Merge pull request #1827 from nextstrain/measurements-x-scale

Limit x-axis by filtered measurements

Author: joverlee521

CHANGELOG.md

@@ -3,6 +3,8 @@
 * Fix bug where app crashed if measurements JSON did not define thresholds ([#1802](https://github.com/nextstrain/auspice/pull/1802))
 * Fix bug where measurements display did not honor the default `measurements_display` ([#1802](https://github.com/nextstrain/auspice/pull/1802))
 * Only display download-JSON button if the dataset name can be parsed from pathname ([#1804](https://github.com/nextstrain/auspice/pull/1804))
+* Fix bug where measurements panel did not display means for measurements that had an "undefined" coloring ([#1827](https://github.com/nextstrain/auspice/pull/1827))
+* Measurement panel's x-axis min/max values are now limited by visible measurements ([#1827](https://github.com/nextstrain/auspice/pull/1827))
 
 ## version 2.56.0 - 2024/07/01
 

src/components/measurements/index.js

@@ -1,4 +1,4 @@
-import React, { useRef, useEffect, useMemo, useState } from "react";
+import React, { useCallback, useRef, useEffect, useState } from "react";
 import { useSelector } from "react-redux";
 import { isEqual, orderBy } from "lodash";
 import { NODE_VISIBLE } from "../../util/globals";
@@ -41,6 +41,17 @@ const useDeepCompareMemo = (value) => {
   return ref.current;
 };
 
+/**
+ * A wrapper around React's useCallback hook that does a deep comparison of the
+ * dependencies.
+ * @param {function} fn
+ * @param {Array} dependencies
+ * @returns
+ */
+const useDeepCompareCallback = (fn, dependencies) => {
+  return useCallback(fn, dependencies.map(useDeepCompareMemo))
+}
+
 // Checks visibility against global NODE_VISIBLE
 const isVisible = (visibility) => visibility === NODE_VISIBLE;
 
@@ -159,9 +170,9 @@ const MeasurementsPlot = ({height, width, showLegend, setPanelTitle}) => {
   }
   const groupedMeasurements = groupMeasurements(filteredMeasurements, groupBy, groupByValueOrder);
 
-  // Memoize D3 scale functions to allow deep comparison to work below for svgData
-  const xScale = useMemo(() => createXScale(width, measurements), [width, measurements]);
-  const yScale = useMemo(() => createYScale(), []);
+  // Cache D3 scale functions to allow deep comparison to work below for svgData
+  const xScale = useDeepCompareCallback(createXScale(width, filteredMeasurements), [width, filteredMeasurements]);
+  const yScale = useCallback(createYScale(), []);
   // Memoize all data needed for basic SVG to avoid extra re-drawings
   const svgData = useDeepCompareMemo({
     containerHeight: height,
@@ -172,8 +183,8 @@ const MeasurementsPlot = ({height, width, showLegend, setPanelTitle}) => {
     groupingOrderedValues,
     groupedMeasurements
   });
-  // Memoize handleHover function to avoid extra useEffect calls
-  const handleHover = useMemo(() => (data, dataType, mouseX, mouseY, colorByAttr=null) => {
+  // Cache handleHover function to avoid extra useEffect calls
+  const handleHover = useCallback((data, dataType, mouseX, mouseY, colorByAttr=null) => {
     let newHoverData = null;
     if (data !== null) {
       // Set color-by attribute as title if provided

src/components/measurements/measurementsD3.js

@@ -58,15 +58,24 @@ const getSubplotDOMId = (groupingValueIndex) => `measurement_subplot_${groupingV
 /**
  * Creates the D3 linear scale for the x-axis with the provided measurements'
  * values as the domain and the panelWidth with hard-coded padding values as
- * the range. Expected to be shared across all subplots.
+ * the range. The optional paddingProportion can be provided to include additional
+ * padding for the domain. Expected to be shared across all subplots.
  * @param {number} panelWidth
  * @param {Array<Object>} measurements
+ * @param {number} [paddingProportion=0.1]
  * @returns {function}
  */
-export const createXScale = (panelWidth, measurements) => {
+export const createXScale = (panelWidth, measurements, paddingProportion = 0.1) => {
+  // Padding the xScale based on proportion
+  // Copied from https://github.com/d3/d3-scale/issues/150#issuecomment-561304239
+  function padLinear([x0, x1], k) {
+    const dx = (x1 - x0) * k / 2;
+    return [x0 - dx, x1 + dx];
+  }
+
   return (
     scaleLinear()
-      .domain(extent(measurements, (m) => m.value))
+      .domain(padLinear(extent(measurements, (m) => m.value), paddingProportion))
       .range([layout.leftPadding, panelWidth - layout.rightPadding])
       .nice()
   );
@@ -377,8 +386,13 @@ export const drawMeansForColorBy = (ref, svgData, treeStrainColors, legendValues
     const ySpacing = (layout.subplotHeight - 4 * layout.subplotPadding) / (numberOfColorByAttributes - 1);
     let yValue = layout.subplotPadding;
     // Order the color groups by the legend value order so that we have a stable order for the means
-    legendValues
-      .filter((attribute) => String(attribute) in colorByGroups)
+    const orderedColorGroups = orderBy(
+      Object.keys(colorByGroups),
+      (key) => legendValues.indexOf(key),
+      "asc"
+    );
+
+    orderedColorGroups
       .forEach((attribute) => {
         const {color, values} = colorByGroups[attribute];
         drawMeanAndStandardDeviation(