Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
Tutorials
1. Installation and Configuration
1.
UNIX vs Windows
2.
Installation
3.
Configuration Files - Syntax, Colors, Fonts and Units
4.
Colors
5.
Data Files
6.
Required Perl Modules
7.
Runtime Parameters
8.
Debugging
9.
Common Errors
10.
PNG Output
11.
SVG Output
2. Quick Start
1.
Hello World
2.
Ticks & Labels
3.
Ideogram Selection, Scale, Color & Orientation
4.
Links & Rules
5.
Histograms
6.
Axes & Backgrounds
7.
Heat Maps & Colors
8.
Text
9.
Automation & Macros
3. Drawing Ideograms
1.
Ideograms
2.
Karyotypes
3.
Filtering
4.
Ordering
5.
Cropping
6.
Spacing and Axis Breaks
7.
Tags
8.
Variable Radius
9.
Labels
10.
Progression and Orientation
4. Highlights
1.
Wedge Highlights
2.
Highlight Parameters - Part I - Embedded in Data File
3.
Highlight Parameters - Part II - Using z-depth
4.
Highlight Parameters - Part III - Radial Position
5.
Ideogram Highlights
6.
Recipe 1 - Ideogram Highlights
7.
Recipe 2 - Focusing on a Genome Region
8.
Recipe 3 - Plot Axis Range Highlights
9.
Drawing on Top of Data
5. Tick Marks, Grids and Labels
1.
Tick Marks - Basics
2.
Tick Marks - Margins
3.
Tick Marks - Label Margins
4.
Tick Marks - Offsets
5.
Grids
6.
Label Formats
7.
Relative Ticks
8.
Ticks at Specific Positions
9.
Tick Rings
6. Links and Relationships
1.
Drawing Basic Links
2.
Link Geometry
3.
Link Formatting
4.
Link Rules - Part I
5.
Link Rules - Part II
6.
Link Rules - Part III
7.
Link Rules - Part IV
8.
Link Rules - Part V
9.
Ribbons
10.
Ribbon Twists
7. 2D Data Tracks
1.
Scatter Plots
2.
Line Plots
3.
Histograms
4.
Tiles
5.
Heat Maps
6.
Text—Basic
7.
Text—Stacking
8.
Text—Rules
9.
Glyphs—Part I
10.
Glyphs—Part II
11.
Connectors
12.
Putting It All Together
8. Axis Scaling
1.
Global Scale Adjustment
2.
Global Relative Scale Adjustment
3.
Adjusting Scale for Regions
4.
Creating Zoomed Regions
5.
Overlapping Zoomed Regions
6.
Smoothing Scale
7.
Combining Scales
8.
Drawing Data with Scale Adjustment
9. Recipes
1.
Microbial Genome
2.
Link Geometry - Detailed Bezier Control
3.
Labeling Karyotype Bands
4.
Image Maps
5.
Image Transparency and Background
6.
Complex 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
10. Helper Tools
1.
Generating Random Link Data
2.
Reordering Ideograms to Minimize Overlap
3.
Bundling Links
4.
Filtering Links
5.
Visualizing Tabular Data
6.
Generate Link Density Tracks
7.
Visualizing Categorical Data
11. Image Maps
1.
Image Maps - Introduction and Clickable Ideograms
2.
Image Maps - Clickable Cytogenetic Bands
3.
Clickable Tick Marks
4.
Clickable Highlights and Data
12. Reference
1.
Best Practices
2.
API
3.
Command Line Parameters
4.
Configuration Structure and Syntax
5.
<image> block
6.
<ideogram> block
7.
<link> block
8.
<plot> block
9.
<rule> block
10.
<background> block
11.
<axis> block
12.
<color> block
13.
<font> block
14.
<patterns> block
15.
<guide> block