clustree

0.5.1

Visualise Clusterings at Different Resolutions

5packages depend

64.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Luke ZappiaFirst published 2018-03-2713 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("clustree", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("lazappi/clustree")

Development version from lazappi/clustree. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-clustree

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-clustree

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-clustree

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.34

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

64.7K

CRAN downloads in the past year

Rank #2,010 · ~177/day · ~5.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.5K30 days

13.5K90 days

64.7K1 year

Compare downloads with other packages →

Also on538 r2u17 autocran7.5K conda_forge

Repository

GitHub ↗ lazappi/clustree

259Stars

15Forks

13Open issues

0Open PRs

8Releases

visualizationvisualisationclusteringclustering-treescran

License GPL-3.0

Stars over time

2025-07-04 · 2302026-07-07 · 259

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5ggraph

Imports (10)

checkmate igraph dplyrgridggplot2 viridismethodsrlang tidygraph ggrepel

LinkingTo (0)

none

Suggests (9)

testthat knitr rmarkdown SingleCellExperiment Seurat covr SummarizedExperiment pkgdown spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

crosshap scRNAstat CIARA MitoHEAR plotthis

Code & Tests

Code Composition

R 2,754 (64%)Rd 1,053 (24%)Vignettes 404 (9%)Other 106 (2%)

Code characteristics

Object systems

S310

Cyclomatic complexity: 3.0 median / 18 max
Test cases: 68 / 0.34 per code line
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

27 2 exported

Complexity

5 avg / 18 max

Call network

27 nodes / 23 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (4)

Maintainer (1)

Luke Zappia

Author, Maintainer

Authors (2)

Luke Zappia

Author, Maintainer

Alicia Oshlack

Author

Contributors (2)

Paul Hoffman

Contributor

Andrea Rau

Contributor

Release timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.5.1Latest
2023-11-05 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.5.0
2022-06-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.4.4
2021-11-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.4.3
2020-06-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.4.2
2020-01-29 · diff ↗
0.4.1
2019-08-21 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.4.0
2019-04-18 · diff ↗
0.3.0
2019-02-24 · diff ↗

Show 7 earlier events

0.2.2
2018-07-10 · diff ↗
0.2.1
2018-07-09 · diff ↗
0.2.0
2018-06-24 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.2
2018-04-20 · diff ↗
0.1.1
2018-03-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-27
Total releases: 13 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 366 KB / 2 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet