Chris (Gentle) YANG

circos-cn

Circos Tutorial Chinese Version Circos教程中文版 By Circos中文社区

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项目简介

Circos教程中文版 翻译自 circos官方的教程 http://circos.ca/documentation/tutorials， 已经过 Circos 作者 Martin 的许可，目前翻译正在进行中。

使用Gitbook发布，地址为 https://www.gitbook.com/read/book/node/circos 。

加入Circos中文社区: QQ群 171307056

章节划分

0 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. Errors
  10. PNG Output
  11. SVG Output

1 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

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 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

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
  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—Basic
  7. Text—Stacking
  8. Text—Rules
  9. Glyphs—Part I
  10. Glyphs—Part II
  11. Connectors
  12. Putting It All Together

##7　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

8 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

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

11 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
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