Surface profile data caveats as a per-track warning in OncoPrint - #5637
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Surface profile data caveats as a per-track warning in OncoPrint#5637inodb wants to merge 1 commit into
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A molecular profile whose profile_description contains a 'Caveat:' marker now shows a warning icon on every OncoPrint track from that profile, with the caveat text in a hover tooltip. Lets curators flag how data should be interpreted (e.g. cell-type fractions from a sorted population) without the caveat being buried in the profile description. - getProfileDescriptionCaveat() parses the 'Caveat:' marker from a description - generic-assay heatmap & categorical track builders set the warning + tooltip - IHeatmapTrackSpec / ICategoricalTrackSpec gain infoTooltip (genetic tracks already had it), wired through DeltaUtils - oncoprintjs track-info view renders non-numeric info verbatim instead of coercing it to 'N/P', so the glyph displays (N/P still shown for the not-profiled sentinel; numeric percents unchanged) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JEbP4a7tGv74r3RtNYt7Jw
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What
A molecular profile whose
profile_descriptioncontains aCaveat:marker now shows a ⚠ warning icon on every OncoPrint track from that profile, with the caveat text in a hover tooltip. This lets study curators flag how data should be interpreted — e.g. cell-type fractions derived from a sorted cell population — without the caveat being buried in the profile description where viewers won't see it.Motivating case: the
msk_spectrum_tme_2022single-cell cell-type fraction profiles are derived from CD45 FACS-sorted scRNA-seq, so a sample's composition reflects its sort gate (some samples are immune-only or non-immune-only) rather than whole-tumor cellularity. A 100%-summing stacked/heatmap track is misleading without surfacing that.Screenshot
Each cell-type track shows a ⚠ (the genetic BRCA1 track is unaffected — numeric percents still render). Hovering the ⚠ shows the caveat text, e.g. "Fractions are derived from CD45 FACS-sorted scRNA-seq, so each sample composition reflects its sort gate (some samples are immune-only or non-immune-only) rather than whole-tumor cellularity."
(Captured locally with the caveat injected, since the live study data doesn't carry the
Caveat:marker until cBioPortal/datahub#2342 merges — the deploy preview won't show the ⚠ until then.)How
getProfileDescriptionCaveat()parses theCaveat:marker (case-insensitive) from a profile description.IHeatmapTrackSpec/ICategoricalTrackSpecgaininfoTooltip(genetic tracks already had it); wired throughDeltaUtilsto$track_info_tooltip_elt.N/P, so the ⚠ glyph displays.N/Pis still shown for the not-profiled sentinel and numeric percents are unchanged.The convention is generic — any profile gets the warning for free by writing
Caveat: …in its description. Companion datahub change: cBioPortal/datahub#2342. Docs change to follow.Preview
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