<code>ggret</code>

<code>ggret</code>: An R package for visualising and manipulating tree‑based phylogenetic networks - Published in JOSS (2025)

https://github.com/grdspcht/ggret

Science Score: 93.0%

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CITATION.cff file
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DOI references
Found 12 DOI reference(s) in README and JOSS metadata
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JOSS paper metadata
Published in Journal of Open Source Software

Last synced: 9 months ago · JSON representation

Repository

ggret: Visualisation of tree-based phylogenetic networks

Basic Info

Host: GitHub
Owner: grdspcht
License: other
Language: R
Default Branch: main
Homepage: https://grdspcht.github.io/ggret/
Size: 2.03 MB

Statistics

Stars: 7
Watchers: 2
Forks: 1
Open Issues: 0
Releases: 1

Created over 3 years ago · Last pushed 12 months ago

Metadata Files

Readme Contributing License

ggret

ggret is an R package for the visualization and annotation of Ancestral Recombination Graphs (ARGs) and other tree-based phylogenetic networks. It extends the functionality of ggtree and ggplot2.

Installation

ggret requires ggplot2, ggtree and ape to function.

``` r

install ggplot2

install.packages("ggplot2")

install ggtree

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ggtree")

install ggret

if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") remotes::installgithub("grdspcht/ggret", dependencies = TRUE, buildvignettes = TRUE) ```

Documentation

In the Web

A website version of the documentation, containing function references and an in-depth vignette about customizing phylogenetic networks (see 'Articles') can be found on: https://grdspcht.github.io/ggret/

In R

Function documentation can be accessed by typing ?function_name. Additionally, you can find multiple examples on how to use ggret effectively in the vignette. To access it call:

r vignette(topic = "intro_to_ggret", package = "ggret")

Contributing & Reporting bugs

Make sure to check out our Contribution guidelines (see CONTRIBUTING.md) for instructions on how to report bugs, suggest improvements or contributing new features to ggret.

Citing ggret

If you use ggret, please cite the associated publication as well as the original ggtree and ape publication:

Specht G, Schmid C, Kühnert D, Kocher A (2025). ggret: An R package for visualising and manipulating tree‑based phylogenetic networks. Journal of Open Source Software, 10(110), 7773, https://doi.org/10.21105/joss.07773
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam^*. “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data”. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi: 10.1111/2041-210X.12628.
Paradis E, Schliep K . “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.” Bioinformatics, 2019, 35, 526-528. doi: 10.1093/bioinformatics/bty633.

Owner

Login: grdspcht
Kind: user
Location: Germany

Repositories: 1
Profile: https://github.com/grdspcht

Bioinformatics Student 🦠👨‍💻

JOSS Publication

<code>ggret</code>: An R package for visualising and manipulating tree‑based phylogenetic networks

Published

June 12, 2025

DOI

10.21105/joss.07773

Volume 10, Issue 110, Page 7773

Authors

Gerd Specht

Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Germany, Transmission, Infection, Diversification & Evolution Group, Max Planck Institute of Geoanthropology, Jena, Germany

Clemens Schmid

Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

Denise Kühnert

Transmission, Infection, Diversification & Evolution Group, Max Planck Institute of Geoanthropology, Jena, Germany, Centre for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany

Arthur Kocher

Transmission, Infection, Diversification & Evolution Group, Max Planck Institute of Geoanthropology, Jena, Germany, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

Editor

Lorena Pantano

GitHub Events

Total

Create event: 4
Release event: 2
Issues event: 6
Watch event: 5
Member event: 1
Issue comment event: 3
Push event: 39
Pull request event: 5
Fork event: 1

Last Year

Create event: 4
Release event: 2
Issues event: 6
Watch event: 5
Member event: 1
Issue comment event: 3
Push event: 39
Pull request event: 5
Fork event: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 16
Total pull requests: 6
Average time to close issues: 29 days
Average time to close pull requests: about 5 hours
Total issue authors: 3
Total pull request authors: 3
Average comments per issue: 0.94
Average comments per pull request: 0.0
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 12
Pull requests: 6
Average time to close issues: 9 days
Average time to close pull requests: about 5 hours
Issue authors: 3
Pull request authors: 3
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

arthurKocher (10)
grdspcht (5)
liamxg (1)

Pull Request Authors

nevrome (2)
grdspcht (2)
arthurKocher (2)

Top Labels

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Dependencies

DESCRIPTION cran

ggplot2 * depends
ggtree * depends
ape * imports
dplyr * imports
magrittr * imports
rlang * imports
tibble * imports
tidytree * imports
treeio * imports