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ggbio

Bioc current

Visualization tools for genomic data

v1.60.0 · software · Artistic-2.0
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.9 · Nov 1, 2011

Current · Requires R 4.6

1.0 In 30 of 49 releases 3.23

Description

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

110 25 exported

Complexity

3.9 avg / 55 max

Call network

110 nodes / 50 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
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Lowest coverage

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

Code

Structure

Lines of code

15,507

Files

146

Compiled share

0%

Has compiled src

No

Language breakdown

R 9,010 (58.1%)Tests 79 (0.5%)Docs 5,299 (34.2%)Vignettes 1,119 (7.2%)

API

Exported functions

31

Internal functions

83

Testing & CI

Has tests

Yes

Test-to-code ratio

0.01

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

45.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

30

First release

2012-02-03

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

29

LOC over versions

v2.9: 3,208 LOCv2.10: 7,924 LOCv2.11: 12,787 LOCv2.12: 13,317 LOCv2.13: 14,862 LOCv2.14: 17,129 LOCv3.0: 17,063 LOCv3.1: 16,643 LOCv3.2: 16,522 LOCv3.3: 16,852 LOCv3.4: 16,890 LOCv3.5: 16,866 LOCv3.6: 16,782 LOCv3.7: 16,808 LOCv3.8: 16,808 LOCv3.9: 16,811 LOCv3.10: 16,813 LOCv3.11: 16,817 LOCv3.12: 16,810 LOCv3.13: 16,060 LOCv3.14: 15,605 LOCv3.15: 15,561 LOCv3.16: 15,561 LOCv3.17: 15,561 LOCv3.18: 15,561 LOCv3.19: 15,561 LOCv3.20: 15,561 LOCv3.21: 15,559 LOCv3.22: 15,559 LOCv3.23: 15,507 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMEYes · 8 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo
Examples that run
86%
Documented parameters
83%
Return-value docs
94%
References docs
0%

Topics

Software › Infrastructure
Software › WorkflowStep › Visualization

Depended on by (38)

Bioconductor (37)

bambu beadarray BOBaFIT CAFE cageminer Damsel derfinderPlot ensembldb FRASER GenomicOZone gwascat intansv msgbsR NanoStringNCTools OUTRIDER R3CPET regionReport ReportingTools RnBeads scafari scruff shiny.gosling SomaticSignatures StructuralVariantAnnotation universalmotif RiboProfiling NanoporeRNASeq Single.mTEC.Transcriptomes SomaticCancerAlterations FourCSeq +7 more

CRAN (1)

PopPsiSeqR

People

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