draw.venn: Draw an area-proportional Venn diagram of 2 or 3 circles

Description Usage Arguments Details Value Examples

View source: R/draw.venn.R

Description

This function creates an area-proportional Venn diagram of 2 or 3 circles, based on lists of (biological) identifiers. It requires three parameters: input lists X, Y and Z. For a 2-circle Venn diagram, one of these lists should be left empty. Duplicate identifiers are removed automatically, and a mapping from Entrez and/or Affymetrix to Ensembl IDs is available. BioVenn is case-sensitive. In SVG mode, text and numbers can be dragged and dropped.

Usage

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draw.venn(
  list_x,
  list_y,
  list_z,
  title = "BioVenn",
  t_f = "serif",
  t_fb = 2,
  t_s = 1.5,
  t_c = "black",
  subtitle = "(C) 2007-2020 Tim Hulsen",
  st_f = "serif",
  st_fb = 2,
  st_s = 1.2,
  st_c = "black",
  xtitle = "ID Set X",
  xt_f = "serif",
  xt_fb = 2,
  xt_s = 1,
  xt_c = "black",
  ytitle = "ID Set Y",
  yt_f = "serif",
  yt_fb = 2,
  yt_s = 1,
  yt_c = "black",
  ztitle = "ID Set Z",
  zt_f = "serif",
  zt_fb = 2,
  zt_s = 1,
  zt_c = "black",
  nrtype = "abs",
  nr_f = "serif",
  nr_fb = 2,
  nr_s = 1,
  nr_c = "black",
  x_c = "red",
  y_c = "green",
  z_c = "blue",
  bg_c = "white",
  width = 1000,
  height = 1000,
  output = "screen",
  filename = NULL,
  map2ens = FALSE
)

Arguments

list_x

(Required) List with IDs from dataset X

list_y

(Required) List with IDs from dataset Y

list_z

(Required) List with IDs from dataset Z

title

(Optional) The title of the Venn diagram (default is "BioVenn")

t_f

(Optional) The font of the main title (default is "serif")

t_fb

(Optional) The font "face" of the main title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)

t_s

(Optional) The size of the main title (cex; relative to the standard size; default is 1.5)

t_c

(Optional) The colour of the main title (default is "black")

subtitle

(Optional) The subtitle of the Venn diagram (default is "(C) 2007-2020 Tim Hulsen")

st_f

(Optional) The font of the subtitle (default is "serif")

st_fb

(Optional) The font "face" of the subtitle (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)

st_s

(Optional) The size of the subtitle (cex; relative to the standard size; default is 1.2)

st_c

(Optional) The colour of the subtitle (default is "black")

xtitle

(Optional) The X title of the Venn diagram (default is "ID set X")

xt_f

(Optional) The font of the X title (default is "serif")

xt_fb

(Optional) The font "face" of the X title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)

xt_s

(Optional) The size of the X title (cex; relative to the standard size; default is 1)

xt_c

(Optional) The colour of the X title (default is "black")

ytitle

(Optional) The Y title of the Venn diagram (default is "ID set Y")

yt_f

(Optional) The font of the Y title (default is "serif")

yt_fb

(Optional) The font "face" of the Y title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)

yt_s

(Optional) The size of the Y title (cex; relative to the standard size; default is 1)

yt_c

(Optional) The colour of the Y title (default is "black")

ztitle

(Optional) The Z title of the Venn diagram (default is "ID set Z")

zt_f

(Optional) The font of the Z title (default is "serif")

zt_fb

(Optional) The font "face" of the Z title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)

zt_s

(Optional) The size of the Z title (cex; relative to the standard size; default is 1)

zt_c

(Optional) The colour of the Z title (default is "black")

nrtype

(Optional) The type of the numbers to be displayed: absolute (abs) numbers or percentages (pct) (default is "abs")

nr_f

(Optional) The font of the numbers (default is "serif")

nr_fb

(Optional) The font "face" of the numbers (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)

nr_s

(Optional) The size of the numbers (cex; relative to the standard size; default is 1)

nr_c

(Optional) The colour of the numbers (default is "black")

x_c

(Optional) The colour of the X circle (default is "red")

y_c

(Optional) The colour of the X circle (default is "green")

z_c

(Optional) The colour of the X circle (default is "blue")

bg_c

(Optional) The background colour (default is "white")

width

(Optional) The width of the output file (in pixels for BMP/JPEG/PNG/TIF or in centiinch for PDF/SVG; default is 1000)

height

(Optional) The height of the output file (in pixels for BMP/JPEG/PNG/TIF or in centiinch for PDF/SVG; default is 1000)

output

(Optional) Output format: "bmp","jpg","pdf","png","svg" or "tif" (anything else writes to the screen; default is "screen")

filename

(Optional) The name of the output file (default is "biovenn" + extension of the selected output format)

map2ens

(Optional) Map from Entrez or Affymetrix IDs to Ensembl IDs (default is FALSE)

Details

When using a BioVenn diagram for a publication, please cite: BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams T. Hulsen, J. de Vlieg and W. Alkema, BMC Genomics 2008, 9 (1): 488

Value

An image of the Venn diagram is generated in the desired output format.

Also returns an object with thirteen lists: X, Y, Z, X only, Y only, Z only, XY, XZ, YZ, XY only, XZ only, YZ only, XYZ.

Examples

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list_x <- c("1007_s_at","1053_at","117_at","121_at","1255_g_at","1294_at")
list_y <- c("1255_g_at","1294_at","1316_at","1320_at","1405_i_at")
list_z <- c("1007_s_at","1405_i_at","1255_g_at","1431_at","1438_at","1487_at","1494_f_at")
biovenn <- draw.venn(list_x, list_y, list_z, subtitle="Example diagram", nrtype="abs")

Example output

[1] "x total: 6"
[1] "y total: 5"
[1] "z total: 7"
[1] "x only: 3"
[1] "y only: 2"
[1] "z only: 4"
[1] "x-y total overlap: 2"
[1] "x-z total overlap: 2"
[1] "y-z total overlap: 2"
[1] "x-y only overlap: 1"
[1] "x-z only overlap: 1"
[1] "y-z only overlap: 1"
[1] "x-y-z overlap: 1"

BioVenn documentation built on Jan. 7, 2021, 9:10 a.m.