upset-plot {ggVennDiagram}

Plot a upset plot

Description

This function generate a upset plot by creating a composite plot which contains subplots generated by ggplot2.

Usage

plot_upset(
  venn,
  nintersects = NULL,
  order.intersect.by = c("size", "name", "none"),
  order.set.by = c("size", "name", "none"),
  relative_height = 3,
  relative_width = 0.3,
  top.bar.color = "grey30",
  top.bar.y.label = NULL,
  top.bar.show.numbers = TRUE,
  top.bar.numbers.size = 3,
  sets.bar.color = "grey30",
  sets.bar.show.numbers = FALSE,
  sets.bar.x.label = "Set Size",
  intersection.matrix.color = "grey30",
  specific = TRUE,
  ...
)

Arguments

venn

a class Venn object

nintersects

number of intersects. If NULL, all intersections will show.

order.intersect.by

'size', 'name', or "none"

order.set.by

'size', 'name', or "none"

relative_height

the relative height of top panel in upset plot

relative_width

the relative width of left panel in upset plot

top.bar.color

default is "grey30"

top.bar.y.label

default is NULL

top.bar.show.numbers

default is TRUE

top.bar.numbers.size

text size of numbers

sets.bar.color

default is "grey30"

sets.bar.show.numbers

default is FALSE

sets.bar.x.label

default is "Set Size"

intersection.matrix.color

default is "grey30"

specific

whether only include specific items in subsets, default is TRUE.

...

useless

Value

an upset plot

Examples

 list = list(A = sample(LETTERS, 20),
             B = sample(LETTERS, 22),
             C = sample(LETTERS, 14),
             D = sample(LETTERS, 30, replace = TRUE))
 venn = Venn(list)
 plot_upset(venn)
 plot_upset(venn, order.intersect.by = "name")
 plot_upset(venn, nintersects = 6)