plot: Plot Venn object

In guokai8/VennDetail: A package for visualization and extract details

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

## 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

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")

guokai8/VennDetail documentation built on July 28, 2021, 1:02 p.m.