User reported: Option to display components of complex or set within the diagram

[adamjohnwright]

Migrated from reactome/PathwayBrowser#46, opened by @nancytli on 2026-03-17. That repository is archived; the Angular pathway browser now lives here.

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User description:

The option to display the components of a complex or set within a diagram is missing in the beta browser. Particularly problematic if wanting to see hits in an analysis.

[adamjohnwright]

This is delivered by the entity popup — verified today against a live analysis rather than assumed.

Ran a 10-gene analysis (TP53, BAX, BCL2, CASP3, CASP9, APAF1, CYCS, BID, BAK1, MCL1 — 195 pathways found, 10 entities found in R-HSA-109606), opened that pathway with the token and right-clicked:

• Complex APAF1:ATP:CYCS → Molecules tab lists CYCS [cytosol] and APAF1:ATP [cytosol], and both carry the found marker (row-hit--found), because both were in the submitted set. So the components are listed and the analysis hits among them are marked, which is the case the issue calls out as most problematic.
• Set BCL2 antagonists → lists its three members (ABT-737, navitoclax, venetoclax), correctly with no hit markers since drugs were not in the gene list.

The popup also carries Pathways and Interactors tabs, and sorts hits and molecules with expression to the top, matching MoleculesTable.sortMolecules in the GWT browser. In the GWT pathway browser this same function lives in ContextDialogPanel / MoleculesDialogPanel, which is what the popup replaces.

Closing on that basis — but flagging the one ambiguity: if "within a diagram" meant drawing the components as nodes inside the diagram canvas rather than listing them in the right-click panel, that is a different and much larger piece of work, and the GWT browser does not do it either (Reactome diagram layouts come from curation and have no in-place expansion). Please reopen if that was the intent.

[adamjohnwright]

Reopening: curators re-tested and it is only half done.

Their words: "OK in tissue expression analysis — the components are shown, but an indication of which component is hit in the analysis is missing."

This was closed on the basis that the right-click panel delivers it. It lists the components, but nothing marks which of them your data hit, which is the part that makes it useful during an analysis. Confirmed visually in the slide deck they sent: the complex's components are listed with no hit indication.

Still not the larger reading of the original request — drawing components as nodes inside the canvas — which the old GWT browser does not do either.