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Scenario Commands

plot2insights is the generic interface. The following commands are specialized applications built on top of the same framework.

bayesmonstr2insights

Source: in_sight/commands/bayesmonstr2insights.py

Use this when you need:

  • BayesMonSTR result database input
  • DuckDB-backed STR result lookup
  • single STR visualization from database records
  • batch visualization and report generation across samples

This command is useful when your primary artifact is a BayesMonSTR result database rather than a mutation TSV or an ad hoc genomic region.

cf2insights

Source: in_sight/commands/cf2insights.py

Use this when you need:

  • mutation-file driven analysis
  • HTML report generation
  • batch processing across many mutation sites
  • optional pseudo-bulk processing

This command is more opinionated than plot2insights. It wraps domain-specific parsing and reporting around the lower-level visualization pipeline.

scrna2insights

Source: in_sight/commands/scrna2insights.py

Use this when you need:

  • STR/mutation rows from a TSV
  • barcode/UMI-aware processing
  • row-by-row visualization orchestration

It is especially useful when your input is already a structured row-wise table rather than a single ad hoc genomic region.

When To Use Which Command

Use plot2insights if:

  • you want a generic BAM-to-plot interface
  • you want a generic CSV-to-plot interface
  • you want to experiment with layouts or custom R scripts

Use cf2insights if:

  • your primary input is a mutation matrix or mutation table
  • you want batch report generation

Use bayesmonstr2insights if:

  • your primary input is a BayesMonSTR result database
  • you want STR-centric visualization from database records
  • you need batch rendering or reporting over STR results

Use scrna2insights if:

  • your primary input is a single-cell STR/mutation TSV
  • you need barcode and UMI aware processing