https://github.com/lazappi/clustree
Visualise Clusterings at Different Resolutions
https://github.com/lazappi/clustree
clustering clustering-trees cran visualisation visualization
Last synced: 9 months ago
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Visualise Clusterings at Different Resolutions
- Host: GitHub
- URL: https://github.com/lazappi/clustree
- Owner: lazappi
- License: gpl-3.0
- Created: 2018-01-22T04:16:14.000Z (almost 8 years ago)
- Default Branch: main
- Last Pushed: 2023-11-08T09:30:46.000Z (about 2 years ago)
- Last Synced: 2025-03-29T01:06:58.336Z (9 months ago)
- Topics: clustering, clustering-trees, cran, visualisation, visualization
- Language: R
- Homepage: https://lazappi.github.io/clustree/
- Size: 36.9 MB
- Stars: 221
- Watchers: 5
- Forks: 15
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
clustree 
=======================================================
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[](https://cran.r-project.org/package=clustree)
[](https://cran.r-project.org/package=clustree)
Deciding what resolution to use can be a difficult question when approaching a
clustering analysis. One way to approach this problem is to look at how samples
move as the number of clusters increases. This package allows you to produce
clustering trees, a visualisation for interrogating clusterings as resolution
increases.
## Installation
You can install the release version of _clustree_ from CRAN with:
``` r
install.packages("clustree")
```
If you want to use the development version that can be installed from GitHub
using the `remotes` package:
``` r
# install.packages("remotes")
remotes::install_github("lazappi/clustree@develop")
```
To also build the vignettes use:
``` r
# install.packages("remotes")
remotes::install_github("lazappi/clustree@develop", dependencies = TRUE,
build_vignettes = TRUE)
```
**NOTE:** Building the vignettes requires the installation of additional
packages.
## Documentation
The documentation for _clustree_ is available from CRAN at
https://cran.r-project.org/package=clustree.
To view the vignette and all the package documentation for the development
version visit http://lazappi.github.io/clustree.
## Citing _clustree_
If you use _clustree_ or the clustering trees approach in your work please cite
our publication ["Zappia L, Oshlack A. Clustering trees: a visualization for
evaluating clusterings at multiple resolutions. Gigascience. 2018;7.
DOI:gigascience/giy083][paper].
```
citation("clustree")
Zappia L, Oshlack A. Clustering trees: a visualization for
evaluating clusterings at multiple resolutions. GigaScience.
2018;7. DOI:gigascience/giy083
A BibTeX entry for LaTeX users is
@Article{,
author = {Luke Zappia and Alicia Oshlack},
title = {Clustering trees: a visualization for evaluating clusterings at
multiple resolutions},
journal = {GigaScience},
volume = {7},
number = {7},
month = {jul},
year = {2018},
url = {http://dx.doi.org/10.1093/gigascience/giy083},
doi = {10.1093/gigascience/giy083},
}
```
## Contributors
Thank you to everyone who has contributed code to the clustree package:
* [@andreamrau](https://github.com/andreamrau) - added the `edge_arrow_ends`
option
* [@mojaveazure](https://github.com/mojaveazure) - added support for _Seurat_
v3 objects
[paper]: https://doi.org/10.1093/gigascience/giy083