gauravj49 / venn_plots

Venn diagram plotting script

Description:

A script for plotting:

• Scaled two and three set venn diagrams
• Unscaled four and five set venn diagrams
• Profile, summary and tabular output for all sets including (six sets or more)

Dependencies:

• numpy
• scipy
• matplotlib
• matplotlib-venn

Usage:

[gjain@gjvbx venn_plots ] $ python scripts/venn_plots.py 

***********************************************
- PROGRAM: venn_plots.py
- CONTACT: Gaurav Jain([e-mail])
***********************************************

usage: venn_plots.py [-h] -if --input_file [-of --output_file] [-od --output_dir] [-cl --cols] [-ci]

arguments:
-h, --help               show this help message and exit
-if --input_file        *Input file (tab separated) with headers
-of --output_file        Output file
-od --output_dir         Output directory
-cl --cols               Comma separated list of columns you want to use to draw venn diagrams: "col0,col1,col2 col5,col9" 
                         for example: -cl="0,1,2,5,9"
                         Its ZERO based indexing i.e. Count the first column as zero 
-ci, --caseInsensitive   if set, use case insensitive comparisions

----------------- SAMPLE USAGE ------------------
- python scripts/venn_plots.py -if=test/test_input.txt -of=test/01_two_sets_venn.txt   -cl=0,1
- python scripts/venn_plots.py -if=test/test_input.txt -of=test/02_three_sets_venn.txt -cl=0,1,3
- python scripts/venn_plots.py -if=test/test_input.txt -of=test/03_four_sets_venn.txt  -cl=0,1,4,6
- python scripts/venn_plots.py -if=test/test_input.txt -of=test/04_five_sets_venn.txt  -cl=1,4,5,6,7
- python scripts/venn_plots.py -if=test/test_input.txt -of=test/05_eight_sets_venn.txt
-------------------------------------------------

Input file (tab-delimited text file with headers):

Set1	Set2	Set3	Set4	Set5	Set6	Set7	Set8
34	50	49	4	35	11	44	20
45	14	5	43	40	23	15	0
7	27	27	1	25	16	16	48
28	31	42	11	17	40	35	37
26	13	44	27	9	36	23	26
15	28	34	22	29	12	38	18
8	39	25	13	4	13	17	22
23	5	15	6	38	46	24	12
18	9	16	50	48	3	39	24
1	42	14	3	32	14	46	25
49	3	1	34	33	48	31	49
12	22	37	35	50	50	22	1
38	4	11	20	27	42	33	19
37	15	31	44	12	34	4	21
42	33	50	17	19	47	5	2
33	26	20	25	0	19	50	42
40		19	12	36	7	14	23
22		0		11	22		8
20		41		22	24		31
21		4					28
4							10

Output files:

1. Plots (png and pdf) for 2 to 5 sets
   

2. Summary file:

   - Set1 = 14
   - Set2 = 9
   - Set1|Set2 = 7
   

3. Profile file:

   > Set1 = 14
   1
   12
   18
   20
   21
   23
   34
   37
   38
   40
   45
   49
   7
   8
   > Set2 = 9
   13
   14
   27
   3
   31
   39
   5
   50
   9
   > Set1|Set2 = 7
   15
   22
   26
   28
   33
   4
   42
   

4. Tabular file (1=PRESENT, 0 = ABSENT):

   #element	Set1	Set2
   28	1	1
   26	1	1
   27	0	1
   20	1	0
   21	1	0
   22	1	1
   49	1	0
   45	1	0
   42	1	1
   40	1	0
   1	1	0
   3	0	1
   5	0	1
   4	1	1
   7	1	0
   9	0	1
   8	1	0
   13	0	1
   38	1	0
   39	0	1
   12	1	0
   15	1	1
   14	0	1
   33	1	1
   18	1	0
   31	0	1
   23	1	0
   37	1	0
   50	0	1
   34	1	0