plot: Plot Venn object

Description Usage Arguments Value Author(s) Examples

Description

The plot function allows users to graphically display the groups and overlap between groups in their venn class object through a variety of graph types such as a bar plot, traditional venn, or venn pie chart.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
## S3 method for class 'Venn'
plot(x, type = "venn", col = "black", sep = "_",
  mycol = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3",
  "orchid3"), cat.cex = 1.5, alpha = 0.5, cex = 2,
  cat.fontface = "bold", margin = 0.05, text.scale = c(1.5, 1.5, 1.5,
  1.5, 1.5, 1.5), filename = NULL, piecolor = NULL,
  revcolor = "lightgrey", any = NULL, show.number = TRUE,
  show.x = TRUE, log = FALSE, base = NULL, percentage = FALSE,
  sets.x.label = "Set Size", mainbar.y.label = "Intersection Size",
  nintersects = 40, abbr = FALSE, abbr.method = "both.sides",
  minlength = 3, ...)

Arguments

x

Venn object

type

Use venn, vennpie or upset (default: venn)

col

Character vector giving the color of the circles.

sep

Character string used to separate the terms when concatenating group names into new column names (colnames)(vennpie).

mycol

Character vector giving the filled color for VennDiagram circles.

cat.cex

Numeric vector giving the size of the category names.

alpha

A number giving the transparency value.

cex

A numerical value giving the text size for venndiagram

cat.fontface

A character giving the fontface (font style) for category name.

margin

Number giving the amount of whitespace around the diagram in grid units

text.scale

Numeric vector of text sizes for upset diagram (ylab, yaxis, xlab, subset name, xaxis, insection).

filename

Filename for output figure.

piecolor

Character vector giving the colors of the subsets(vennpie).

revcolor

Character giving the color for the non-selected subsets(vennpie).

any

Number to indicate selected subsets, such as 1 means any unique subsets, 2 means any subsets shared by two groups(vennpie).

show.number

Boolean indicating whether to display the element numbers of the subsets or not (default: TRUE)(vennpie).

show.x

Boolean indicating whether to show subset labels outside the circle (default: TRUE)(vennpie).

log

Boolean indicating whether to transform the data in log scale(vennpie).

base

Base value for log transformation(vennpie).

percentage

Boolean indicating whether to display subset percentages (default: FALSE)(vennpie).

sets.x.label

x-axis label (upset)

mainbar.y.label

y-axis label (upset)

nintersects

Number of intersections to plot. If subset to NA, all intersections will be plotted.

abbr

Boolean indicating whether to abbreviate subset names (default: FALSE).

abbr.method

a character string specifying the method used. Partial matches allowed. (default: both side).

minlength

Minmal length for the subset name.

...

further arguments passed to or from other methods

Value

different type of graphics based on user chose

Author(s)

Kai Guo

Examples

1
2
3
4
5
A <- sample(1:100, 40, replace = FALSE)
B <- sample(1:100, 60, replace = FALSE)
C <- sample(1:100, 40, replace = FALSE)
res <- venndetail(list(A = A, B = B, C = C))
plot(res, type = "venn")

Example output



VennDetail documentation built on Nov. 8, 2020, 8:25 p.m.