Help for package venny

Title:

Venn Diagram

Version:

0.0.2

Description:

Generate Venn plots, summary tables, and ellipse paths for polygon clipping. Provides direct access to subsets of interest and offers flexible customization of Venn diagrams. Summary tables are also available when Venn diagram visualization is not suitable.

License:

MIT + file LICENSE

Encoding:

UTF-8

RoxygenNote:

7.3.3

Imports:

ggplot2, polyclip

Depends:

R (≥ 4.1)

LazyData:

true

Suggests:

tidyr, dplyr, BiocManager, org.At.tair.db, DESeq2, clusterProfiler, testthat (≥ 3.0.0)

Config/testthat/edition:

NeedsCompilation:

Packaged:

2026-05-18 02:17:01 UTC; ABRC

Author:

Joon-Keat Lai

[aut, cre, cph]

Maintainer:

Joon-Keat Lai <p10911004@gmail.com>

Repository:

CRAN

Date/Publication:

2026-05-21 12:30:02 UTC

RNA-seq data

Description

A list of essential information for RNA-seq analysis and an example for demonstration.

Usage

LGL23

Format

An object of class list of length 4.

Details

sample_info: the information for the sample IDs noted in the count matrix.
GFD: A data.frame of gene functional description.
count_matrix: A matrix of the gene expression count reads for each sample. The row names are gene IDs; the column names are sample IDs.
DEGs: An example demonstrating differentially expressed genes across four conditions.

Create a bits matrix

Description

Produce a bits matrix for all possible combinations of the input sets.

Usage

bits_encoding(x, rownames = TRUE, sep = "")

Arguments

x

A character vector.

rownames

Logical (default: TRUE). Whether to show rownames.

sep

A character used to separate the group names (default is ""). Only working when rownames = TRUE.

Value

A numeric matrix with values of 0 or 1.

Examples

bits_encoding(c("A", "B", "C", "D"))

Control the ellipse textures

Description

This is used to generate the ellipse line color and transparency parameters, for passing into the venny()s ellipse.line argument.

Usage

ellipse_line(
  linetype = "blank",
  linewidth = 0.5,
  color = c("#CC79A7", "#009E73", "#E69F00", "#56B4E9"),
  alpha = 0.5
)

ellipse_fill(
  color = c("#CC79A7", "#009E73", "#E69F00", "#56B4E9"),
  alpha = 0.2
)

Arguments

linetype

A character. The options are: blank, solid, dashed, dotted, dotdash, longdash, twodash.

linewidth

A number (default: 0.5).

color

A character vector (default: c("#009E73", "#E69F00", "#CC79A7", "#56B4E9")).

alpha

A number range from 0 to 1 (default: 0.5). Set the line transparency.

Value

A list contains "color" and "alpha" values.

Examples

ellipse_line()

Ellipse positions

Description

This is an internal function used to generate the ellipse parameters that was used by the generate_ellipse_path() function. It returns a list encompassing 3 lists. Each list consists of the x0, y0, long-arm, short-arm, and angle default values for generating 2, 3, or 4 ellipses.

Usage

ellipse_position()

Value

A two-layer nested list.

Examples

ellipse_position()

Fixed Length Vector

Description

Create a desired length of vector by trimming/extending the x vector.

Usage

fixed_length(x, len, fill_with = NULL)

Arguments

x

A vector.

len

Desired length.

fill_with

Element used to extend the vector length. If set to NULL, extend by itself (default: NULL).

Value

A vector

Examples

# Extend `x` to fulfill the `len` requirement
fixed_length(1:5, 7)
# Trim `x` to fulfill the `len` requirement
fixed_length(1:5, 3)

Generate Ellipse Path

Description

Generate Ellipse Path

Usage

generate_ellipse_path(x0 = 0, y0 = 0, a = 2, b = 1, angle = 0, density = 200)

Arguments

x0

The coordinate x of the polygon center point (default: 0).

y0

The coordinate y of the polygon center point (default: 0).

a

Long arm (default: 2).

b

Short arm (default: 1).

angle

Rotation angle in degree (default: 0).

density

Greater amount of points yield smoother ellipse (default: 200).

Value

A data.frame with the point coordinates (x, y) to construct the polygon

Examples

library(ggplot2)
# Draw a circle
circle <- generate_ellipse_path(a = 1, b = 1)
ggplot(circle, aes(x, y)) +
    geom_polygon() +
    coord_fixed()
# Draw an ellipse
ellipse <- generate_ellipse_path(a = 2, b = 1, angle = 45)
ggplot(ellipse, aes(x, y)) +
    geom_polygon() +
    coord_fixed()

Draw polygons to highlight subsets

Description

A handy wrapper for the ggplot2::geom_polygon() used to represent the result of set operations.

Usage

highlight(
  venn,
  setops,
  color = "transparent",
  linewidth = 1.5,
  linetype = "solid",
  fill = "black",
  alpha = 0.4,
  ...
)

Arguments

venn

Venn diagram produced from venny::venny().

setops

The result of set operations.

color

Character (default: "transparent"). The polygon line color.

linewidth

Numeric (default: 1.5). The polygon linewidth.

linetype

Character (default: "solid"). The polygon linetype.

fill

Character (default: "black"). The polygon color.

alpha

Numeric (default: 0.4). The polygon transparency (0-1).

...

The other arguments passed into ggplot2::geom_polygon.

Value

A ggplot object.

Examples

data <- list(
    Set_A = c(10:100, 500:600),
    Set_B = c(5:150, 550:650),
    Set_C = c(80:180, 580:680),
    Set_D = c(120:220, 520:620)
)
out <- venny(data, detail = TRUE)
p0 <- out$venn
ep <- out$ellipse_path
res <- intersect(ep$Set_A, ep$Set_B, ep$Set_D)
highlight(p0, res)

How many subsets

Description

Calculate the number of combinations that can be derived from the given character vector.

Usage

how_many_subsets(x, detail = FALSE)

Arguments

x

A character vector.

detail

Logical (default: FALSE). Whether to output the combinations.

Value

An integer value or a list.

Examples

how_many_subsets(c("qqa", "bnk", "sdf", "123"))

Set labels

Description

This is an internal function for venny() to automatically generate set labels, when the input list is unnamed.

Usage

set_label_default(n_sets)

Arguments

n_sets

An integer.

Value

A list.

Examples

set_label_default(3)

Set label font

Description

Generate a list of the available set label font parameters.

Usage

set_label_font(
  family = "sans",
  face = "bold",
  size = 5,
  color = c("#CC79A7", "#009E73", "#E69F00", "#56B4E9"),
  angle = NULL
)

subset_label_font(
  family = "sans",
  face = "bold.italic",
  size = 4,
  color = "black",
  angle = 0
)

subset_count_font(
  family = "sans",
  face = "plain",
  size = 4,
  color = "grey20",
  angle = 0
)

subset_percentage_font(
  family = "sans",
  face = "plain",
  size = 4,
  color = "grey20",
  angle = 0
)

Arguments

family

Character (default: "sans").

face

Character (default: "bold").

size

Numeric (default: 5).

color

Character (default: c("#009E73", "#E69F00", "#CC79A7", "#56B4E9")).

angle

Numeric | NULL (default: NULL).

Value

A list.

Examples

set_label_font()

Set label position

Description

Generate the coordinates for the set labels. This is passed into the venny()'s set.label.position arguments.

Usage

set_label_position(hjust = 0, vjust = 0, show = NULL, hide = NULL)

subset_label_position(hjust = 0, vjust = 0, show = NULL, hide = NULL)

subset_count_position(hjust = 0, vjust = 0, show = NULL, hide = NULL)

Arguments

hjust

A numeric vector (default: 0). Horizontal adjustment, adjust the x-axis coordinates of the set labels.

vjust

A numeric vector (default: 0). Vertical adjustment, adjust the y-axis coordinates of the set labels.

show

A character vector (default: NULL). Show only the specified set labels. By default, show all labels.

hide

A character vector (default: NULL). Do not show the specified set labels. By default, show all labels.

Value

A list contains 3 named list. Each named list contains the x, y coordinates of the set labels for different venn diagram (2, 3, or 4 ellipses), respectively.

Examples

set_label_position()

Set operations

Description

Perform intersection (intersect()), union (union()), and difference (setdiff()) for multiple venny_ep objects representing sets. They are handy wrappers of the polyclip::polyclip() function.

Usage

intersect(x, y, ...)

union(x, y, ...)

setdiff(x, y, ...)

## S3 method for class 'venny_setops'
intersect(x, y, ...)

## S3 method for class 'venny_setops'
union(x, y, ...)

## S3 method for class 'venny_setops'
setdiff(x, y, ...)

Arguments

x

A two-column matrix consists of the point coordinates (x, y) used to construct the ellipse. This is the reference-ellipse used to be clipped by the others.

y

A two-column matrix consists of the point coordinates (x, y) used to construct the ellipse. This is the object-ellipse used to clip the reference ellipse, i.e. x.

...

The other object-ellipses.

Details

These functions override the base versions to make them generic so that venny can provide methods to proceed the venny_ep class object. The default methods call the base versions.

Value

A list contains one or multiple two-column dataframe. Each dataframe is the point coordinates (x, y) used to construct a polygon.

Examples

data <- list(
    Set_A = c(10:100, 500:600),
    Set_B = c(5:150, 550:650),
    Set_C = c(80:180, 580:680),
    Set_D = c(120:220, 520:620)
)
out <- venny(data, detail = TRUE)
p0 <- out$venn
ep <- out$ellipse_path

#------------- Intersection -------------#
res <- intersect(ep$Set_A, ep$Set_B, ep$Set_D)
highlight(p0, res)

#----------------- Union ----------------#
res <- union(ep$Set_A, ep$Set_C, ep$Set_D)
highlight(p0, res)

#--------------- Difference -------------#
res <- setdiff(ep$Set_B, ep$Set_D, ep$Set_A, ep$Set_C)
highlight(p0, res)

#---------- Multiple operations ---------#
res <- union(ep$Set_A, ep$Set_B, ep$Set_C) |>
    intersect(ep$Set_D) |>
    setdiff(ep$Set_B)
highlight(p0, res)

Create a `venny` summary data.frame

Description

A data.frame consists of each combination of the input sets.

Usage

venn_summary(data = list(), show_elements = FALSE)

Arguments

data

A named list contains 2 ~ 26 sets of elements. For example, list(set1 = 1:5, set2 = 3:7).

show_elements

Logical (default: FALSE). List out the elements of each zone in the dataframe.

Value

A data frame contains necessary information for subsequent inferences and plotting.

Examples

venn_summary(LGL23$DEGs)

Venn diagram

Description

Venn diagram

Usage

venny(
  data,
  detail = FALSE,
  ellipse.line = ellipse_line(),
  ellipse.fill = ellipse_fill(),
  ellipse.density = 200L,
  set.label = TRUE,
  set.label.position = set_label_position(),
  set.label.font = set_label_font(),
  subset.label = TRUE,
  subset.label.position = subset_label_position(),
  subset.label.font = subset_label_font(),
  subset.count = TRUE,
  subset.count.position = subset_count_position(),
  subset.count.font = subset_count_font(),
  subset.percentage = TRUE,
  subset.percentage.position = subset_count_position(vjust = -0.3),
  subset.percentage.font = subset_percentage_font(),
  subset.percentage.rounding = 1L
)

Arguments

data

A list with 2 to 4 vectors

detail

Logical (default: TRUE). If TRUE, output a list contains the venn diagram and summary table. Otherwise, output only venn diagram.

ellipse.line

A list. See ellipse_line().

ellipse.fill

A list. See ellipse_fill().

ellipse.density

An integer (default: 200L). Higher value yield smoother ellipse.

set.label

Logical (default: TRUE). If TRUE, show the set labels.

set.label.position

A list. See set_label_position().

set.label.font

A list. See set_label_font().

subset.label

Logical (default: TRUE). If TRUE, show the subset labels. If a named list is provided, then the selected subset name will be renamed. For example, list(AB = "new_AB") will change the original subset AB name to "new_AB".

subset.label.position

A list. See subset_label_position().

subset.label.font

A list. See subset_label_font().

subset.count

Logical (default: TRUE). If TRUE, show the element counts for each subset.

subset.count.position

A list. See subset_count_position().

subset.count.font

A list. See subset_count_font().

subset.percentage

Logical (default: TRUE). If TRUE, show the percentages of the counts.

subset.percentage.position

A list. See subset_percentage_position().

subset.percentage.font

A list. See subset_percentage_font().

subset.percentage.rounding

An integer (default: 1L). How many decimal points.

Value

A venn diagram which is a ggplot object.

Examples

lst <- LGL23$DEGs
venny(lst)

Package {venny}

RNA-seq data

Description

Usage

Format

Details

Create a bits matrix

Description

Usage

Arguments

Value

Examples

Control the ellipse textures

Description

Usage

Arguments

Value

See Also

Examples

Ellipse positions

Description

Usage

Value

Examples

Fixed Length Vector

Description

Usage

Arguments

Value

Examples

Generate Ellipse Path

Description

Usage

Arguments

Value

Examples

Draw polygons to highlight subsets

Description

Usage

Arguments

Value

Examples

How many subsets

Description

Usage

Arguments

Value

Examples

Set labels

Description

Usage

Arguments

Value

Examples

Set label font

Description

Usage

Arguments

Value

Examples

Set label position

Description

Usage

Arguments

Value

Examples

Set operations

Description

Usage

Arguments

Details

Value

Examples

Create a venny summary data.frame

Description

Usage

Arguments

Value

Examples

Venn diagram

Create a `venny` summary data.frame