Floor genome-wide scatter y-axis so deep deletions don't distort it (gh#385)

[etal]

Summary

Plotting homozygous deletions (very large negative log2) distorted the y-axis of cnvkit.py scatter. The region/chromosome view was fixed long ago — it clamps its auto-scaled lower limit at -5.0 and flags clipped segments (commits ca8d5cc / 0920829). The genome-wide view (cnv_on_genome) never got the same treatment.

Root cause

cnv_on_genome computed y_min = np.nanmin([seg_auto_vals.min() - 0.2, -1.5]) with no lower bound. A single homozygous-deletion segment (log2 ≈ -12) drove y_min to ≈ -12.2, compressing all real signal into the top ~10% of the plot.

Empirically, before the fix:

view	ylim with a log2≈-12 segment
region (cnv_on_chromosome)	(-5.0, 0.3) ✓
genome (cnv_on_genome)	(-12.2, 1.5) ✗

Fix

• Add a shared AUTO_Y_MIN_FLOOR = -5.0 constant.
• Apply it in cnv_on_genome: max(AUTO_Y_MIN_FLOOR, np.nanmin([seg.min() - 0.2, -1.5])). This keeps the existing -1.5 default-extend (quiet genomes are unaffected), extends to fit moderate deletions, and floors pathological ones at -5.0.
• Warn when segments are clipped below the floor — parity with the region view — pointing users to --y-min.
• Switch the region view's literal -5.0 to the shared constant (no behavior change).

After the fix: genome (-5.0, 1.5); quiet genome (no deep deletion) still (-1.5, 1.5); explicit --y-min -15 still honored.

Tests

• New PlotTests::test_scatter_genome_y_floor (test/test_commands.py): asserts the genome-wide y-axis is floored at AUTO_Y_MIN_FLOOR for a deep-deletion dataset, and that an explicit --y-min overrides it. Written failing first (-12.2 not >= -5.0), passes with the fix.
• test_commands.py (74) and test_cnvlib.py (30) pass; mypy and ruff clean.

Clinical-impact note

Plotting-only. Genome-wide scatter plots containing very deep deletions now render with a -5.0 lower bound instead of an arbitrarily low one (this is the intended fix). No change to .cnr/.cns/.cnn/SEG/VCF output, so downstream pipelines are unaffected. The --y-min escape hatch is preserved.

Closes #385.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 83.33333% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 67.83%. Comparing base (86bf4da) to head (a2742cf).

Files with missing lines	Patch %	Lines
cnvlib/scatter.py	83.33%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1079      +/-   ##
==========================================
+ Coverage   67.81%   67.83%   +0.02%     
==========================================
  Files          74       74              
  Lines        7686     7691       +5     
  Branches     1366     1368       +2     
==========================================
+ Hits         5212     5217       +5     
  Misses       2034     2034              
  Partials      440      440              

Flag	Coverage Δ
unittests	67.83% <83.33%> (+0.02%)	⬆️

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