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Plot a Venn Diagram from Genomic or Set Overlap Results

Source: R/plotVenn.R
plotVenn.Rd

This function creates a Venn diagram using the eulerr package to visualize intersections across multiple sets. Supports both GenomicOverlapsResult and SetOverlapsResult objects.

Usage

plotVenn(
  overlap_object,
  fills = TRUE,
  edges = TRUE,
  labels = FALSE,
  quantities = list(type = "counts"),
  legend = "right",
  main = NULL,
  ...
)

Arguments

overlap_object

A GenomicOverlapsResult or SetOverlapsResult object returned by computeOverlaps.

fills

Controls the fill appearance of the diagram. Can be:

  • logical: TRUE (default) shows fills, FALSE hides them

  • character vector: Colors for the fills. Default colors are: c("#2B70AB", "#FFB027", "#3EA742", "#CD3301", "#9370DB", "#008B8B", "#D87093")

  • list: Fine control with graphical parameters including fill (colors), alpha (transparency 0-1)

edges

Controls the edge/border appearance. Can be:

  • logical: TRUE (default) shows edges, FALSE hides them

  • character vector: Colors for the edges

  • list: Fine control with col (colors), alpha (transparency 0-1), lty (line type), lwd (line width), lex (line expansion)

labels

Controls set labels. Can be:

  • logical: TRUE shows default labels, FALSE hides them

  • character vector: Custom text for labels

  • list: Fine control with col (text color), fontsize, font (1=plain, 2=bold, 3=italic, 4=bold italic), fontfamily, cex (character expansion), alpha (transparency 0-1)

quantities

Controls intersection quantities display. Can be:

  • logical: TRUE shows counts, FALSE hides them

  • character vector: Custom text labels

  • list: Fine control with type (c("counts", "percent")), col (text color), fontsize, font, fontfamily, cex, alpha

legend

Controls the legend. Can be:

  • logical: FALSE to disable

  • character: Position ("right", "top", "bottom", "left")

  • list: Fine control with side (position), labels (custom labels), col, fontsize, cex, fontfamily

main

Title for the plot. Can be character, expression, or list with label (text), col, fontsize, font, fontfamily

...

Additional arguments passed to plot.euler.

Value

A Venn diagram plot generated by eulerr.

Examples

# Example with gene sets
data(gene_list)
res_sets <- computeOverlaps(gene_list)

# Basic plot
plotVenn(res_sets)


# Customize fills with transparency and custom colors
plotVenn(res_sets,
         fills = list(fill = c("#FF6B6B", "#4ECDC4", "#45B7D1"),
                      alpha = 0.6))


# Customize edges
plotVenn(res_sets,
         edges = list(col = "darkgray", lwd = 2, lty = 2))


# Customize labels
plotVenn(res_sets,
         labels = list(col = "white", font = 2, fontsize = 14))


# Show both counts and percentages
plotVenn(res_sets,
         quantities = list(type = c("counts", "percent"),
                          col = "black", fontsize = 10))


# Add a title
plotVenn(res_sets,
         main = list(label = "Gene Set Overlaps",
                     col = "navy", fontsize = 16, font = 2))


# Transparent fills with colored borders only
plotVenn(res_sets,
         fills = "transparent",
         edges = list(col = c("red", "blue", "green"), lwd = 3))


# Custom legend
plotVenn(res_sets,
         legend = list(side = "bottom",
                      labels = c("Treatment A", "Treatment B", "Control"),
                      fontsize = 12))