Visualise Clusterings at Different Resolutions

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.


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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.

clustree is currently unavailable from CRAN, please use the GitHub installation instructions

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 "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},
  }

Contributors

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

  • @andreamrau - added the edge_arrow_ends option

News

clustree 0.2.2 (2018-07-10)

  • Replace SingleCellExperiment and Seurat example datasets with a list
  • Add additional checks for suggested packages
  • Remove links to suggested packages in documentation

clustree 0.2.1.9001 (2018-07-10)

  • Add additional checks for suggested packages
  • Remove links to suggested packages in documentation

clustree 0.2.1.9000 (2018-07-10)

  • Replace SingleCellExperiment and Seurat example datasets with a list

clustree 0.2.1 (2018-07-09)

  • Bump version for CRAN

clustree 0.2.0 (2018-06-24)

  • Calculate the SC3 stability index for cluster nodes
  • Improvements to the clustree function:
    • Add option to use core network to calculate layout
    • Add option to highlight core network
    • Add option to return plot, graph or layout
  • New clustree_overlay function
    • Allows overlaying of clustering trees on other data dimensions
  • Store trees as tbl_graph instead of igraph objects
  • Switch to GPL-3 license
  • Updates to vignette, documentation and tests

clustree 0.1.2.9005 (2018-06-23)

  • Add plot_sides argument to clustree_overlay

clustree 0.1.2.9004 (2018-06-22)

  • Add clustree_overlay function

clustree 0.1.2.9003 (2018-06-20)

  • Add checks for suggested packages

clustree 0.1.2.9002 (2018-05-22)

  • Store tree as tbl_graph instead of igraph object
  • Update vignette

clustree 0.1.2.9001 (2018-05-09)

  • Add option to use core network to calculate layout
  • Add option to highlight core network
  • Add option to return plot, graph or layout

clustree 0.1.2.9000 (2018-05-08)

  • Add functions to calculate the SC3 stability index
  • Switch to GPL-3 license

clustree 0.1.2 (2018-04-11)

  • Adjust tests to work with new checkmate version (v1.8.6)
  • Update R requirement to >= 3.4 (for compatibility with SingleCellExperiment)
  • Add CITATION file and update author entries in DESCRIPTION

clustree 0.1.1.9002 (2018-04-11)

  • Add CITATION file
  • Update author entries in DESCRIPTION

clustree 0.1.1.9001 (2018-04-11)

  • Update R requirement to >= 3.4

clustree 0.1.1.9000 (2018-04-11)

  • Adjust tests to match checkmate messages

clustree 0.1.1 (2018-03-23)

  • Add edge_arrow_ends argument

clustree 0.1.0 (2018-03-01)

  • First release
  • Remove theme_clustree function

clustree 0.0.0.9013 (2018-02-28)

  • Fix resolution colour ordering

clustree 0.0.0.9012 (2018-02-15)

  • Switch from using function for aggregation to function names
  • Improve naming of aesthetics
  • Set alpha scale limits
  • Add Sugiyama layout
  • Update vignette
  • Tidy code

clustree 0.0.0.9011 (2018-02-09)

  • Fix missing node when all aesthetics static

clustree 0.0.0.9010 (2018-02-05)

  • Check that at least two resolutions have been provided
  • Add node text colour option
  • Improve example scRNA-seq datasets

clustree 0.0.0.9009 (2018-02-02)

  • Add data option to exprs for Seurat objects

clustree 0.0.0.9008 (2018-01-27)

  • Add vignettes

clustree 0.0.0.9007 (2018-01-27)

  • Add tests and run checks

clustree 0.0.0.9006 (2018-01-27)

  • Add documentation
  • Add parameter checks

clustree 0.0.0.9005 (2018-01-27)

  • Add Seurat example data
  • Add Seurat method

clustree 0.0.0.9004 (2018-01-26)

  • Add SingleCellExperiment example data
  • Add SingleCellExperiment method

clustree 0.0.0.9003 (2018-01-25)

  • Add more control over aesthetics

clustree 0.0.0.9002 (2018-01-24)

  • Add node aesthetic options

clustree 0.0.0.9001 (2018-01-23)

  • Implement basic plotting

clustree 0.0.0.9000 (2018-01-22)

  • Start development

Reference manual

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install.packages("clustree")

0.2.2 by Luke Zappia, 5 months ago


https://github.com/lazappi/clustree


Report a bug at https://github.com/lazappi/clustree/issues


Browse source code at https://github.com/cran/clustree


Authors: Luke Zappia [aut, cre] , Alicia Oshlack [aut] , Andrea Rau [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports checkmate, igraph, dplyr, grid, ggplot2, viridis, methods, rlang, tidygraph, ggrepel

Depends on ggraph

Suggests testthat, knitr, rmarkdown, SingleCellExperiment, Seurat, covr, SummarizedExperiment


See at CRAN