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vennDiagramLab ships three complementary visualizations of the same underlying region structure. This vignette explains when to use which.
library(vennDiagramLab)
result <- analyze(load_sample("dataset_real_cancer_drivers_4"))
length(result@dataset@set_names)| # of sets | Recommended primary view | Why |
|---|---|---|
| 2 | Venn | obvious, area-proportional possible |
| 3 | Venn | classic three-circle layout reads instantly |
| 4 | Venn (Edwards) | still readable as a Venn |
| 5–6 | UpSet | Venn becomes hard to read; UpSet bars are clearer |
| 7+ | UpSet (primary) + Network (relationships) | Venn is essentially unusable |
For high set counts (5+), the Network view adds something neither representation provides: it shows the pairwise relationships as a graph, where edge weight is intersection size or significance.
svg <- render_venn_svg(result, title = "4-set Venn (cancer drivers)")
nchar(svg)The SVG is plain text — embed it in a notebook with htmltools::HTML(svg) or save to disk and reference from Markdown.
render_upset(result, sort_by = "size", color_mode = "depth")(The chunk above is gated on R >= 4.6 because the CRAN release of ComplexUpset (1.3.3) is incompatible with ggplot2 >= 4.0 on older R.)
render_network(result, edge_metric = "intersection")Each node is a set, sized by inclusive cardinality. Each edge is a pair, weighted by the chosen edge_metric ("intersection", "jaccard", "fold_enrichment", or "overlap_coefficient"). Edges below the significance threshold are colored differently.
Sometimes a region looks “small” on a Venn but lights up bright on a Network because the fold-enrichment is high relative to expectation. That’s not a contradiction — Venn shows raw counts, Network can show normalized strength. Use both.
vignette("v05_statistics_deep_dive") — what the network’s significance threshold actually means.vignette("v07_pdf_reports") — generate a single PDF that includes all three views.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.