[2] L.J.P. van der Maaten. Barnes-Hut-SNE. In Proceedings of the International Conference on Learning Representations, 2013.

[3] http://homepage.tudelft.nl/19j49/t-SNE.html

News

Rtsne 0.15

  • Substantial speed increase by fixing the possible embedding dimensionalities to 1, 2 or 3
  • Clarification of the licensing of different parts of the package
  • Support for using, more efficient, partial PCA (by Daniel Wells)
  • Made the normalization optional and the normalization function used available (by Aaron Lun)
  • Support for using precomputed nearest neighbour matrices (by Aaron Lun)
  • Added OpenMP support
  • Default verbose value is now the global setting (by Richard Cotton)
  • Added a NEWS.md file to track changes to the package.

Reference manual

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install.packages("Rtsne")

0.15 by Jesse Krijthe, 5 months ago


https://github.com/jkrijthe/Rtsne


Browse source code at https://github.com/cran/Rtsne


Authors: Jesse Krijthe [aut, cre] , Laurens van der Maaten [cph] (Author of original C++ code)


Documentation:   PDF Manual  


file LICENSE license


Imports Rcpp, stats

Suggests irlba, testthat

Linking to Rcpp


Imported by AutoPipe, CINNA, FateID, HDclust, PAC, RaceID, Rdimtools, Seurat, Spectrum, densityClust, diceR, projector, randomcoloR, scRNAtools, visvow.

Suggested by coRanking, dimRed, stm, themetagenomics.


See at CRAN