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:

install.packages("clustree")

If you want to use the development version that can be installed from GitHub using with:

# install.packages("devtools")
devtools::install_github("lazappi/clustree")

To also build the vignettes use:

# install.packages("devtools")
devtools::install_github("lazappi/clustree", 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 in your work please cite our preprint ā€œZappia L, Oshlack A. Clustering trees: a visualisation for evaluating clusterings at multiple resolutions. bioRxiv. 2018; doi:10.1101/274035ā€.

  @Article{,
    author = {Luke Zappia and and Alicia Oshlack},
    title = {Clustering trees: a visualisation for evaluating clusterings at
              multiple resolutions},
    journal = {bioRxiv},
    year = {2018},
    url = {https://doi.org/10.1101/274035},
    doi = {10.1101/274035},
  }

Contributors

Thank you to everyone who has contributed code to the clustree package: