Headless Venn Diagram Analysis and Rendering
Overview
Headless companion to the 'Venn Diagram Lab' web tool (https://www.venndiagramlab.org/). Build, render, and statistically analyze Venn / 'UpSet' diagrams from 'CSV' / 'TSV' / 'GMT' / 'GMX' inputs. Provides the same 44 SVG models, intersection / 'Jaccard' / hypergeometric statistics, and PDF report layout as the web tool, with byte-equivalent 'TSV' exports (parity-tested against the published Python package). Integrates with 'ggplot2', 'tidygraph', and 'broom'.
Feature release following CRAN 2.4.2. The version numbers 2.5.0–2.8.0 were
lockstep bumps shared with the web tool and were never submitted to CRAN;
everything below is new relative to 2.4.2. All changes are additive — no
removed or changed APIs, no new dependencies. Every TSV / JSON / network
output is byte-identical to the web tool and the Python / npm companions
(parity goldens regenerated; tests/testthat/test-parity-*.R).
Statistics
fold_enrichment_ci(N, K, n, k)(new export): approximate 95% CI for the fold enrichment (log-scale Wald with Jeffreys-style continuity correction, finite at k = 0). Monte Carlo null coverage: 95.6% over 20,000 trials (scripts/bio_validation.py, section F).one_vs_rest_enrichment()(new export): each set tested against the union of all other sets (hypergeometric P, BH-FDR, Bonferroni, fold enrichment).
Show all changes in 2.9.0Hide the rest of the changes in 2.9.0
compute_pairwise()/ the hypergeometric long-form table gainp_bonferroni,p_two_sided(two-sided Fisher's exact, log-space point-mass sum),jaccard_ci_low/high,dice_ci_low/high(Wilson score intervals) andfe_ci_low/highcolumns.- Display formatters floor underflowed p-values to
< 1e-300.
Export
to_statistics_tsv()now writes 24 columns (Bonferroni,P_two_sided,Jaccard_CI_low/high,Dice_CI_low/high,FE_CI_low/highadded).to_one_vs_rest_tsv()(new export).to_result_json()(new export): full region result + statistics as JSON, 6-decimal rounding,-0normalised, regions radix-sorted.to_network_graphml()/to_network_sif()(new exports): Cytoscape-ready set-relationship network (nodes = sets, edges = all pairwise overlaps weighted by intersection size and carrying jaccard, foldEnrichment, overlapCoeff, dice, pValue, fdr and significant attributes), using the same background N as every other output.
Data quality
analyze_data_quality()andvalidate_dataset()(new exports): duplicate identifiers, empty / whitespace cells and case-only collisions are reported viawarning()without changing any identifier.
Documentation / infrastructure
- pkgdown reference index lists all new functions;
fold_enrichment_ci()man page and the Rd text of the data-quality / SIF helpers are ASCII-clean and passR CMD checkon R release, devel and oldrel-1 (Linux, macOS, Windows). to_result_json()man page: the JSON schema block is now a\preformatted{}section with escaped braces (clears acheckRd"Lost braces" NOTE).- PDF report Credits & Cite section lists the npm companion package.
- DESCRIPTION Date 2026-10-05.
From NEWS.md in the release
Install
Health
- OK13 OK2026-08-04
- NOTE12 OK, 1 NOTE2026-08-01
- OK13 OK2026-06-09
- ERROR12 OK, 1 ERROR2026-06-07
- OK5 OK2026-05-19
Documentation
- Help pages
- 58
- Examples that run
- 91%48 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Downloads
Repository
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Commits over time
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/zoliqua/venn-diagram-lab on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-12 · The repository has a site deploy workflow
This repository shows signs of AI coding tools.
- Claude Codefirst seen 2026-01-07Seen in the repository: CLAUDE.mdNamed in .gitignore: .claude, CLAUDE.md
Dependencies
Installing vennDiagramLab adds 54 packages (35 with compiled code, 60 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB. 1 more not on CRAN is not measured.
Code & Tests
Datasets
People & History
Pick two releases to compare their code metrics.
- 2.9.0Latest2026-10-06 · current release · diff ↗ ··
added 8 exports
analyze_data_quality, fold_enrichment_ci, one_vs_rest_enrichment, to_network_graphml, to_network_sif, to_one_vs_rest_tsv, to_result_json, validate_datasetlisted once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-06 08:22 UTC, so it stayed less than the time between readings. - 2.4.22026-06-10 · diff ↗ ·
added 12 exports
cluster_set_order, exclusive_items, intersection_items, item_share_distribution, parse_region_expression, render_cluster_heatmap, render_enrichment_bar, render_enrichment_lollipop, render_share_distribution, to_excel_workbook, to_zip_report, union_items - 2.0.52026-05-18
- RR 4.6.0 released · 2026-04-24
Package metadata
- First published
- 2026-05-18
- Total releases
- 3 / 1 yrs
- License
- MIT + file LICENSE OSI
- Minimum R
- ≥ 4.2
- Download size
- 4.2 MB
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("vennDiagramLab")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
The repository also keeps a CITATION.cff.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.