| Title: | Create Area-Proportional Venn Diagrams from Biological Lists |
|---|---|
| Description: | Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen (2021) <doi:10.3233/DS-210032>. |
| Authors: | Tim Hulsen [aut, cre] |
| Maintainer: | Tim Hulsen <[email protected]> |
| License: | GPL-3 |
| Version: | 1.1.3 |
| Built: | 2024-10-31 07:00:04 UTC |
| Source: | CRAN |
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.
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 )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 )
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) |
When using a BioVenn diagram for a publication, please cite: BioVenn - an R and Python package for the comparison and visualization of biological lists using area-proportional Venn diagrams T. Hulsen, Data Science 2021, 4 (1): 51-61 https://dx.doi.org/10.3233/DS-210032
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.
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")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")