Tutorial Images
Each tutorial consists of configuration and data files to create an image that demonstrates a particular feature of Circos. Some tutorials (e.g. debugging, perl modules) don't have an associated image.
Click on an image to see its tutorial.
0 : Installation and Configuration
0.1 UNIX vs Windows
0.2 Installation
0.3 Configuration Files - Syntax, Colors, Fonts and Units
0.4 Colors
0.5 Data Files
0.6 Required Perl Modules
0.7 Runtime Parameters
0.8 Debugging
0.9 Common Errors
0.10 PNG Output
0.11 SVG Output
1 : Quick Start
1.1 Hello World
1.2 Ticks & Labels
1.3 Ideogram Selection, Scale, Color & Orientation
1.4 Links & Rules
1.5 Histograms
1.6 Axes & Backgrounds
1.7 Heat Maps & Colors
1.8 Text
1.9 Automation & Macros
2 : Drawing Ideograms
2.1 Ideograms
2.2 Karyotypes
2.3 Filtering
2.4 Ordering
2.5 Cropping
2.6 Spacing and Axis Breaks
2.7 Tags
2.8 Variable Radius
2.9 Labels
2.10 Progression and Orientation
3 : Highlights
3.1 Wedge Highlights
3.2 Highlight Parameters - Part I - Embedded in Data File
3.3 Highlight Parameters - Part II - Using z-depth
3.4 Highlight Parameters - Part III - Radial Position
3.5 Ideogram Highlights
3.6 Recipe 1 - Ideogram Highlights
3.7 Recipe 2 - Focusing on a Genome Region
3.8 Recipe 3 - Plot Axis Range Highlights
3.9 Drawing on Top of Data
4 : Tick Marks, Grids and Labels
4.1 Tick Marks - Basics
4.2 Tick Marks - Margins
4.3 Tick Marks - Label Margins
4.4 Tick Marks - Offsets
4.5 Grids
4.6 Label Formats
4.7 Relative Ticks
4.8 Ticks at Specific Positions
4.9 Tick Rings
5 : Links and Relationships
5.1 Drawing Basic Links
5.2 Link Geometry
5.3 Link Formatting
5.4 Link Rules - Part I
5.5 Link Rules - Part II
5.6 Link Rules - Part III
5.7 Link Rules - Part IV
5.8 Link Rules - Part V
5.9 Ribbons
5.10 Ribbon Twists
6 : 2D Data Tracks
6.1 Scatter Plots
6.2 Line Plots
6.3 Histograms
6.4 Tiles
6.5 Heat Maps
6.6 Text—Basic
6.7 Text—Stacking
6.8 Text—Rules
6.9 Glyphs—Part I
6.10 Glyphs—Part II
6.11 Connectors
6.12 Putting It All Together
7 : Axis Scaling
7.1 Global Scale Adjustment
7.2 Global Relative Scale Adjustment
7.3 Adjusting Scale for Regions
7.4 Creating Zoomed Regions
7.5 Overlapping Zoomed Regions
7.6 Smoothing Scale
7.7 Combining Scales
7.8 Drawing Data with Scale Adjustment
8 : Recipes
8.1 Microbial Genome
8.2 Link Geometry - Detailed Bezier Control
8.3 Labeling Karyotype Bands
8.4 Image Maps
8.5 Image Transparency and Background
8.6 Complex Histograms
8.7 Variable Radius Link Ends
8.8 Stacked Histograms
8.9 Transparent Links
8.10 ID Fields
8.11 Heat Map Links
8.12 Inverted Links
8.13 Copy Number Data
8.14 Directed Links
8.15 Pattern Fills
8.16 Automating Tracks
8.17 Automating Heatmaps
8.18 Circular Stacked Bar Plots
8.19 Cortical Maps—Connectograms
8.20 Cell Cycle—Part 1
8.21 Cell Cycle—Part 2
8.22 Nature Cover Encode Diagram
8.23 Naming Names
9 : Helper Tools
9.1 Generating Random Link Data
9.2 Reordering Ideograms to Minimize Overlap
9.3 Bundling Links
9.4 Filtering Links
9.5 Visualizing Tabular Data
9.6 Generate Link Density Tracks
9.7 Visualizing Categorical Data
10 : Image Maps
10.1 Image Maps - Introduction and Clickable Ideograms
10.2 Image Maps - Clickable Cytogenetic Bands
10.3 Clickable Tick Marks
10.4 Clickable Highlights and Data
11 : Reference
11.1 Best Practices
11.2 API
11.3 Command Line Parameters
11.4 Configuration Structure and Syntax
11.5 <image> block
11.6 <ideogram> block
11.7 <link> block
11.8 <plot> block
11.9 <rule> block
11.10 <background> block
11.11 <axis> block
11.12 <color> block
11.13 <font> block
11.14 <patterns> block
11.15 <guide> block