Circos
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This document provides an overview of Circos, a software package for visualizing data in circular forms. It discusses Circos' technical requirements, data formats, and configuration files. The document also provides examples of commands to generate Circos plots from data files.
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Circos
- 1. Genome Visualization: Akkal Bahadur Bist AI Developer || Data Science Intern BSC.CSIT Swastik College, Tribhuvan University Email: akkalbist55@gmail.com GitHub: github.com/akkalbist55 CIRCOS PLOT 1
- 2. Outlines ❖ Circos: Introduction ❖ Technical Requirements ❖ Chromosomes and Ideogram ❖ Standardization ❖ Circos Configuration file format ❖ Circos Distribution ❖ Circos Process ❖ Data Format ❖ Circos Plot: Examples 2
- 3. Introduction ● Software package for visualizing data in circular form. ● If you are researcher, data analyst, visual artist in large data sets, circos is for you. ● Data represent level wise in circular form. What is circos? 3
- 4. cont….. ● It’s adopted biological scientific community worldwide. ● It appeared in many top scientific journals. 4
- 6. cont... ● Platform: Windows/Linux/Mac OS ● perl 5, version 20, subversion 1 (v5.20.1) or latest version 6
- 7. Additional Perl Models Perl is a high-level general-purpose programming language. Config::General (v2.50 or later) Font::TTF GD List::MoreUtils Math::Bezier Math::Round Math::VecStat Params::Validate Readonly Regexp::Common Set::IntSpan (v1.16 or later) Text::Format 7
- 8. cont... ➢ Installed modules check in your computer. ➢ Use -modules perl circos -modules 8
- 10. 10
- 11. standardization ● All input files are in “txt” format ● Output form “PNG” or “SVG” format ● It’s require “configuration” files in “conf” format ● Conf specify circos layout & data format ● It does not do any analysis only visualization ● Run on command line 11
- 12. Circos Configuration “.conf” file format ● Image generation process is driven by a central configuration file. ● Circos configuration “.conf” file is text file with some parameter that define the image, including input files, image size, coloring, formatting etc. ● This file is usually import other configuration files Eg.12
- 13. cont... 13 ❖ Configuration syntax ➢ Variable assignment variable = value ➢ Block <ideogram> thickness = 30p fill = yes … </ideogram> ❖ Global vs Local <plots> #start of plots block type = heatmap min = 0 max = 1 <plot> #start of inner plot block file = data.1.txt r1 = 0.6r r0 = 0.5r … </plot> #end of inner plot block <plot> file = data.2.txt r1 = 0.7r r0 = 0.6r … </plot> </plots> #end of plots block Global to all plots Specific to do data.1.txt.plot
- 14. Circos Distribution 14 Circos executable file Contains karyotype files Necessary configuration files
- 15. Circos Process 15 Command to run circos: circos -conf <configFile>
- 16. Data Format Data format for different tracks for circos plot is 4 column data. char start stop values 16 Before creating any plot “chr” need to be change to “hs” header should be removed . hs10 60001 134200 CALY hs10 134201 234000 ------ hs10 234001 317600 UNC5B hs10 317601 445100 ……. …………………………………………….. chr10 60001 134200 chr10 134201 234000 chr10 234001 317600 chr10 317601 445100 ……………………………………
- 17. Circos Plot Example 17 $~cd example $~./run Command to use