Skip to content

User Guide Overview

The user-facing experience is built around one command:

  • in_sight/commands/plot2insights.py

This command gives you a stable top-level interface while the project keeps multiple internal workflows and multiple R plotting layouts under the hood.

Primary Use Cases

  • Plot a genomic region directly from a BAM file.
  • Re-render a plot from normalized CSV intermediates.
  • Switch between layouts such as base, plain, bulkmonster, or barcode-aware workflows.
  • Replace the bundled R plotting script with your own custom script.

Specialized Commands

You may still use the scenario-specific commands directly when you need their extra orchestration:

  • in_sight/commands/cf2insights.py
  • in_sight/commands/scrna2insights.py

Those commands are documented in Scenario Commands.

  1. Install the project.
  2. Start with plot2insights --help.
  3. Use plot2insights --list-layouts.
  4. Start with a simple base layout from BAM mode.
  5. Customize the R script only if the bundled output is not enough.