gramene-search 2.40.0 → 2.41.0

package/dist/index.js

@@ -8362,18 +8362,6 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
         studies,
         geneStudyIds
     ]);
-    // Without a baseline study the EBI Studies heatmap has nothing to draw (its
-    // request fails rather than coming back empty), so the tab says so and
-    // points at the differential EBI studies the gene does appear in -- e.g.
-    // Medicago truncatula, whose studies are all differential.
-    const ebiDifferential = (0, $gXNCa$react.useMemo)(()=>{
-        if (!geneStudyIds || !studies) return [];
-        const mine = new Set(geneStudyIds);
-        return studies.filter((e)=>mine.has(e._id) && $9e29a4f60318db7a$var$isDifferential(e) && !$9e29a4f60318db7a$var$isJgiStudy(e)).sort((a, b)=>$9e29a4f60318db7a$var$studyLabel(a) < $9e29a4f60318db7a$var$studyLabel(b) ? -1 : 1);
-    }, [
-        studies,
-        geneStudyIds
-    ]);
     const allJgiKey = JSON.stringify(allJgiStudies.map((e)=>[
             e._id,
             e.name
@@ -8478,32 +8466,21 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                         children: [
                             gene.name || gene._id,
                             " is not in any baseline expression study, so there is no heatmap here.",
-                            ebiDifferential.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                            paralogQuery && atlasExperiment && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
                                 children: [
                                     ' ',
-                                    "It has results in ",
-                                    ebiDifferential.length === 1 ? 'a differential study' : `${ebiDifferential.length} differential studies`,
-                                    " at Expression Atlas:",
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("ul", {
-                                        className: "mt-1 mb-0",
-                                        children: ebiDifferential.map((e)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
-                                                children: [
-                                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
-                                                        href: `${$9e29a4f60318db7a$var$EBI_GXA}experiments/${encodeURIComponent(e._id)}/Results?geneQuery=${encodeURIComponent(JSON.stringify([
-                                                            {
-                                                                value: geneQuery
-                                                            }
-                                                        ]))}`,
-                                                        target: "_blank",
-                                                        rel: "noopener noreferrer",
-                                                        children: e.description || e._id
-                                                    }),
-                                                    " (",
-                                                    e._id,
-                                                    ")"
-                                                ]
-                                            }, e._id))
-                                    })
+                                    "To explore the differential expression of this gene and its paralogs, use the",
+                                    ' ',
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                                        variant: "link",
+                                        size: "sm",
+                                        className: "p-0 align-baseline",
+                                        onClick: ()=>setExpression({
+                                                activeTab: 'paralogs'
+                                            }),
+                                        children: "Paralogs tab"
+                                    }),
+                                    "."
                                 ]
                             })
                         ]
@@ -8818,6 +8795,32 @@ function $cd8bc494277e92a4$export$965a6b1d7408d496(docs, tree) {
 }
 const $cd8bc494277e92a4$var$gridBorder = '1px solid var(--tbrowse-grid-line, rgba(0,0,0,0.06))';
 const $cd8bc494277e92a4$var$stressWidth = (width, organCount)=>Math.max($cd8bc494277e92a4$var$STRESS_MIN, width - organCount * $cd8bc494277e92a4$var$ORGAN_CELL_W - $cd8bc494277e92a4$var$MAXTPM_W);
+// "Expressed only" toggle. Homology applies it: while on (and the zone is
+// visible) it prunes every branch with no gene that has expression
+// attributes, and turning it on expands the branches that remain.
+const $cd8bc494277e92a4$var$ExpressedOnlyToggle = ({ on: on, onChange: onChange })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("label", {
+        title: "Prune branches without expression data and expand the rest",
+        style: {
+            display: 'inline-flex',
+            alignItems: 'center',
+            gap: 3,
+            fontSize: 10,
+            cursor: 'pointer',
+            whiteSpace: 'nowrap',
+            margin: 0
+        },
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                type: "checkbox",
+                checked: on,
+                onChange: (e)=>onChange(e.target.checked),
+                style: {
+                    margin: 0
+                }
+            }),
+            "expressed only"
+        ]
+    });
 const $cd8bc494277e92a4$var$ExprHeader = ({ zoneState: zoneState, setZoneState: setZoneState, width: width, data: data, hoveredNodeId: hoveredNodeId })=>{
     const ea = data.hostData && data.hostData.exprAttrs || {};
     const organs = ea.organs || [];
@@ -8850,6 +8853,13 @@ const $cd8bc494277e92a4$var$ExprHeader = ({ zoneState: zoneState, setZoneState:
                                     name: next
                                 }))
                     }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($cd8bc494277e92a4$var$ExpressedOnlyToggle, {
+                        on: !!zoneState?.expressedOnly,
+                        onChange: (on)=>setZoneState((s)=>({
+                                    ...s ?? {},
+                                    expressedOnly: on
+                                }))
+                    }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
                         style: {
                             display: 'flex',
@@ -9312,6 +9322,30 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         const keepGeneId = this.gene && this.gene._id;
         return (0, $gXNCa$tbrowsecore.maximalExcludedClades)(snap.tree, (leaf)=>leaf.taxonomyId != null && activeSet.has(String(leaf.taxonomyId)) || leaf.geneId === keepGeneId);
     }
+    // The Expression zone's "expressed only" toggle (zoneStates.expression
+    // .expressedOnly): while it is on and the zone is visible, prune the largest
+    // branches with no leaf carrying expression attributes. The gene of interest
+    // stays, as with the genome prunes, so the root is never pruned.
+    getExpressionPrunedIds(vs, hostProps) {
+        const zs = vs && vs.zoneStates && vs.zoneStates.expression;
+        if (!zs || !zs.expressedOnly) return [];
+        if (!(vs.zones || []).some((z)=>z.id === 'expression' && z.visible)) return [];
+        const ea = hostProps && hostProps.hostData && hostProps.hostData.exprAttrs;
+        if (!ea || !ea.byNode || !hostProps.tree) return [];
+        const keepGeneId = this.gene && this.gene._id;
+        return (0, $gXNCa$tbrowsecore.maximalExcludedClades)(hostProps.tree, (leaf)=>ea.byNode.hasOwnProperty(leaf.id) || leaf.geneId === keepGeneId);
+    }
+    // Turning "expressed only" on also expands every branch, so the expressed
+    // genes left after pruning are all in view. Done here, in the same update
+    // as the toggle, rather than by a second viewer action that would race it.
+    expandOnExpressedOnly(prev, next) {
+        const was = !!(prev && prev.zoneStates && prev.zoneStates.expression && prev.zoneStates.expression.expressedOnly);
+        const is = !!(next && next.zoneStates && next.zoneStates.expression && next.zoneStates.expression.expressedOnly);
+        return !was && is ? {
+            ...next,
+            collapsedNodeIds: []
+        } : next;
+    }
     // Seed the bundle with a pivot-computed initial tbrowse view state once the
     // loader has the tree and the user is actually looking at the tbrowse
     // viewer, from lifecycle (not render) to avoid dispatching mid-render. The
@@ -9454,12 +9488,17 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             },
             children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Spinner), {})
         });
-        // Layer the genome-limit prune set on top of the user's own prunes for the
-        // controlled view state, but persist only the user's prunes (the layer
-        // strips the genome-derived ones in onViewStateChange) so the bundle stays
-        // free of filter-derived state and re-applies cleanly when the filter
-        // changes.
-        const pruneLayer = (0, $gXNCa$tbrowsecore.createDerivedPruneLayer)(this.getGenomePrunedIds());
+        // Layer the genome-limit and "expressed only" prune sets on top of the
+        // user's own prunes for the controlled view state, but persist only the
+        // user's prunes (the layer strips the derived ones in onViewStateChange) so
+        // the bundle stays free of derived state and re-applies cleanly when the
+        // filter or toggle changes.
+        const pruneLayer = (0, $gXNCa$tbrowsecore.createDerivedPruneLayer)([
+            ...new Set([
+                ...this.getGenomePrunedIds(),
+                ...this.getExpressionPrunedIds(tbrowseVS, hostProps)
+            ])
+        ]);
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
             children: [
                 /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
@@ -9473,7 +9512,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                         zones: this.getTbrowseZones(),
                         nodeOfInterest: this.gene._id,
                         viewState: pruneLayer.effective(tbrowseVS),
-                        onViewStateChange: (next)=>this.setTbrowseViewState(pruneLayer.onChange(next)),
+                        onViewStateChange: (next)=>this.setTbrowseViewState(this.expandOnExpressedOnly(tbrowseVS, pruneLayer.onChange(next))),
                         densityControls: true,
                         defaultOpenSections: {
                             zones: true,