Package index • vennDiagramLab

Loading data

Read CSV / TSV / GMT / GMX files into a VennDataset, or load one of the five bundled samples.

load_csv(): Load a delimited file (CSV/TSV) into a [`VennDataset-class`]
load_tsv(): Load a tab-separated file into a [`VennDataset-class`]
load_gmt(): Load a GMT (Gene Matrix Transposed) file into a [`VennDataset-class`]
load_gmx(): Load a GMX file (transposed GMT) into a [`VennDataset-class`]
load_sample(): Load a bundled sample dataset by name
list_samples(): List bundled sample dataset names
list_models(): List all bundled Venn diagram models

Compute regions and pairwise statistics from a VennDataset.

analyze(): Analyze a Venn diagram dataset
statistics(): Lazy pairwise statistics for a RegionResult
effective_universe(): Effective hypergeometric universe size for a RegionResult

Generate SVG, ggplot2-based UpSet / Network plots, and multi-page PDF reports.

render_venn_svg(): Render a RegionResult onto its model SVG and return the raw SVG string
render_upset(): Render an UpSet plot from a RegionResult
render_network(): Render a force-directed network plot from a RegionResult
to_pdf_report(): Compose a multi-page PDF report from a RegionResult

Byte-equivalent TSV writers for region summaries, item-membership matrices, and pairwise statistics tables.

Embed venns in ggplot chains and convert results to tidyverse-friendly tibbles.

geom_venn(): Embed a rendered Venn diagram as a ggplot2 layer
tidy(<RegionResult>): Tidy method for RegionResult (broom-compatible)
glance(<RegionResult>): Glance method for RegionResult (broom-compatible)
augment(<RegionResult>): Augment method for RegionResult (broom-compatible)

Stateless functions for individual metrics. Useful for ad-hoc calculations outside of analyze().

jaccard(): Jaccard similarity index
dice(): Sorensen-Dice coefficient
overlap_coefficient(): Szymkiewicz-Simpson overlap coefficient
hypergeometric_p_value(): One-sided hypergeometric p-value (over-representation)
fold_enrichment(): Fold enrichment (observed / expected ratio)
bh_fdr(): Benjamini-Hochberg FDR adjustment
compute_pairwise(): Compute all 5 pairwise statistical tables

Low-level geometry solvers behind analyze(model = "proportional").

solve_2set(): Area-proportional 2-set circle layout
solve_3set(): Area-proportional 3-set circle layout (Wilkinson 2012-style triangulation)
circle_intersection_area(): Lens-shaped intersection area of two circles
generate_proportional_svg(): Generate an area-proportional SVG for a 2- or 3-set RegionResult

Result types returned by the loaders and analyzers.

VennDataset-class: VennDataset: in-memory representation of a Venn-diagram input
RegionData-class: RegionData: one region of a Venn diagram
RegionResult-class: RegionResult: result of analyze()
StatisticsResult-class: StatisticsResult: container for pairwise statistical metric tables