BioVenn 1.0.3

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 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

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")