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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. InstallationYou 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 the remotes package: # install.packages("remotes") remotes::install_github("lazappi/clustree@develop")To also build the vignettes use: # install.packages("remotes") remotes::install_github("lazappi/clustree@develop", dependencies = TRUE, build_vignettes = TRUE)NOTE: Building the vignettes requires the installation of additional packages. DocumentationThe 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 clustreeIf 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. 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}, } ContributorsThank you to everyone who has contributed code to the clustree package: @andreamrau - added the edge_arrow_ends option @mojaveazure - added support for Seurat v3 objects |
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