ggtreeExtra
Bioc currentAn R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
47 12 exported
Complexity
4 avg / 23 max
Call network
47 nodes / 40 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
3,323
Files
45
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
18
Internal functions
35
Testing
Has tests
Yes
Test-to-code ratio
0.02
testthat edition
3
Docs
Roxygen coverage
94.4%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
6
Dep constraint coverage
20%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2021-04-26
Latest release
2026-06-04
Avg cadence
178 days
Cold removal rate
100%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14 (1 internal)
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 46%
- Documented parameters
- 82%
- Return-value docs
- 46%
- Help pages citing references
- 0%
- ggtreeExtra HTML
Repository practices
3 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/yulab-smu/ggtreeextra on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| first_ring_discrete | data.frame | 1,024 × 3 | No other package |
| second_ring_continuous | data.frame | 200 × 3 | No other package |
| second_ring_point | data.frame | 80 × 3 | No other package |
| tree_tippoint_bar | data.frame | 230 × 5 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (4)
People
- Shuangbin Xu author maintainer
- Guangchuang Yu author contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("ggtreeExtra")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/molbev/msab166.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.