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Changelog

misha.browser 0.1.1

New Features

  • Intervals panels: show_direction option to plot intervals as arrows (triangles) by strand, for directional features like CTCF motifs. Uses strand column (BED col 6 or misha intervals). direction_field to specify custom column name.

  • Simplified browser_add_vtrack() and YAML vtrack configuration to use a single inferred expression field. When src/func are present, expression wraps the created vtrack during extraction; otherwise it defines a pure expression vtrack. Legacy expr is still accepted as a compatibility alias.

misha.browser 0.1.0

Initial Release

Core Features

  • YAML-based genome browser configuration with profile support
  • Interactive Shiny application for genome exploration
  • ggplot2/patchwork-based multi-panel genome visualization
  • Support for data, annotation, intervals, and ideogram panel types
  • Virtual track (vtrack) system with configurable extraction functions
  • Transform pipeline: smooth, log2, log10, sqrt, zscore, minmax, clip, quantile, and custom expressions
  • Faceting and grouping by track metadata (e.g., source/mark)
  • Vertical line overlays from files, misha tracks, or inline coordinates
  • Horizontal reference lines (fixed y-value or statistical summaries)
  • Color management with named palettes, auto-generation, and suffix fallbacks

Shiny Application

  • Real-time navigation: zoom, pan, go-to-gene
  • In-app configuration editor for all settings
  • Upload support for intervals (BED/TSV) and PSSMs (TSV/MEME/JASPAR)
  • Navigator dropdown for region selection from interval sets
  • Smooth window slider with live updates
  • Download current plot as PNG
  • Region highlight overlay

Performance

  • Two-tier LRU cache (memory + optional disk)
  • Three extraction modes: fixed, dynamic, and dynamic_smooth
  • Optional parallel panel extraction via future/promises

Deployment

Programmatic API