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0 : Installation and Configuration

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0.1 UNIX vs Windows zoom

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0.2 Installation zoom

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0.3 Configuration Files - Syntax, Colors, Fonts and Units zoom

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0.4 Colors zoom

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0.5 Data Files zoom

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0.6 Required Perl Modules zoom

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0.7 Runtime Parameters zoom

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0.8 Debugging zoom

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0.9 Common Errors zoom

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0.10 PNG Output zoom

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0.11 SVG Output zoom

1 : Quick Start

1.1 Hello World zoom

1.2 Ticks & Labels zoom

1.3 Ideogram Selection, Scale, Color & Orientation zoom

1.4 Links & Rules zoom

1.5 Histograms zoom

1.6 Axes & Backgrounds zoom

1.7 Heat Maps & Colors zoom

1.8 Text zoom

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1.9 Automation & Macros zoom

2 : Drawing Ideograms

2.1 Ideograms zoom

2.2 Karyotypes zoom

2.3 Filtering zoom

2.4 Ordering zoom

2.5 Cropping zoom

2.6 Spacing and Axis Breaks zoom

2.7 Tags zoom

2.8 Variable Radius zoom

2.9 Labels zoom

2.10 Progression and Orientation zoom

3 : Highlights

3.1 Wedge Highlights zoom

3.2 Highlight Parameters - Part I - Embedded in Data File zoom

3.3 Highlight Parameters - Part II - Using z-depth zoom

3.4 Highlight Parameters - Part III - Radial Position zoom

3.5 Ideogram Highlights zoom

3.6 Recipe 1 - Ideogram Highlights zoom

3.7 Recipe 2 - Focusing on a Genome Region zoom

3.8 Recipe 3 - Plot Axis Range Highlights zoom

3.9 Drawing on Top of Data zoom

4 : Tick Marks, Grids and Labels

4.1 Tick Marks - Basics zoom

4.2 Tick Marks - Margins zoom

4.3 Tick Marks - Label Margins zoom

4.4 Tick Marks - Offsets zoom

4.5 Grids zoom

4.6 Label Formats zoom

4.7 Relative Ticks zoom

4.8 Ticks at Specific Positions zoom

4.9 Tick Rings zoom

5 : Links and Relationships

5.1 Drawing Basic Links zoom

5.2 Link Geometry zoom

5.3 Link Formatting zoom

5.4 Link Rules - Part I zoom

5.5 Link Rules - Part II zoom

5.6 Link Rules - Part III zoom

5.7 Link Rules - Part IV zoom

5.8 Link Rules - Part V zoom

5.9 Ribbons zoom

5.10 Ribbon Twists zoom

6 : 2D Data Tracks

6.1 Scatter Plots zoom

6.2 Line Plots zoom

6.3 Histograms zoom

6.4 Tiles zoom

6.5 Heat Maps zoom

6.6 Text—Basic zoom

6.7 Text—Stacking zoom

6.8 Text—Rules zoom

6.9 Glyphs—Part I zoom

6.10 Glyphs—Part II zoom

6.11 Connectors zoom

6.12 Putting It All Together zoom

7 : Axis Scaling

7.1 Global Scale Adjustment zoom

7.2 Global Relative Scale Adjustment zoom

7.3 Adjusting Scale for Regions zoom

7.4 Creating Zoomed Regions zoom

7.5 Overlapping Zoomed Regions zoom

7.6 Smoothing Scale zoom

7.7 Combining Scales zoom

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7.8 Drawing Data with Scale Adjustment zoom

8 : Recipes

8.1 Microbial Genome zoom

8.2 Link Geometry - Detailed Bezier Control zoom

8.3 Labeling Karyotype Bands zoom

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8.4 Image Maps zoom

8.5 Image Transparency and Background zoom

8.6 Complex Histograms zoom

8.7 Variable Radius Link Ends zoom

8.8 Stacked Histograms zoom

8.9 Transparent Links zoom

8.10 ID Fields zoom

8.11 Heat Map Links zoom

8.12 Inverted Links zoom

8.13 Copy Number Data zoom

8.14 Directed Links zoom

8.15 Pattern Fills zoom

8.16 Automating Tracks zoom

8.17 Automating Heatmaps zoom

8.18 Circular Stacked Bar Plots zoom

8.19 Cortical Maps—Connectograms zoom

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8.20 Cell Cycle—Part 1 zoom

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8.21 Cell Cycle—Part 2 zoom

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8.22 Nature Cover Encode Diagram zoom

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8.23 Naming Names zoom

9 : Helper Tools

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9.1 Generating Random Link Data zoom

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9.2 Reordering Ideograms to Minimize Overlap zoom

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9.3 Bundling Links zoom

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9.4 Filtering Links zoom

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9.5 Visualizing Tabular Data zoom

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9.6 Generate Link Density Tracks zoom

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9.7 Visualizing Categorical Data zoom

10 : Image Maps

10.1 Image Maps - Introduction and Clickable Ideograms zoom

10.2 Image Maps - Clickable Cytogenetic Bands zoom

10.3 Clickable Tick Marks zoom

10.4 Clickable Highlights and Data zoom

11 : Reference

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11.1 Best Practices zoom

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11.2 API zoom

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11.3 Command Line Parameters zoom

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11.4 Configuration Structure and Syntax zoom

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11.5 <image> block zoom

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11.6 <ideogram> block zoom

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11.7 <link> block zoom

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11.8 <plot> block zoom

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11.9 <rule> block zoom

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11.10 <background> block zoom

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11.11 <axis> block zoom

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11.12 <color> block zoom

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11.13 <font> block zoom

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11.14 <patterns> block zoom

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11.15 <guide> block zoom