https://github.com/jkrijthe/Rtsne

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding
https://github.com/jkrijthe/Rtsne

Last synced: 18 days ago
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R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

• Host: GitHub
• URL: https://github.com/jkrijthe/Rtsne
• Owner: jkrijthe
• License: other
• Created: 2014-01-22T16:34:59.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2023-12-07T01:23:02.000Z (11 months ago)
• Last Synced: 2024-05-21T01:06:16.141Z (6 months ago)
• Language: C++
• Size: 608 KB
• Stars: 253
• Watchers: 19
• Forks: 66
• Open Issues: 4
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

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README

        
---

output:

  github_document:

    html_preview: false

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```

[![CRAN version](http://www.r-pkg.org/badges/version/Rtsne)](https://cran.r-project.org/package=Rtsne/)

[![R-CMD-check](https://github.com/jkrijthe/Rtsne/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jkrijthe/Rtsne/actions/workflows/R-CMD-check.yaml)

[![codecov.io](https://codecov.io/github/jkrijthe/Rtsne/coverage.svg?branch=master)](https://app.codecov.io/github/jkrijthe/Rtsne?branch=master)

[![CRAN mirror downloads](http://cranlogs.r-pkg.org/badges/Rtsne)](https://cran.r-project.org/package=Rtsne/)

# R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding 

## Installation

To install from CRAN:

```{r, eval = FALSE}

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

```

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

```{r, eval = FALSE}

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).

```{r example, fig.path="tools/"}

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. "Accelerating t-SNE using tree-based algorithms." Journal of Machine Learning Research 15.1:3221-3245, 2014.

[3] https://lvdmaaten.github.io/tsne/