# Headless Venn Diagram Analysis and Rendering

## Documentation for package ‘vennDiagramLab’ version 2.4.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

analyze | Analyze a Venn diagram dataset
augment.RegionResult | Augment method for RegionResult (broom-compatible)
bh_fdr | Benjamini-Hochberg FDR adjustment
circle_intersection_area | Lens-shaped intersection area of two circles
cluster_set_order | Hierarchical clustering on a symmetric distance matrix.
compute_pairwise | Compute all 5 pairwise statistical tables
dice | Sorensen-Dice coefficient
effective_universe | Effective hypergeometric universe size for a RegionResult
effective_universe-method | Effective hypergeometric universe size for a RegionResult
exclusive_items | Items exclusive to a specific set combination
fold_enrichment | Fold enrichment (observed / expected ratio)
generate_proportional_svg | Generate an area-proportional SVG for a 2- or 3-set RegionResult
geom_venn | Embed a rendered Venn diagram as a ggplot2 layer
glance.RegionResult | Glance method for RegionResult (broom-compatible)
hypergeometric_p_value | One-sided hypergeometric p-value (over-representation)
intersection_items | Items in the intersection of the named sets
item_share_distribution | Item Share Distribution
jaccard | Jaccard similarity index
list_models | List all bundled Venn diagram models
list_samples | List bundled sample dataset names
load_csv | Load a delimited file (CSV/TSV) 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
load_tsv | Load a tab-separated file into a ['VennDataset-class']
overlap_coefficient | Szymkiewicz-Simpson overlap coefficient
parse_region_expression | Parse a Boolean region expression into bitmasks
RegionData-class | RegionData: one region of a Venn diagram
RegionResult-class | RegionResult: result of analyze()
render_cluster_heatmap | Render a cluster-ordered Jaccard similarity heatmap
render_enrichment_bar | Render the pairwise enrichment bar chart
render_enrichment_lollipop | Render the pairwise enrichment lollipop chart
render_network | Render a force-directed network plot from a RegionResult
render_share_distribution | Render the Item Share Distribution histogram
render_upset | Render an UpSet plot from a RegionResult
render_venn_svg | Render a RegionResult onto its model SVG and return the raw SVG string
solve_2set | Area-proportional 2-set circle layout
solve_3set | Area-proportional 3-set circle layout (Wilkinson 2012-style triangulation)
statistics | Lazy pairwise statistics for a RegionResult
statistics-method | Lazy pairwise statistics for a RegionResult
StatisticsResult-class | StatisticsResult: container for pairwise statistical metric tables
SvgImage-class | SvgImage: wrapper for rendered SVG output
tidy.RegionResult | Tidy method for RegionResult (broom-compatible)
to_excel_workbook | Write a 3-sheet Excel workbook matching the webtool's ZIP bundle
to_matrix_tsv | Write the Item Matrix TSV
to_matrix_tsv-method | Write the Item Matrix TSV
to_pdf_report | Compose a multi-page PDF report from a RegionResult
to_region_summary_tsv | Write the Region Summary TSV
to_region_summary_tsv-method | Write the Region Summary TSV
to_statistics_tsv | Write the pairwise Statistics TSV
to_statistics_tsv-method | Write the pairwise Statistics TSV
to_zip_report | Write a Full Report ZIP bundle
union_items | Items in the union of the named sets
vdl_version | Get the vennDiagramLab package version
VennDataset-class | VennDataset: in-memory representation of a Venn-diagram input