uwot

An R package implementing the UMAP dimensionality reduction method.

https://github.com/jlmelville/uwot

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
✓
Academic publication links
Links to: arxiv.org
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Committers with academic emails
1 of 9 committers (11.1%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary

Keywords

dimensionality-reduction r umap

Keywords from Contributors

bioconductor human-cell-atlas bioinformatics

Last synced: 6 months ago · JSON representation

Repository

An R package implementing the UMAP dimensionality reduction method.

Basic Info

Host: GitHub
Owner: jlmelville
License: gpl-3.0
Language: R
Default Branch: master
Homepage: https://jlmelville.github.io/uwot/
Size: 91.2 MB

Statistics

Stars: 339
Watchers: 21
Forks: 31
Open Issues: 18
Releases: 24

Topics

dimensionality-reduction r umap

Created over 7 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License

uwot

An R implementation of the Uniform Manifold Approximation and Projection (UMAP) method for dimensionality reduction of McInnes et al. (2018). Also included are the supervised and metric (out-of-sample) learning extensions to the basic method. Translated from the Python implementation.

News

February 24 2025 uwot version 0.2.3 has been released to CRAN. This release mainly fixes some bugs, including one that was causing an error with an upcoming version of R-devel. One new feature: set rng_type = "deterministic" to use a deterministic sampling of vertices during the optimization phase which will give faster and more reproducible output at the cost of accuracy. The idea for this came straight from Leland McInnes via Reddit.

April 21 2024 As ordained by prophecy, version 0.2.2 of uwot has been released to CRAN. RSpectra is back as a main dependency and I thought I had worked out a clever scheme to avoid the failures seen in some installations with the irlba/Matrix interactions. This releases fixes the problem on all the systems I have access to (including GitHub Actions CI) but some CRAN checks remain failing. How embarrassing. That said, if you have had issues, it's possible this new release will help you too.

Installing

From CRAN

R install.packages("uwot")

From github

uwot makes use of C++ code which must be compiled. You may have to carry out a few extra steps before being able to build this package:

Windows: install Rtools and ensure C:\Rtools\bin is on your path.

Mac OS X: using a custom ~/.R/Makevars may cause linking errors. This sort of thing is a potential problem on all platforms but seems to bite Mac owners more. The R for Mac OS X FAQ may be helpful here to work out what you can get away with. To be on the safe side, I would advise building uwot without a custom Makevars.

R install.packages("devtools") devtools::install_github("jlmelville/uwot")

Example

```R library(uwot)

umap2 is a version of the umap() function with better defaults

iris_umap <- umap2(iris)

but you can still use the umap function (which most of the existing

documentation does)

iris_umap <- umap(iris)

Load mnist from somewhere, e.g.

devtools::install_github("jlmelville/snedata")

mnist <- snedata::download_mnist()

mnistumap <- umap(mnist, nneighbors = 15, mindist = 0.001, verbose = TRUE) plot( mnistumap, cex = 0.1, col = grDevices::rainbow(n = length(levels(mnist$Label)))[as.integer(mnist$Label)] |> grDevices::adjustcolor(alpha.f = 0.1), main = "R uwot::umap", xlab = "", ylab = "" )

I recommend the following optional packages

for faster or more flexible nearest neighbor search:

install.packages(c("RcppHNSW", "rnndescent")) library(RcppHNSW) library(rnndescent)

Installing RcppHNSW will allow the use of the usually faster HNSW method:

mnistumaphnsw <- umap(mnist, nneighbors = 15, mindist = 0.001, nn_method = "hnsw")

nndescent is also available

mnistumapnnd <- umap(mnist, nneighbors = 15, mindist = 0.001, nn_method = "nndescent")

umap2 will choose HNSW by default if available

mnist_umap2 <- umap2(mnist) ```

MNIST UMAP

Documentation

https://jlmelville.github.io/uwot/. For more examples see the get started doc. There are plenty of articles describing various aspects of the package.

License

GPLv3 or later.

Citation

If you want to cite the use of uwot, then use the output of running citation("uwot") (you can do this with any R package).

The UMAP reference implementation and publication.
The UMAP R package (see also its github repo), predates uwot's arrival on CRAN.
Another R package is umapr, but it is no longer being maintained.
umappp is a full C++ implementation, and yaumap provides an R wrapper. The batch implementation in umappp are the basis for uwot's attempt at the same.
uwot uses the RcppProgress package to show a text-based progress bar when verbose = TRUE.

Owner

Name: James Melville
Login: jlmelville
Kind: user
Location: San Diego

Repositories: 12
Profile: https://github.com/jlmelville

"The work of a lazy, self-indulgent man"

GitHub Events

Total

Create event: 1
Release event: 1
Issues event: 12
Watch event: 18
Issue comment event: 18
Push event: 56

Last Year

Create event: 1
Release event: 1
Issues event: 12
Watch event: 18
Issue comment event: 18
Push event: 56

Committers

Last synced: 9 months ago

All Time

Total Commits: 993
Total Committers: 9
Avg Commits per committer: 110.333
Development Distribution Score (DDS): 0.015

Past Year

Commits: 56
Committers: 1
Avg Commits per committer: 56.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
James Melville	j**e@g**m	978
sirusb	d**d@g**m	3
LTLA	i**s@g**m	3
Dirk Eddelbuettel	e**d@d**g	3
Keith Hughitt	k**t@g**m	2
james-vivodyne	j**e@v**m	1
Tim Triche, Jr	t**e@g**m	1
Yuhan Hao	h**y@s**g	1
Aaron Lun	a**n@w**u	1

Committer Domains (Top 20 + Academic)

wehi.edu.au: 1 satijalab05.nygenome.org: 1 vivodyne.com: 1 debian.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 110
Total pull requests: 15
Average time to close issues: 9 months
Average time to close pull requests: about 7 hours
Total issue authors: 75
Total pull request authors: 6
Average comments per issue: 6.13
Average comments per pull request: 2.8
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 7
Pull requests: 0
Average time to close issues: 2 months
Average time to close pull requests: N/A
Issue authors: 7
Pull request authors: 0
Average comments per issue: 1.57
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jlmelville (15)
LTLA (5)
PedroMilanezAlmeida (4)
ilyakorsunsky (3)
SamGG (3)
akhst7 (3)
juba (2)
OuNao (2)
jielab (2)
mytarmail (2)
Harini-107 (2)
jianshu93 (2)
ummel (2)
yuhanH (2)
Ax3man (1)

Pull Request Authors

jlmelville (9)
eddelbuettel (3)
sirusb (2)
LTLA (2)
khughitt (1)
yuhanH (1)

Top Labels

Issue Labels

enhancement (20) bug (16) help wanted (1)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- cran 37,159 last-month
Total docker downloads: 174,289

Total dependent packages: 36
(may contain duplicates)
Total dependent repositories: 169
(may contain duplicates)
Total versions: 38
Total maintainers: 1

cran.r-project.org: uwot

The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction

Homepage: https://github.com/jlmelville/uwot
Documentation: http://cran.r-project.org/web/packages/uwot/uwot.pdf
License: GPL (≥ 3)
Latest release: 0.2.3
published 12 months ago

Versions: 15
Dependent Packages: 32
Dependent Repositories: 165
Downloads: 37,159 Last month
Docker Downloads: 174,289

Rankings

Docker downloads count: 0.0%

Stargazers count: 1.4%

Dependent repos count: 1.5%

Average: 1.7%

Downloads: 2.4%

Forks count: 2.4%

Dependent packages count: 2.5%

Maintainers (1)

jlmelville@gmail.com

Last synced: 6 months ago

proxy.golang.org: github.com/jlmelville/uwot

Documentation: https://pkg.go.dev/github.com/jlmelville/uwot#section-documentation
License: gpl-3.0
Latest release: v0.2.3
published 12 months ago

Versions: 15
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

conda-forge.org: r-uwot

Homepage: https://github.com/jlmelville/uwot
License: GPL-3.0-or-later
Latest release: 0.1.14
published over 3 years ago

Versions: 8
Dependent Packages: 4
Dependent Repositories: 4

Rankings

Dependent packages count: 12.5%

Dependent repos count: 16.1%

Average: 20.3%

Stargazers count: 22.6%

Forks count: 30.2%

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

Matrix * depends
FNN * imports
Rcpp * imports
RcppAnnoy >= 0.0.17 imports
irlba * imports
methods * imports
RSpectra * suggests
bigstatsr * suggests
covr * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/lint.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

uwot

Science Score: 46.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

uwot

News

Installing

From CRAN

From github

Example

umap2 is a version of the umap() function with better defaults

but you can still use the umap function (which most of the existing

documentation does)

Load mnist from somewhere, e.g.

devtools::install_github("jlmelville/snedata")

mnist <- snedata::download_mnist()

I recommend the following optional packages

for faster or more flexible nearest neighbor search:

Installing RcppHNSW will allow the use of the usually faster HNSW method:

nndescent is also available

umap2 will choose HNSW by default if available

Documentation

License

Citation

See Also

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: uwot

Rankings

Maintainers (1)

proxy.golang.org: github.com/jlmelville/uwot

Rankings

conda-forge.org: r-uwot

Rankings

Dependencies