protvista-uniprot 4.3.5 → 4.3.7

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "4.3.5",
+  "version": "4.3.7",
   "files": [
     "dist",
     "src"
@@ -36,8 +36,8 @@
     "@nightingale-elements/nightingale-manager": "5.6.0",
     "@nightingale-elements/nightingale-navigation": "5.6.0",
     "@nightingale-elements/nightingale-sequence": "5.6.0",
-    "@nightingale-elements/nightingale-sequence-heatmap": "5.6.0",
-    "@nightingale-elements/nightingale-structure": "5.6.1",
+    "@nightingale-elements/nightingale-sequence-heatmap": "5.6.2",
+    "@nightingale-elements/nightingale-structure": "5.6.2",
     "@nightingale-elements/nightingale-track-canvas": "5.6.0",
     "@nightingale-elements/nightingale-variation": "5.6.0",
     "color-hash": "2.0.2",

package/src/adapters/alphamissense-pathogenicity-adapter.ts

@@ -1,15 +1,38 @@
 import { AlphafoldPayload } from './types/alphafold';
 
-// from example data
-// benign: [0.0448,0.3397]: x < 0.34
-// ambiguous: [0.34,0.564]: 0.34 <= x <= 0.564
-// pathogenic: [0.5646,0.9999]: 0.564 < x
-const benign = 0.34;
-const pathogenic = 0.564;
+// from color scale B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1
+const certainlyBenign = 0;
+const benign = 0.1132;
+const veryLikelyBenign = 0.2264;
+const likelyBenign = 0.3395;
+const ambiguous = 0.4527;
+const likelyAmbiguous = 0.5895;
+const likelyPathogenic = 0.7264;
+const pathogenic = 0.8632;
+const certainlyPathogenic = 1;
 
 export const rowSplitter = /\s*\n\s*/;
 export const cellSplitter = /^(.)(\d+)(.),(.+),(\w+)$/;
 
+const pathogenicityCategories = [
+  { min: certainlyBenign, max: benign, code: 'H' },
+  { min: benign, max: veryLikelyBenign, code: 'V' },
+  { min: veryLikelyBenign, max: likelyBenign, code: 'L' },
+  { min: likelyBenign, max: ambiguous, code: 'A' },
+  { min: ambiguous, max: likelyAmbiguous, code: 'l' },
+  { min: likelyAmbiguous, max: likelyPathogenic, code: 'h' },
+  { min: likelyPathogenic, max: pathogenic, code: 'p' },
+  { min: pathogenic, max: certainlyPathogenic, code: 'P' },
+];
+
+const getPathogenicityCode = (score) => {
+  for (const { min, max, code } of pathogenicityCategories) {
+    if (score >= min && score < max) {
+      return code;
+    }
+  }
+};
+
 type Row = {
   wildType: string;
   position: number;
@@ -48,7 +71,6 @@ const parseCSV = (rawText: string): string => {
 
   const out = [];
   for (const position of positions) {
-    let letter = 'A';
     // maximum
     // const value = Math.max(
     //   ...position.map((variation) => variation.pathogenicityScore)
@@ -59,11 +81,7 @@ const parseCSV = (rawText: string): string => {
         (acc, variation) => acc + +variation.pathogenicityScore,
         0
       ) / position.length;
-    if (value > pathogenic) {
-      letter = 'P';
-    } else if (value < benign) {
-      letter = 'B';
-    }
+    const letter = getPathogenicityCode(value);
     out.push(letter);
   }
 

package/src/config.ts

@@ -815,8 +815,8 @@ const config: ProtvistaConfig = {
       name: 'ALPHAMISSENSE_PATHOGENICITY',
       label: 'AlphaMissense',
       trackType: 'nightingale-colored-sequence',
-      scale: 'P:100,A:50,B:0',
-      'color-range': '#9a131a:100,#a8a9ad:50,#3d5493:0',
+      scale: 'B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1',
+      'color-range': '#2166ac:0,#4290bf:0.1132,#8cbcd4:0.2264,#c3d6e0:0.3395,#e2e2e2:0.4527,#edcdba:0.5895,#e99e7c:0.7264,#d15e4b:0.8632,#b2182b:1',
       tracks: [
         {
           name: 'alphamissense_pathogenicity',

package/src/protvista-uniprot.ts

@@ -16,6 +16,7 @@ import NightingaleSequenceHeatmap from '@nightingale-elements/nightingale-sequen
 import NightingaleFilter, {
   Filter,
 } from '@nightingale-elements/nightingale-filter';
+import { amColorScale } from '@nightingale-elements/nightingale-structure';
 
 // adapters
 import featureAdapter from './adapters/feature-adapter';
@@ -294,6 +295,11 @@ class ProtvistaUniprot extends LitElement {
                 ...new Set(heatmapData.map((hotMapItem) => hotMapItem.yValue)),
               ] as string[];
               heatmapComponent.setHeatmapData(xDomain, yDomain, heatmapData);
+              heatmapComponent.updateComplete.then(() => {
+                heatmapComponent.heatmapInstance.setColor((d) =>
+                  amColorScale(d.score)
+                );
+              });
             }
           }
         }