https://github.com/lazappi/clustree

Visualise Clusterings at Different Resolutions
https://github.com/lazappi/clustree

clustering clustering-trees cran visualisation visualization

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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 (over 6 years ago)
• Default Branch: main
• Last Pushed: 2023-11-08T09:30:46.000Z (11 months ago)
• Last Synced: 2024-07-21T15:08:25.129Z (2 months ago)
• Topics: clustering, clustering-trees, cran, visualisation, visualization
• Language: R
• Homepage: https://lazappi.github.io/clustree/
• Size: 36.9 MB
• Stars: 207
• Watchers: 6
• Forks: 16
• Open Issues: 12
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
clustree 

=======================================================

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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