@sjcrh/proteinpaint-server 2.151.0 → 2.152.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.151.0",
+  "version": "2.152.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -64,8 +64,8 @@
     "@sjcrh/proteinpaint-python": "2.151.0",
     "@sjcrh/proteinpaint-r": "2.149.0",
     "@sjcrh/proteinpaint-rust": "2.150.0",
-    "@sjcrh/proteinpaint-shared": "2.150.0",
-    "@sjcrh/proteinpaint-types": "2.150.0",
+    "@sjcrh/proteinpaint-shared": "2.152.0",
+    "@sjcrh/proteinpaint-types": "2.152.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.sampleScatter.js

@@ -31,6 +31,8 @@ function init({ genomes }) {
     }
     const g = genomes[q.genome];
     const ds = g.datasets[q.dslabel];
+    if (q.singleCellPlot)
+      return getSingleCellScatter(req, res, ds);
     try {
       let refSamples = [], cohortSamples;
       const terms = [];
@@ -116,6 +118,55 @@ function init({ genomes }) {
     }
   };
 }
+async function getSingleCellScatter(req, res, ds) {
+  const q = req.query;
+  const { name, sample } = q.singleCellPlot;
+  const tw = q.colorTW;
+  try {
+    const data = await ds.queries.singleCell.data.get({ plots: [name], sample });
+    const plot = data.plots[0];
+    const cells = [...plot.expCells, ...plot.noExpCells];
+    const samples = cells.map((cell) => {
+      const hidden = {
+        category: tw?.q?.hiddenValues ? cell.category in tw.q.hiddenValues : false
+      };
+      return {
+        sample: cell.cellId,
+        sampleId: cell.cellId,
+        x: cell.x,
+        y: cell.y,
+        z: 0,
+        category: cell.category,
+        shape: "Ref",
+        hidden
+      };
+    });
+    const [xMin, xMax, yMin, yMax] = samples.reduce(
+      (s, d) => [d.x < s[0] ? d.x : s[0], d.x > s[1] ? d.x : s[1], d.y < s[2] ? d.y : s[2], d.y > s[3] ? d.y : s[3]],
+      [samples[0].x, samples[0].x, samples[0].y, samples[0].y]
+    );
+    const categories = new Set(samples.map((s) => s.category));
+    const colorMap = {};
+    const k2c = getColors(categories.size);
+    for (const category of categories) {
+      const color = k2c(category);
+      colorMap[category] = {
+        sampleCount: samples.filter((s) => s.category == category).length,
+        color,
+        key: category
+      };
+    }
+    const shapeLegend = [["Ref", { sampleCount: samples.length, shape: 0, key: "Ref" }]];
+    const colorLegend = Object.entries(colorMap);
+    res.send({
+      result: { Default: { samples, colorLegend, shapeLegend } },
+      range: { xMin, xMax, yMin, yMax }
+    });
+  } catch (e) {
+    console.log(e);
+    res.send({ error: e.message || e });
+  }
+}
 async function getSamples(ds, plot) {
   if (!plot.filterableSamples) await loadFile(plot, ds);
   return [readSamples(plot.referenceSamples), readSamples(plot.filterableSamples)];