Advanced Usage

Guides for setting up a PangyPlot instance

• Quick Start
  • Prerequisites
  • Quick Start - Running PangyPlot
  • Quick Start - Loading Prepared Data
  • Quick Start - Preparing Data
• Dotenv Setup
  • Environment Variables
• Organisms and Cytobands
  • Built-in Organisms
  • Custom Organisms
• Subcommands
  • pangyplot setup
  • pangyplot preprocess
  • pangyplot add
  • pangyplot annotate
  • pangyplot status
  • pangyplot run
  • pangyplot version
• Calculating Graph Layout
  • odgi Layout
  • Bandage Layout
• Calculating Bubbles
  • Structure Definitions
  • Compacting the Graph
• On-Disk Data Layout
  • Directory Layout
  • SQLite Databases
  • Memory-Mapped Indexes (*.mmapindex/)
  • Paths (paths/)
  • Skeleton and Polychain (skeleton/ and polychain.mmapindex/)
  • Annotations
• Rendering Architecture
  • Two-Tier Viewer
  • Node Types
  • Representing Segment Length
  • Force Simulation