PDF reports

In vennDiagramLab: Headless Venn Diagram Analysis and Rendering

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
# Skip evaluation of all chunks on CRAN's auto-check farm to fit the
# 10-minute build budget. Locally, on CI, and under devtools::check(),
# NOT_CRAN=true and all chunks evaluate normally. The vignette source
# (which CRAN users see in browseVignettes() / vignette()) is unchanged.
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
knitr::opts_chunk$set(eval = NOT_CRAN)

PDF reports

to_pdf_report() produces a multi-page US-Letter-landscape PDF combining the venn diagram, UpSet plot, statistics tables, network view, and a methodology page — equivalent to the web tool's "Generate Report" button.

library(vennDiagramLab)
result <- analyze(load_sample("dataset_real_cancer_drivers_4"))

Generating the report

Save to a temporary file (vignettes shouldn't write into the package directory):

out <- tempfile(fileext = ".pdf")
to_pdf_report(result, path = out, title = "Cancer driver overlap")
file.exists(out)
file.size(out)   # bytes

(The chunk above is gated on R >= 4.6 because the report embeds an UpSet panel via ComplexUpset, whose CRAN release (1.3.3) is incompatible with ggplot2 >= 4.0 on older R. See ?vennDiagramLab::to_pdf_report for context and workarounds.)

What the report contains

By default, every report has 5 page types:

1. Overview — metadata (timestamp, dataset, set count) + set-size table.
2. Venn + UpSet — rasterized venn (left) + UpSet plot (right).
3. Statistics — Jaccard / Dice / Hypergeometric tables (per-page on 7+ sets).
4. Network — set-relationship graph + significant edges list.
5. About — methodology notes (Venn / UpSet / Network / metric definitions).

Pages 4 (network) and 5 (about) can be turned off:

to_pdf_report(result, "venn_only.pdf",
              include_network = FALSE,
              include_about   = FALSE)

What's next

• vignette("v02_real_cancer_drivers") — see the analysis that feeds the report.
• vignette("v08_custom_styling_and_export") — multi-format export beyond PDF (SVG, PNG).

vennDiagramLab documentation built on May 19, 2026, 1:07 a.m.