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PDF reports

Source: vignettes/v07_pdf_reports.Rmd
v07_pdf_reports.Rmd

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")
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ComplexUpset package.
#>   Please report the issue at
#>   <https://github.com/krassowski/complex-upset/issues>.
#> This warning is displayed once per session.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
file.exists(out)
#> [1] TRUE
file.size(out)   # bytes
#> [1] 120553

(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