pathview
Bioc currenta tool set for pathway based data integration and visualization
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
37 22 exported
Complexity
10.5 avg / 55 max
Call network
37 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
4,803
Files
82
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
22
Internal functions
6
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
33.3%
Unsafe pattern score
6
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
GPL (>=3.0)
License flags
not SPDX, not OSI
History
Versions
27
First release
2013-06-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 86%
- Return-value docs
- 100%
- References docs
- 76%
Topics
Depended on by (20)
Bioconductor (17)
CRAN (3)
People
Weijun Luo
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("pathview")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.