Tutorials

1. Directory Structure and Configuration

1. Distribution Directory Structure
2. Configuration Files - Syntax, Colors, Fonts and Units
3. Required Perl Modules
4. Debugging
5. Common Errors
6. PNG Output
7. SVG Output

2. 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

3. Highlights

1. Wedge Highlights
2. Highlight Parmaeters - Part I - Embedded in Data File
3. Highlight Parmaeters - Part II - Using z-depth
4. Highlight Parmaeters - 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

4. 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

5. 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

6. 2D Data Tracks

1. Scatter Plots
2. Line Plots
3. Histograms
4. Tiles
5. Heat maps
6. Text Labels
7. Arranging Text Labels
8. Applying Rules to Text Labels
9. Glyphs
10. Connectors
11. Putting it All Together

7. Axis Scaling

1. Global Scale Adjustment
2. Adjusting Scale for Regions
3. Creating Zoomed Regions
4. Overlapping Zoomed Regions
5. Smoothing Scale
6. Combining Scales
7. Drawing Data with Scale Adjustment

8. Recipes

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

9. 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

10. Image Maps

1. Image Maps - Introduction and Clickable Ideograms
2. Image Maps - Clickable Cytogenetic Bands
3. Clickable Tick Marks
4. Clickable Highlights and Data