Venn Diagram — venn • ClinicoPathDescriptives

Venn Diagram

Usage

venn(
  data,
  var1,
  var1true,
  var2,
  var2true,
  var3 = NULL,
  var3true,
  var4 = NULL,
  var4true,
  var5 = NULL,
  var5true,
  var6 = NULL,
  var6true,
  var7 = NULL,
  var7true,
  show_upsetR = FALSE,
  show_complexUpset = FALSE,
  show_ggvenn = FALSE,
  show_ggVennDiagram = FALSE,
  sortBy = "freq",
  minSize = 0,
  showAnnotations = FALSE,
  explanatory = FALSE,
  aboutAnalysis = FALSE,
  clinicalSummary = FALSE,
  reportSentences = FALSE,
  assumptions = FALSE,
  shapeType = "auto",
  regionLabels = "count",
  labelGeometry = "label",
  labelPrecisionDigits = 1,
  setNameSize = 5,
  labelSize = 4,
  edgeSize = 1,
  edgeColor = "black",
  edgeLineType = "solid",
  edgeAlpha = 1,
  fillAlpha = 0.5,
  showSetLabels = TRUE,
  setLabelColor = "black",
  fillColorMapping = TRUE,
  colorPalette = "default",
  showSetCalculations = FALSE,
  calculateOverlap = FALSE,
  calculateDiscern = FALSE,
  calculateUnite = FALSE,
  showMembershipTable = FALSE,
  showGlossary = FALSE
)

Arguments

data: The dataset as a data frame containing the variables for analysis.
var1: A string naming the primary variable from data for the diagram.
var1true: The level in var1 that represents the positive condition.
var2: A string naming the secondary variable from data used in the diagram.
var2true: The level in var2 that represents the positive condition.
var3: An optional variable from data to include in the diagram.
var3true: The level in var3 that represents the positive condition.
var4: An optional variable from data for additional overlap analysis.
var4true: The level in var4 that represents the positive condition.
var5: Fifth variable for 5-set Venn diagrams (automatically switches to advanced engine).
var5true: The level in var5 that represents the positive condition.
var6: Sixth variable for 6-set Venn diagrams (uses advanced engine automatically).
var6true: The level in var6 that represents the positive condition.
var7: Seventh variable for 7-set Venn diagrams (uses advanced engine automatically).
var7true: The level in var7 that represents the positive condition.
show_upsetR: .
show_complexUpset: .
show_ggvenn: .
show_ggVennDiagram: .
sortBy: How to sort the intersections in the UpSet plot.
minSize: Minimum size of intersections to display.
showAnnotations: Add percentage labels to intersection sizes in ComplexUpset plots or enhanced text scaling in UpSetR plots.
explanatory: Add detailed explanatory footnotes with interpretation guidance for Venn diagrams and set operations.
aboutAnalysis: Display detailed information about Venn diagram analysis and interpretation.
clinicalSummary: Display clinical interpretation of overlap patterns and key findings.
reportSentences: Generate copy-ready sentences for clinical reports and publications.
assumptions: Display interpretation guidelines and statistical assumptions.
shapeType: Shape type for ggVennDiagram. Auto selects optimal shape based on number of sets.
regionLabels: What to display in Venn diagram regions (available for advanced diagrams).
labelGeometry: Whether to use label geometry (with background) or text geometry for region labels.
labelPrecisionDigits: Number of decimal places for percentage labels (available for advanced diagrams).
setNameSize: Font size for set names (available for advanced diagrams).
labelSize: Font size for region labels (available for advanced diagrams).
edgeSize: Width of set boundary lines (available for advanced diagrams).
edgeColor: Color of set boundary lines (available for advanced diagrams).
edgeLineType: Line type for set boundaries in ggVennDiagram.
edgeAlpha: Transparency level for set boundary lines (0=transparent, 1=opaque).
fillAlpha: Transparency level for region fills (0=transparent, 1=opaque).
showSetLabels: Whether to display set names on the diagram.
setLabelColor: Color for set name labels.
fillColorMapping: Map fill colors to intersection sizes (available for advanced diagrams).
colorPalette: Color palette for Venn diagram regions (available for advanced diagrams).
showSetCalculations: Display detailed set calculations including overlaps, unique members, and unions.
calculateOverlap: Calculate and display overlap intersections between sets.
calculateDiscern: Calculate and display unique members for each set (discern operation).
calculateUnite: Calculate and display union of all sets.
showMembershipTable: Display detailed membership table showing which items belong to which sets.
showGlossary: Display glossary of statistical terms and clinical interpretations.

Value

A results object containing:

`results$welcome`					a html
`results$todo`					a html
`results$summary`					a table
`results$plotGgvenn`					an image
`results$plotGgVennDiagram`					an image
`results$plotUpsetR`					an image
`results$plotComplexUpset`					an image
`results$aboutAnalysis`					a html
`results$clinicalSummary`					a html
`results$reportSentences`					a html
`results$assumptions`					a html
`results$setCalculations`					a html
`results$membershipTable`					a table
`results$membershipGroups`					an output
`results$glossary`					a html

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$summary$asDF

as.data.frame(results$summary)