Headless Venn Diagram Analysis and Rendering
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Documentation for package ‘vennDiagramLab’ version 2.4.2
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 |