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BioVenn-1.1.3
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BioVenn: Create Area-Proportional Venn Diagrams from Biological Lists
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | BioVenn-1.1.3 |
| نام | BioVenn |
| نسخه کتابخانه | 1.1.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Tim Hulsen |
| ایمیل نویسنده | thulsen@gmail.com |
| آدرس صفحه اصلی | https://www.biovenn.nl |
| آدرس اینترنتی | https://pypi.org/project/BioVenn/ |
| مجوز | - |
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:
[T. Hulsen, BioVenn - an R and Python package for the comparison and visualization of biological lists using area-proportional Venn diagrams. Data Science 2021, 4 (1): 51-61, https://dx.doi.org/10.3233/ds-210032](https://dx.doi.org/10.3233/ds-210032)
and
[T. Hulsen, BioVenn: Create Area-Proportional Venn Diagrams from Biological Lists. Python Package Version 1.1.3, https://pypi.org/project/BioVenn/](https://pypi.org/project/BioVenn/)
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")
نیازمندی
| مقدار | نام |
|---|---|
| >=0.9.2 | biomart |
| >=3.3.3 | matplotlib |
| >=1.19.4 | numpy |
نحوه نصب
نصب پکیج whl BioVenn-1.1.3:
pip install BioVenn-1.1.3.whl
نصب پکیج tar.gz BioVenn-1.1.3:
pip install BioVenn-1.1.3.tar.gz