huangziyan11111 / cirgo

CirGO

! *CirGO (Circular Gene Ontology) Version 1.0 for Python 2+ is available 01/03/2018  
! *CirGO (Circular Gene Ontology) Version 2.0 for Pyhton 3+ is available 24/04/2020  

© Copyright (C) 2020
https://github.com/IrinaVKuznetsova/CirGO.git

Software development:
Irina Kuznetsova | email: [email protected]
Artur Lugmayr | email: [email protected]

CirGO manual was designed to help people with limited or no programming experience to install the CirGO software

• For CirGO installation instructions for Version 1.0 for Python 2+
• For CirGO installation instructions for Version 2.0 for Python 3+

General Usage Notes

Description: CirGO (Circular Gene Ontology) is an alternative way of visualising GO terms in 2D space that is suitable for publishing and presenting gene expression Ontology data

Software architecture:
CirGO can be run on Windows, Unix/Linux and Mac OS as:
      (1) Graphical User Interface (GUI)
      (2) Command Line (CMD)
      (3) Interactive Command Line (INT)

Brief Algorithm Description

Briefly, CirGO visualisation algorithm consists of three steps that are described at the Supplementary Material of the CirGO: an alternative circular way of visualising gene ontology terms publication:
      (1) Formatting of the csv input file obtained from the TreeMap tab on REVIGIO page
      (2) Values calculation
      (3) GO visualisation as two-layer full hierarchies

Input Data Format

REVIGIO csv input file

Note: four header lines are omitted

term_ID	description	frequencyInDb	log10pvalue	uniqueness	dispensability	representative
GO:0002376	immune system process	0.6%	-7.6615	0.994	0	immune system process
GO:0006950	response to stress	4.58%	-24.6003	0.937	0	response to stress
GO:1901700	response to oxygen-containing compound	0.5%	-9.8297	0.943	0.683	response to stress
GO:0023051	regulation of signaling	0.93%	-9.5272	0.817	0.636	response to stress
...	...	...	...	...	...	...

Formatted three columns input for visualisation

Note: there is no header

immune system process	7.6615	immune system process
response to stress	24.6003	response to stress
response to oxygen-containing compound	9.8297	response to stress
regulation of signaling	9.5272	response to stress
...	...	...
..

Version control CirGO Version 1.0 Python 2+:
       Tested on Windows 7 Professional / Windows 10
       Conda 4.3.25
       Python 2.7
       NumPy 1.13.1
       Matplotlib 2.1.0
       Seaborn 0.8.1

Version control CirGO Version 2.0 Python 3+:
       Tested on Windows 10
       Conda 4.8.3
       Python 3.7
       NumPy 1.18.1
       Matplotlib 3.2.1
       Seaborn 0.10.0

Visualisation Example

Example Dataset

The example dataset was obtained from GSE83471

Copyright Notice

This project is licensed under the terms of the GNU version 3 general public license

Cite

Kuznetsova I, Lugmayr A, Siira SJ, Rackham O, Filipovska A. CirGO: an alternative circular way of visualising gene ontology terms. BMC Bioinformatics [Internet]. 2019 Feb 18;20(1):84. Available from: https://doi.org/10.1186/s12859-019-2671-2