Hwinata fix h padding - #190
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test-linear.R built its plot with horizontal.padding = -1. That squeezed the plot area until the gene annotations collapsed into unreadable coloured specks and the axis tick labels crowded over the polygon -- the "test plots are not right" symptom in issue #186. The fixture was the only place a negative horizontal padding was exercised, so nothing else caught it. Sweeping the parameter shows -1 and 0 both crush the annotations, 1 and 2 render them cleanly outside the polygon, and 3 pushes the axis titles off the edge. Use 1, which keeps the pre-#190 layout (PGA left, SNV right, ticks outside the plot) while leaving space between the polygon and the axes. The gene labels TP53/CDKN2A/CSMD1/FHIT/TERT/MYC and NOTCH1/SOX2/TP63/PIK3CA/EGFR are legible again. Regenerate the snapshots. Comparing every stored grob against its predecessor with compare.trees confirms only two changed: linear.example (this padding change) and fish.example (the CCF axis is now flush with the polygon rather than overhanging it, which is what "make axes flush against polygon" in #190 set out to do). The other nine are unchanged, so the regeneration accepted nothing silently. Two fixes to update-snapshots.R were needed to run it at all: * pkg.root used dirname(sys.frame(1)$ofile), which only resolves under source(). Invoked the documented way -- Rscript tests/update-snapshots.R -- sys.frame(1) raised "not that many frames on the stack" and the script died before loading the package. Resolve the path from --file= first, fall back to sys.frames()[[1]]$ofile, then getwd(). * Swap devtools::load_all for pkgload::load_all. devtools is not in Suggests and merely re-exports load_all from pkgload.
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Description
Fix
horizontal.paddingfor polygon plot use case, ensuring its translated tovertical.paddingin horizontal fishplots.Checklist
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CHANGELOG.mdunder the next release version or unreleased, and updated the date.Footnotes
UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩
The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩
Genetic information is considered PHI.
Forensic assays can identify patients with as few as 21 SNPs ↩
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