[jpfisher72]

fix #138
fix #141
fix #143
fix #145
fix #146
fix #147
fix #148

Summary

Beta-testing feedback: header and explorer polish, a new status palette and age bin, one default sort for every sample table, and removing participant IDs, status and age from the WGS Ancestry PCA payload.

Changes

Header (#138)

• "About" shows the external-link icon. On mobile it now also opens in a new tab, as on desktop.
• "Explore Data" lists Molecular Data (/omes, new), Clinical & Phenotypic Data, then Dimensionality Reduction.

Explorer "Go to ome" (#141)

• Now a text button with an arrow instead of a caption link. It's not outlined, so it can't be mistaken for another ome toggle.

WGS Ancestry PCA (#143, #145)

• The X/Y menus list each PC's percent variance. The select itself still shows the bare PC.
• MOHD rows lose sample ID, case status and age on the server, and status and age are no longer queried. MOHD tooltips have no title row (PlotTooltip.title is now optional). 1000G+HGDP samples keep their public IDs.
• MOHD rows are sorted by PC1, then PC2, before they're sent. The API returns them in sample ID order, the same order the WGS downloads catalog lists those IDs with status, so row n would otherwise still be the nth ID.
• Status and Age are gone from MOHD's Color by. The age-only sequential ramp in groups.ts went with them.

Age bin 13-18 (#146)

• AGE_BIN_LABELS and the catalog script's AGE_BINS are updated. A comment notes that 18 is in two bins on purpose.
• Genome browser JSON is regenerated from the API. That brings the new bins, plus 106 samples now marked pending.

Table sort (#147)

• Every sample table starts sorted by site ascending: ome scatter and heatmap pages, and the downloads datasets table.
• The field columns share one behavior (sampleFieldColumn). QC rows sort last in every field column, in both directions, after participants with no value. Age sorts in bin order.
• The downloads table now groups QC rows the way the ome pages do, so both display and sort them the same.
• Heatmap columns follow table order, so heatmaps now group samples by site.

Status colors (#148)

• Case (red) and control (blue) are unchanged. High and low risk are a dark/light purple pair, and pending is green.
• Validated as a scatter palette across all pairs: ≥ 11.7 ΔE under protanopia and deuteranopia, ≥ 20.9 with normal vision. The old case/high-risk pair failed the 15 ΔE floor even for normal vision.
• The genome browser's status sort includes pending.

Cleanup

• One PC label formatter and one PC_COUNT in common/components/pcAxis.ts, replacing three copies (explorer, ome pages, WGS).
• Removed the unreachable "unknown" entries from the status and age color maps. "Neutral group" now has a single definition in sampleFields/fields.ts.
• Exposomics: removed AGELESS_OMES and now selects age_bin, since every participant has one. Its heatmap and empty DR page moved to the private _heatmap and _dimensionalityReduction folders, so they can't be routed.
• Removed stale "WGS has no age" comments. Mobile menu links use LinkComponent.
• Regenerated the GraphQL types, which also picked up some unrelated upstream schema drift.

Testing

• tsc, lint, React Doctor 100/100.
• Served WGS page HTML: no MOHD IDs, statuses or age bins. All 3,400 sample_ids belong to reference samples, and MOHD rows come in PC1 order.
• Dev server checks:
  • Metabolomics scatter and downloads tables sort identically: QC last when sorting by site or status, ascending and descending.
  • Header, desktop and mobile.
  • Axis labels on the explorer, the RNA ome page and WGS.
  • Exposomics heatmap and DR routes return 404, and /omes/exposomics still redirects to downloads.
• The bulk-download service was restarted and now serves 13-18 and pending.

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Project	Deployment	Actions	Updated
mohd	Ready	Preview	Oct 19, 2026 12:28pm UTC

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