clustree

0.5.1

Visualise Clusterings at Different Resolutions

5packages depend

65.3Kdownloads / year

80.6%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: 5.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.34

80.6%

Coverage · measured lines

100%

Documentation · exports

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

Documentation

READMEYes · 200 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

65.3K

CRAN downloads in the past year

Rank #1,848 · ~179/day · ~5.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.8K30 days

14K90 days

65.3K1 year

Compare downloads with other packages →

Also on538 r2u39 autocran7.5K conda_forge

Repository

GitHub ↗ lazappi/clustree

259Stars

15Forks

13Open issues

0Open PRs

8Releases

283Commits

5Contributors

visualizationvisualisationclusteringclustering-treescran

License GPL-3.0 · 283 commits · Last activity 2025-06-21 · +0.4% stars, 30d

Stars over time

2025-07-21 · 2332026-07-19 · 259

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/lazappi/clustree on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

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

Test coverage

Line coverage

81%

Expression

75.1%

Tests / Examples

80.6% / 41% ex

Functions

27 2 exported

Complexity

5 avg / 18 max

Call network

27 nodes / 23 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

27 functions

Function	Cyclo	Coverage
clustree.SingleCellExperiment	6	0%
clustree.seurat	5	0%
clustree_overlay.SingleCellExperiment	14	0%
clustree_overlay.seurat	12	0%
assert_node_aes	6	81%
clustree.Seurat	7	84%

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
nba_clusts	data.frame	150 × 12	–

People & History

People (4)

Maintainer (1)

Luke Zappia

Author, Maintainer

Authors (2)

Luke Zappia

Author, Maintainer

Alicia Oshlack

Author

Contributors (2)

Paul Hoffman

Contributor · added in 0.4.0

Andrea Rau

Contributor

Package 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 10 earlier events

0.2.2
2018-07-10 · diff ↗
0.2.1
2018-07-09 · diff ↗
archivedRemoved from CRAN
2018-07-09
check problems were again not corrected Unconditional use of packages including 'Seurat' and 'SingleCellExperiment'
unarchivedReturned to CRAN
2018-07-09
archivedRemoved from CRAN
2018-06-30
check problems were not corrected despite reminders and an update
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

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