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.
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.
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.
If you use clustree in your work please cite our preprint “Zappia L, Oshlack A. Clustering trees: a visualisation for evaluating clusterings at multiple resolutions. bioRxiv. 2018; doi:10.1101/274035”.
@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},
}Thank you to everyone who has contributed code to the clustree package:
edge_arrow_ends option