Changelog • misha.browser

misha.browser 0.1.2

The panel name now appears as the legend title for data panels (e.g. a panel named "signal" shows “signal” above the track-name list in the legend).
browser_add_panel() gains show_name (default FALSE), which renders the panel name as a bold left-side strip label (UCSC-style). Off by default to avoid visual noise; opt in with show_name = TRUE.
browser_add_panel() accepts type = "ggplot" and a plot argument to render an arbitrary user-supplied static ggplot object as a panel. Useful for sample-metadata heatmaps, logos, and other annotations that don’t depend on the genomic region. The plot is static (does not re-render on navigation), gets no vline/highlight overlay, and cannot be saved to YAML — browser_save_config() drops ggplot panels with a warning listing the dropped names.
browser_add_panel() gains raw (default NULL, inheriting from cfg$plot$raw), which renders the panel without smoothing and surfaces NAs as gaps. Useful for sparse data tracks where smoothing is misleading. Precedence at render time: Shiny Raw view checkbox > per-panel raw > global cfg$plot$raw > FALSE.
Shiny UI gains a “Raw view” checkbox next to the smooth slider. When active, smoothing is skipped session-wide and the smooth slider is visually disabled.

browser_add_intervals_panel(): programmatic API for adding intervals panels. Accepts a misha intervals name, a file path, or an in-memory data frame (intervals = my_df). Data-frame panels are runtime-only and are skipped by browser_save_config().
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.

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