Interactors are hard to find: the control says "Overlay", and the count badge is ~8px at default zoom

[adamjohnwright]

Two separate discoverability problems, both found by a reader who could not see a feature that was working correctly. Nothing here is broken — the interactor overlay draws, the badges appear, clicking one opens that entity's interactors. It just cannot be found.

1. The control is called "Overlay"

On beta the switch is a dropdown in the page header, beside Species, labelled Overlay. Nothing in that word says interactors, and it sits above the page chrome rather than on the diagram it affects.

Production puts it in the diagram toolbar, next to the search box, where the thing it changes is.

Neither site shows interactors by default, so both require finding this control first — but production's at least lives beside the diagram.

2. The badge is about 8 pixels at the default zoom

R-HSA-1368108 opens at zoom 0.283. The count badge is a filled purple circle on the entity's top-right corner, which at that zoom is roughly 8px across. All nine badges on that diagram are inside the viewport — the problem is size, not position.

Measured on beta, after Overlay → IntAct:

Node	interactors
BHLHE40	73
KLF15	46
PPARA	26
CCRN4L	14
SERPINE1	14
AVP(20-28)	11
NAMPT	6
F7(21-466)	2
BHLHE41	1

Zoomed in, the badge is perfectly clear. At the zoom a pathway actually opens at, it reads as a speck.

Worth noting the colour differs too: production's badge is red, beta's is purple. Not a bug on its own, but it means someone looking for "the red dot" does not find it.

Suggestions, in order of how cheap they are

1. Rename the control to say interactors — "Overlay" is the category, not the thing.
2. Move it to the diagram toolbar, beside search, matching production and putting it next to what it changes.
3. Make the badge hold a minimum on-screen size as the diagram zooms out, the way a map pin does, so it stays findable at the zoom a pathway opens at.
4. Consider matching production's red, so existing users' expectations transfer.

How to reproduce

1. Open https://beta.reactome.org/PathwayBrowser/R-HSA-1368108
2. Click Overlay (top left, beside Species) → IntAct
3. Look at the top-right corner of BHLHE40 in the right-hand column

Two of us missed it before zooming in.

[adamjohnwright]

Two additions.

An alternative to "minimum on-screen size"

Suggestion: the badge could appear only once zoomed in, rather than shrinking to a speck at overview zoom. That is arguably better than keeping it at a floor size — at the zoom a pathway opens at, a badge on every entity is clutter nobody can read anyway, and its appearing as you zoom in is a clear signal that there is something to click.

I could not confirm production does this, and I want to be plain about that rather than let a plausible claim settle in:

• SummaryItemAbstractRenderer.draw(...) in reactome/pwp-diagram scales the badge by factor (the zoom) and has no threshold in it — nothing that skips drawing below a zoom level.
• InteractorEntityAbstractRenderer similarly only checks item.isVisible(), which is not about zoom.

So on the evidence I have, production's badge is probably also small when zoomed out, and the difference we saw is more likely #201 — production remembering the resource selection, so the badges are simply there more often.

That does not weaken the suggestion. It just means it would be our improvement rather than parity with production, and it should not be justified by "production does it" unless someone confirms that on the running site.

The overlay cannot be unselected

Related, and found while testing this: clicking the selected resource again does not turn it off. Measured on beta, R-HSA-1368108, counting InteractorOccurrences:

action	badges
select IntAct	9
click IntAct again	9
"Clear overlays"	0

So the only way off is a separate button, which is easy to miss when the obvious gesture — click the highlighted thing again — appears to do nothing. Worth fixing alongside the naming, since both are the same class of problem: the control does not behave the way its appearance suggests.

[adamjohnwright]

Withdrawing suggestion 3, and replacing it with the opposite. I suggested giving the badge a minimum on-screen size so it stays findable when zoomed out. That is wrong, and production settles it.

Production does not shrink the badge — it does not draw it at all below zoom 0.5. The diagram swaps whole renderer sets by zoom:

// RendererManager.setFactor
if (factor < 0.5)      { this.current = this.s000; }   // most simplified
else if (factor < 1)   { this.current = this.s050; }
else if (factor < 3)   { this.current = this.s100; }

and the summary badge is drawn only from the second tier up:

renderer	zoom	calls to drawSummaryItems
ProteinRenderer000	< 0.5	0
ProteinRenderer050	0.5 – 1	2

R-HSA-1368108 opens at zoom 0.283. So at the zoom a reader actually arrives at, production shows no badge whatsoever, and we show a handful of unreadable pixels. That difference is the whole of this issue, and a minimum size would have preserved the clutter rather than removed it.

I said earlier in this thread that I could not confirm this and that production's badge was "probably also small when zoomed out". That was wrong — I had looked at SummaryItemAbstractRenderer, which indeed has no threshold, and missed the level-of-detail system one layer above it that chooses which renderer runs at all.

Revised suggestion 3

Do not draw the interactor badge below a zoom threshold, and pick the threshold deliberately rather than copying 0.5 without thinking: cytoscape's zoom and GWT's factor are not guaranteed to mean the same thing, so the number should be chosen by looking at when the badge becomes legible in this implementation.

Already fixed, and the reason this mattered

The confidence control used to appear only once an entity's interactors had been drawn — which made clicking a badge the only route to it. Combined with the above, that meant the threshold was unreachable at the zoom a pathway opens at. The control now appears as soon as a resource is chosen, so hiding the badge when zoomed out no longer strands anything.