feat: Add x-axis windowing for long read visualization #160
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Adds x-axis position windowing to aggregate plots to support visualization of long nanopore reads (1000-2000 nt) without cramming all data into view. ## UI Changes - Added dual-handle range slider (rc-slider) for position range selection - Slider auto-populates min/max from selected reference's BAM alignment data - "Reset to Full Range" button to restore default view - Fixed horizontal scrollbar and control cutoff issues in Plot Options panel ## API Changes - Added x_axis_min/x_axis_max parameters to plotting functions - Added get_reference_range() function to query BAM alignment ranges - Updated SquiggyRuntimeAPI.generatePlot() signature - Added requestReferenceRange message for webview communication ## Implementation - Data windowing approach: filters positions before plotting - Explicit x-axis range setting with Bokeh Range1d - Handles position-keyed dicts (pileup, signal) vs non-position dicts (mods) - Implemented for aggregate.py strategy ## Styling Fixes - Fixed Plot Options panel overflow issues - Added box-sizing: border-box globally - Prevented horizontal scrolling in webview base HTML - Uniform padding matching other panels (Samples) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Implements windowing for remaining plot strategies and fixes lints. ## Implementation - **single_read.py**: Data filtering based on x-axis type (time, position, genomic) - Filters signal arrays and seq_to_sig_map - Handles base positions and modification annotations - **eventalign.py**: View windowing with Range1d - Takes precedence over clip_x_to_alignment - Works with both position and time modes - **overlay.py**: View windowing for multi-read overlays - **stacked.py**: View windowing for stacked reads ## Lint Fixes - Added get_reference_range to __all__ in __init__.py - Fixed raise statement to include 'from e' in io.py All plot strategies now support x_axis_min/x_axis_max parameters. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
…owing Remove archived rc-slider dependency in favor of two native HTML number inputs. This eliminates an unmaintained dependency, reduces bundle size by ~36 KiB, and provides better UX for precise position entry. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Update PlotOptionsViewProvider test to include new x-axis windowing fields in aggregate plot event expectations. Also apply code formatting fixes from ruff and prettier. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #160 +/- ##
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- Coverage 73.47% 71.74% -1.73%
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Files 27 27
Lines 4404 4538 +134
Branches 883 917 +34
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+ Hits 3236 3256 +20
- Misses 1168 1282 +114
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Summary
Adds x-axis position windowing to aggregate plots to support visualization of long nanopore reads (1000-2000 nt) without cramming all data into view. Users can interactively select a position range using a dual-handle slider, with automatic bounds detection from BAM alignments.
Changes
UI Components
API Updates
x_axis_min/x_axis_maxparameters toplot_aggregate()get_reference_range(bam_path, reference)functionSquiggyRuntimeAPI.generatePlot()signaturerequestReferenceRangeandupdateReferenceRangemessagesPython Implementation
Range1daggregate.pystrategyBug Fixes
box-sizing: border-boxglobally for proper width calculationsTesting
Tested with:
Screenshots
[User to add screenshots showing slider in action]
Future Work
The following plot strategies still need windowing implementation:
single_read.pyeventalign.pyoverlay.pystacked.pyAdditional enhancements:
🤖 Generated with Claude Code