@sjcrh/proteinpaint-server 2.145.1 → 2.145.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.145.1",
+  "version": "2.145.2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -63,9 +63,9 @@
     "@sjcrh/augen": "2.143.0",
     "@sjcrh/proteinpaint-python": "2.144.0",
     "@sjcrh/proteinpaint-r": "2.145.1-0",
-    "@sjcrh/proteinpaint-rust": "2.145.1",
-    "@sjcrh/proteinpaint-shared": "2.145.1-0",
-    "@sjcrh/proteinpaint-types": "2.145.1-1",
+    "@sjcrh/proteinpaint-rust": "2.145.2",
+    "@sjcrh/proteinpaint-shared": "2.145.2",
+    "@sjcrh/proteinpaint-types": "2.145.2",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.boxplot.js

@@ -2,9 +2,7 @@ import { boxplotPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { sortPlot2Values } from "./termdb.violin.ts";
-import { roundValueAuto } from "#shared/roundValue.js";
-import { getMean, getVariance } from "#shared/descriptive.stats.js";
-const minSampleSize = 5;
+import { summaryStats, getDescriptiveStats, summaryStatsFromStats } from "#shared/descriptive.stats.js";
 const api = {
   endpoint: "termdb/boxplot",
   methods: {
@@ -31,6 +29,9 @@ function init({ genomes }) {
       if (q.divideTw) terms.push(q.divideTw);
       const data = await getData({ filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__ }, ds);
       if (data.error) throw data.error;
+      const samples = Object.values(data.samples);
+      const values = samples.map((s) => s?.[q.tw.$id]?.value).filter((v) => typeof v === "number");
+      const statsAllSummary = summaryStats(values).values;
       const sampleType = `All ${data.sampleType?.plural_name || "samples"}`;
       const overlayTerm = q.overlayTw;
       const divideTerm = q.divideTw;
@@ -45,24 +46,30 @@ function init({ genomes }) {
       if (!absMin && absMin !== 0) throw "absMin is undefined [termdb.boxplot init()]";
       if (!absMax && absMax !== 0) throw "absMax is undefined [termdb.boxplot init()]";
       const charts = {};
+      let outlierMin = Number.POSITIVE_INFINITY, outlierMax = Number.NEGATIVE_INFINITY;
       for (const [chart, plot2values] of chart2plot2values) {
         const plots = [];
-        for (const [key, values] of sortPlot2Values(data, plot2values, overlayTerm)) {
-          const sortedValues = values.sort((a, b) => a - b);
+        for (const [key, values2] of sortPlot2Values(data, plot2values, overlayTerm)) {
+          const sortedValues = values2.sort((a, b) => a - b);
           const vs = sortedValues.map((v) => {
             const value = { value: v };
             return value;
           });
-          const boxplot = boxplot_getvalue(vs);
+          const stats = getDescriptiveStats(sortedValues);
+          if (q.removeOutliers) {
+            outlierMin = Math.min(outlierMin, stats.outlierMin);
+            outlierMax = Math.max(outlierMax, stats.outlierMax);
+          }
+          const descrStats = summaryStatsFromStats(stats, true).values;
+          const boxplot = boxplot_getvalue(vs, q.removeOutliers);
           if (!boxplot) throw "boxplot_getvalue failed [termdb.boxplot init()]";
-          const descrStats = setDescrStats(boxplot, sortedValues);
           const _plot = {
             boxplot,
             descrStats
           };
           if (overlayTerm) {
             const _key = overlayTerm?.term?.values?.[key]?.label || key;
-            const plotLabel = `${_key}, n=${values.length}`;
+            const plotLabel = `${_key}, n=${values2.length}`;
             const overlayBins = numericBins(overlayTerm, data);
             const plot = Object.assign(_plot, {
               color: overlayTerm?.term?.values?.[key]?.color || null,
@@ -73,7 +80,7 @@ function init({ genomes }) {
             plot.boxplot.label = plotLabel;
             plots.push(plot);
           } else {
-            const plotLabel = `${sampleType}, n=${values.length}`;
+            const plotLabel = `${sampleType}, n=${values2.length}`;
             const plot = Object.assign(_plot, {
               key: sampleType
             });
@@ -89,10 +96,11 @@ function init({ genomes }) {
         charts[chart] = { chartId: chart, plots };
       }
       const returnData = {
-        absMin,
-        absMax,
+        absMin: q.removeOutliers ? outlierMin : absMin,
+        absMax: q.removeOutliers ? outlierMax : absMax,
         charts,
-        uncomputableValues: setUncomputableValues(uncomputableValues)
+        uncomputableValues: setUncomputableValues(uncomputableValues),
+        descrStats: statsAllSummary
       };
       res.send(returnData);
     } catch (e) {
@@ -114,24 +122,6 @@ function setHiddenPlots(term, plots) {
   }
   return plots;
 }
-function setDescrStats(boxplot, sortedValues) {
-  if (sortedValues.length < minSampleSize) return [{ id: "total", label: "Total", value: sortedValues.length }];
-  const mean = getMean(sortedValues);
-  const variance = getVariance(sortedValues);
-  const sd = Math.sqrt(variance);
-  return [
-    { id: "total", label: "Total", value: sortedValues.length },
-    { id: "min", label: "Minimum", value: roundValueAuto(sortedValues[0], true) },
-    { id: "p25", label: "1st quartile", value: roundValueAuto(boxplot.p25, true) },
-    { id: "median", label: "Median", value: roundValueAuto(boxplot.p50, true) },
-    { id: "mean", label: "Mean", value: roundValueAuto(mean, true) },
-    { id: "p75", label: "3rd quartile", value: roundValueAuto(boxplot.p75, true) },
-    { id: "max", label: "Maximum", value: roundValueAuto(sortedValues[sortedValues.length - 1], true) },
-    { id: "sd", label: "Standard deviation", value: isNaN(sd) ? null : roundValueAuto(sd, true) },
-    { id: "variance", label: "Variance", value: roundValueAuto(variance, true) },
-    { id: "iqr", label: "Inter-quartile range", value: roundValueAuto(boxplot.iqr, true) }
-  ];
-}
 function setUncomputableValues(values) {
   if (Object.entries(values)?.length) {
     return Object.entries(values).map(([label, v]) => ({ label, value: v }));