UI release

[khoroshevskyi]

Changes:

• Updated UMAP

TODO:

• Version of pepdbagent updated in __version__.py file
• Changelog updated

[Copilot]

Pull request overview

Updates the UI embedding/UMAP experience by switching category assignment to a “top 20 + Other” scheme and aligning legend/pinning behavior with the new categorization.

Changes:

• Reworked assay_category / cell_line_category assignment to rank by frequency and cap at 20 (“Other”).
• Updated legend querying/rendering to group long tails into “Other”, show counts, and add “Pin All / Unpin All”.
• Bumped UI package version to 0.12.5.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
ui/src/contexts/mosaic-coordinator-context.tsx	Recomputes assay/cell line category IDs based on frequency and caps at “Other”.
ui/src/const.ts	Keeps the current UMAP URL and adds a commented-out alternative.
ui/src/components/umap/bed-embedding-view.tsx	Updates legend query + UI (counts, Other bucket, Pin All/Unpin All) and category color handling.
ui/src/components/umap/bed-embedding-plot.tsx	Extends the color palette to include an “Other” color.
ui/package.json	Version bump for the UI package.

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[Copilot]

The categorization query uses inner joins on assay and cell_line. If either column can be NULL in the UMAP JSON, rows with NULL values will be dropped because NULL = NULL does not match, causing points to disappear from the embedding. Consider using LEFT JOIN plus a default rank/category, or join with IS NOT DISTINCT FROM to preserve NULL-valued rows.

Suggested change

	CASE WHEN ac.rank < 20 THEN ac.rank ELSE 20 END AS assay_category,
	CASE WHEN cc.rank < 20 THEN cc.rank ELSE 20 END AS cell_line_category
	FROM data d
	JOIN assay_counts ac ON d.assay = ac.assay
	JOIN cell_line_counts cc ON d.cell_line = cc.cell_line` as any,
	CASE
	WHEN ac.rank IS NULL OR ac.rank >= 20 THEN 20
	ELSE ac.rank
	END AS assay_category,
	CASE
	WHEN cc.rank IS NULL OR cc.rank >= 20 THEN 20
	ELSE cc.rank
	END AS cell_line_category
	FROM data d
	LEFT JOIN assay_counts ac ON d.assay IS NOT DISTINCT FROM ac.assay
	LEFT JOIN cell_line_counts cc ON d.cell_line IS NOT DISTINCT FROM cc.cell_line` as any,

[Copilot]

Pin All builds the filter predicate with vg.or(...) unconditionally. Elsewhere in this file, single-category cases are handled with vg.eq(...) to avoid relying on vg.or behavior with a single argument. Update Pin All to mirror that logic so pinning works correctly when the legend only contains one category.

Suggested change

	const predicate = vg.or(...categories.map((cat: any) => vg.eq(colorGrouping, cat)));
	const predicates = categories.map((cat: any) => vg.eq(colorGrouping, cat));
	const predicate =
	predicates.length === 1 ? predicates[0] : vg.or(...predicates);

[Copilot]

Avoid committing commented-out alternative UMAP_URL values (especially ones that reference window.location). If you need an override for local testing, prefer an env var (e.g. VITE_UMAP_URL) or remove this line before release to prevent confusion about the canonical data source.

Suggested change

// export const UMAP_URL = `${window.location.origin}/feb08_3_13.json`;

[Copilot]

PR description TODOs mention updating pepdbagent __version__.py and the changelog, but this PR only shows UI changes (UMAP logic + UI version bump). Either update the PR description to match or include the missing version/changelog changes so the release notes are accurate.