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Circos

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Circos is a circular visualization tool that can be used to display relationships between different types of data. It allows users to create publication-quality circular layouts through a plain-text configuration file. Typical Circos images feature ideograms, histograms, links between data, and other customizable elements. The tool is useful for visualizing genomic, chemical, and network data and has been applied in a variety of publications.

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Introduction of Circos Yunyun Zhou 03/11/2014
Introduction PRETTY Circular visualization POPULAR --- APPEARED IN A VARIETY OF PUBLICATIONS
Overview CIRCOS Features Methods Applications Questions http://circos.ca/
Features CIRCOS is only a circular visualization tool, no analysis Creation of images is controlled through a plain-text configuration file Circos can be used to display any kind of information. ---initially, design specific to genomics ---currently, any relationship among data. i.e. chemical reactivity, tracking transactions visualizing tables
Typical Circos Image (A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
CIRCOS installation 1. System requirement: Unix/Linux/Mac 2. Download & Install circos software 3. Install Required Perl modules 4. Download Tutorial (Best practice examples)
Plain Text Input Files > circos -conf etc/circos.conf
Configuration file (circos.conf) <ticks> <<include ../etc/ticks.conf>> <ticks> ticks.conf
Genome to Genome link
Clickable image Associate areas of the image with web links. Any element in the image (ideogram, tick, band, highlight, ribobn, etc) can have an associated URL. FEATURES: MAKING IDEOGRAMS CLICKABLE <ideogram> ideogram_url = http://www.google.com/search?q=[chr] <ideogram> chr - hs1 1 0 247249719 chr1 url=special_script?chr=[chr] chr - hs2 2 0 242951149 chr2 url=another_special_script?chr=[chr] chr - hs3 3 0 199501827 chr3 DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS METHODS:
Image map
1. Microbial Genome 2. Link Geometry - Detailed Bezier Control 3. Labeling Karyotype Bands 4. Image Maps 5. Image Transparency and Background 6. Manipulating Histograms 7. Variable Radius Link Ends 8. Stacked Histograms 9. Transparent Links 10. ID Fields 11. Heat Map Links 12. Inverted Links 13. Copy Number Data 14. Directed Links 15. Pattern Fills 16. Automating Tracks 17. Automating Heatmaps 18. Circular Stacked Bar Plots 19. Cortical Maps Connectograms 20. Cell Cycle Part 1 21. Cell Cycle Part 2 22. Nature Cover Encode Diagram 23. Naming Names Recipes Configuration files Input data file Output images Provided files:
Copy number variation scatter plot chrom start end logFC hs3 7683536 8465787 1.43 hs11 465784 756867 -0.65 gc.txt
track for [0,3] CNV data range [-3,3] Different background for the positive and negative CNV values <plot> type = scatter file = data/8/13/data.cnv.txt r0 = 0.6r r1 = 0.75r min = -3 max = 0 glyph = circle glyph_size = 8 color = red <axes> <axis> color = lred thickness = 2 spacing = 0.1r </axis> </axes> <backgrounds> <background> color = vlred_a5 </background> </backgrounds> .. track for [-3,0] <plot> type = scatter file = data/8/13/data.cnv.txt r0 = 0.75r r1 = 0.9r min = 0 max = 3 glyph = circle glyph_size = 8 color = green <axes> <axis> color = lgreen thickness = 2 spacing = 0.1r </axis> </axes> <backgrounds> <background> color = vlred_a5 </background> </backgrounds> ..
Visualizing Biological Data http://vizbi.org/ Genomic alignments Phylogenies macromolecular structures system biology
Circos

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Circos

  • 2. Introduction PRETTY Circular visualization POPULAR --- APPEARED IN A VARIETY OF PUBLICATIONS
  • 4. Features CIRCOS is only a circular visualization tool, no analysis Creation of images is controlled through a plain-text configuration file Circos can be used to display any kind of information. ---initially, design specific to genomics ---currently, any relationship among data. i.e. chemical reactivity, tracking transactions visualizing tables
  • 5. Typical Circos Image (A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
  • 6. CIRCOS installation 1. System requirement: Unix/Linux/Mac 2. Download & Install circos software 3. Install Required Perl modules 4. Download Tutorial (Best practice examples)
  • 7. Plain Text Input Files > circos -conf etc/circos.conf
  • 8. Configuration file (circos.conf) <ticks> <<include ../etc/ticks.conf>> <ticks> ticks.conf
  • 10. Clickable image Associate areas of the image with web links. Any element in the image (ideogram, tick, band, highlight, ribobn, etc) can have an associated URL. FEATURES: MAKING IDEOGRAMS CLICKABLE <ideogram> ideogram_url = http://www.google.com/search?q=[chr] <ideogram> chr - hs1 1 0 247249719 chr1 url=special_script?chr=[chr] chr - hs2 2 0 242951149 chr2 url=another_special_script?chr=[chr] chr - hs3 3 0 199501827 chr3 DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS METHODS:
  • 12. 1. Microbial Genome 2. Link Geometry - Detailed Bezier Control 3. Labeling Karyotype Bands 4. Image Maps 5. Image Transparency and Background 6. Manipulating Histograms 7. Variable Radius Link Ends 8. Stacked Histograms 9. Transparent Links 10. ID Fields 11. Heat Map Links 12. Inverted Links 13. Copy Number Data 14. Directed Links 15. Pattern Fills 16. Automating Tracks 17. Automating Heatmaps 18. Circular Stacked Bar Plots 19. Cortical Maps Connectograms 20. Cell Cycle Part 1 21. Cell Cycle Part 2 22. Nature Cover Encode Diagram 23. Naming Names Recipes Configuration files Input data file Output images Provided files:
  • 13. Copy number variation scatter plot chrom start end logFC hs3 7683536 8465787 1.43 hs11 465784 756867 -0.65 gc.txt
  • 14. track for [0,3] CNV data range [-3,3] Different background for the positive and negative CNV values <plot> type = scatter file = data/8/13/data.cnv.txt r0 = 0.6r r1 = 0.75r min = -3 max = 0 glyph = circle glyph_size = 8 color = red <axes> <axis> color = lred thickness = 2 spacing = 0.1r </axis> </axes> <backgrounds> <background> color = vlred_a5 </background> </backgrounds> .. track for [-3,0] <plot> type = scatter file = data/8/13/data.cnv.txt r0 = 0.75r r1 = 0.9r min = 0 max = 3 glyph = circle glyph_size = 8 color = green <axes> <axis> color = lgreen thickness = 2 spacing = 0.1r </axis> </axes> <backgrounds> <background> color = vlred_a5 </background> </backgrounds> ..
  • 15. Visualizing Biological Data http://vizbi.org/ Genomic alignments Phylogenies macromolecular structures system biology