BioVenn 1.0.16

BioVenn: Create Area-Proportional Venn Diagrams from Biological Lists

Draw an area-proportional Venn diagram of 2 or 3 circles

The draw_venn 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.

When using this BioVenn Python package 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
and
BioVenn - Create Area-Proportional Venn Diagrams from Biological Lists. T. Hulsen, Python package version 1.0.16

Parameters

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 (default is "bold")
t_s (Optional) The size of the main title (default is 20)
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 (default is "bold")
st_s (Optional) The size of the subtitle (default is 15)
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 (default is "bold")
xt_s (Optional) The size of the X title (default is 10)
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 (default is "bold")
yt_s (Optional) The size of the Y title (default is 10)
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 (default is "bold")
zt_s (Optional) The size of the Z title (default is 10)
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 (default is "bold")
nr_s (Optional) The size of the numbers (default is 10)
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)

Returns

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.

Example

list_x = ("1007_s_at","1053_at","117_at","121_at","1255_g_at","1294_at")
list_y = ("1255_g_at","1294_at","1316_at","1320_at","1405_i_at")
list_z = ("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")