Merge pull request #1668 from nextstrain/node-name

Extend usefulness of tip labels

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+* Any `node_attr` in the tree can be used as a tip label, as well as the special-cases of strain-name and "none".
+  Previously we only allowed valid colorings.
+  ([#1668](https://github.com/nextstrain/auspice/pull/1668))
+* The specified tip label is surfaced more prominently within the the on-hover info boxes & on-click modals.
+  ([#1668](https://github.com/nextstrain/auspice/pull/1668))
+
 ## version 2.56.1 - 2024/08/22
 
 

src/actions/recomputeReduxState.js

@@ -578,9 +578,9 @@ const checkAndCorrectErrorsInState = (state, metadata, genomeMap, query, tree, v
 
   /* check tip label is valid. We use the function which generates the options for the dropdown here.
    * state.defaults.tipLabelKey is set by the JSON's display_defaults (default: strainSymbol)
-   * state.tipLabelKey is first set the JSON and then overridden via the URL query (default: state.defaults.tipLabelKey)
+   * state.tipLabelKey is initially the same value and then overridden via the URL query (default: state.defaults.tipLabelKey)
    */
-  const validTipLabels = collectAvailableTipLabelOptions(metadata.colorings).map((o) => o.value);
+  const validTipLabels = collectAvailableTipLabelOptions(tree.nodeAttrKeys, metadata.colorings).map((o) => o.value);
   if (!validTipLabels.includes(state.defaults.tipLabelKey)) {
     console.error("Invalid JSON-defined tip label:", state.defaults.tipLabelKey);
     state.defaults.tipLabelKey = strainSymbol;

src/components/controls/choose-tip-label.js

@@ -8,7 +8,7 @@ import CustomSelect from "./customSelect";
 
 @connect((state) => ({
   selected: state.controls.tipLabelKey,
-  options: collectAvailableTipLabelOptions(state.metadata.colorings)
+  options: collectAvailableTipLabelOptions(state.tree.nodeAttrKeys, state.metadata.colorings)
 }))
 class ChooseTipLabel extends React.Component {
   constructor(props) {
@@ -43,11 +43,17 @@ const WithTranslation = withTranslation()(ChooseTipLabel);
 export default WithTranslation;
 
 /**
- * collect available tip labellings -- currently this is based on the available
- * colorings but we ignore genotype (this could be implemented in the future,
- * but it's not straightforward)
+ * available tip labellings are all observed node_attrs as well as two special cases:
+ * no tip labels / hide & the node name ("sample name"). If a node_attr is a coloring
+ * then we display the coloring title.
+ * 
+ * Note that this only considers the main (LHS) tree. It is trivial for this function
+ * to consider the RHS tree, however the logic in `recomputeReduxState.js` doesn't
+ * make it straightforward to provide the RHS `nodeAttrKeys` when we construct these.
+ * 
+ * In the future we could add genotype, but it's not straightforward.
  */
-export function collectAvailableTipLabelOptions(colorings) {
+export function collectAvailableTipLabelOptions(nodeAttrKeys, colorings) {
   return [
     /**
      * We should consider using a Symbol for the 'none' value so that it
@@ -56,10 +62,7 @@ export function collectAvailableTipLabelOptions(colorings) {
      */
     {value: 'none', label: "none"},
     {value: strainSymbol, label: "Sample Name"},
-    ...Object.entries(colorings)
-      .filter((keyValue) => keyValue[0] !== 'gt' && keyValue[0] !== 'none')
-      .map(([key, value]) => {
-        return {value: key, label: value.title};
-      })
+    ...Array.from(nodeAttrKeys)
+      .map((key) => ({value: key, label: (colorings[key]||{})?.title||key}))
   ];
 }

src/components/tree/infoPanels/click.js

@@ -1,11 +1,12 @@
 import React from "react";
-import { isValueValid } from "../../../util/globals";
+import { isValueValid, strainSymbol } from "../../../util/globals";
 import { infoPanelStyles } from "../../../globalStyles";
 import { numericToCalendar } from "../../../util/dateHelpers";
 import { getTraitFromNode, getFullAuthorInfoFromNode, getVaccineFromNode,
   getAccessionFromNode, getUrlFromNode } from "../../../util/treeMiscHelpers";
 import { MutationTable } from "./MutationTable";
 import { lhsTreeId} from "../tree";
+import { nodeDisplayName } from "./helpers";
 
 export const styles = {
   container: {
@@ -241,9 +242,10 @@ const Trait = ({node, trait, colorings, isTerminal}) => {
  * @param  {Object}   props.colorings
  * @param  {Object}   props.observedMutations
  * @param  {function} props.geneSortFn
+ * @param  {string|symbol} props.tipLabelKey
  * @param  {function} props.t
  */
-const NodeClickedPanel = ({selectedNode, nodesLhsTree, nodesRhsTree, clearSelectedNode, colorings, observedMutations, geneSortFn, t}) => {
+const NodeClickedPanel = ({selectedNode, nodesLhsTree, nodesRhsTree, clearSelectedNode, colorings, observedMutations, geneSortFn, tipLabelKey, t}) => {
   if (!selectedNode) return null;
   const node = (selectedNode.treeId===lhsTreeId ? nodesLhsTree : nodesRhsTree)?.[selectedNode.idx];
   if (!node) {
@@ -252,25 +254,23 @@ const NodeClickedPanel = ({selectedNode, nodesLhsTree, nodesRhsTree, clearSelect
   }
   const panelStyle = { ...infoPanelStyles.panel};
   panelStyle.maxHeight = "70%";
+
+  /* We have `isTerminal` and `isTip` to differentiate between clicking on a branch leading to a tip
+   * vs clicking on the tip (circle) itself */
   const isTerminal = !node.hasChildren;
   const isTip = !selectedNode.isBranch;
-
-  const title = isTip ?
-    node.name :
-    isTerminal ?
-      `Branch leading to ${node.name}` :
-      "Internal branch";
+  const shouldShowNodeName = tipLabelKey!==strainSymbol;
 
   return (
     <div style={infoPanelStyles.modalContainer} onClick={() => clearSelectedNode(selectedNode)}>
       <div className={"panel"} style={panelStyle} onClick={(e) => stopProp(e)}>
-        <StrainName>{title}</StrainName>
+        <StrainName>{nodeDisplayName(t, node, tipLabelKey, !isTip)}</StrainName>
         <table>
           <tbody>
-            {!isTip && item(t("Number of terminal tips"), node.fullTipCount)}
+            {!isTerminal && item(t("Number of terminal tips"), node.fullTipCount)}
+            {shouldShowNodeName && item(t("Node name"), node.name)}
             {isTip && <VaccineInfo node={node} t={t}/>}
             <SampleDate isTerminal={isTerminal} node={node} t={t}/>
-            {!isTip && item("Node name", node.name)}
             {isTip && <PublicationInfo node={node} t={t}/>}
             {getTraitsToDisplay(node).map((trait) => (
               <Trait node={node} trait={trait} colorings={colorings} key={trait} isTerminal={isTerminal}/>

src/components/tree/infoPanels/helpers.js

@@ -0,0 +1,23 @@
+import { getTraitFromNode } from "../../../util/treeMiscHelpers";
+import { numericToCalendar } from "../../../util/dateHelpers";
+
+
+/**
+ * Attempt to display the best name we can for a node, depending on how we are looking at a node.
+ * The returned string will be rendered on a line of its own, so an empty string will look ok
+ * Future enhancement: we could examine the coloring metadata (if available) and format the value accordingly
+ */
+export function nodeDisplayName(t, node, tipLabelKey, branch) {
+  let tipLabel = getTraitFromNode(node, tipLabelKey)
+  if (tipLabelKey==='num_date' && tipLabel) tipLabel = numericToCalendar(tipLabel)
+  const terminal = !node.hasChildren;
+
+  if (branch) {
+    if (terminal) {
+      return tipLabel ? t("Branch leading to {{tipLabel}}", {tipLabel}) : t("Terminal branch") // hover + click
+    }
+    return t("Internal branch")  // branch click only
+  }
+  /* TIP */
+  return tipLabel;
+}

src/components/tree/infoPanels/hover.js

@@ -5,9 +5,10 @@ import { getTipColorAttribute } from "../../../util/colorHelpers";
 import { isColorByGenotype, decodeColorByGenotype } from "../../../util/getGenotype";
 import { getTraitFromNode, getDivFromNode, getVaccineFromNode,
   getFullAuthorInfoFromNode, getTipChanges, getBranchMutations } from "../../../util/treeMiscHelpers";
-import { isValueValid } from "../../../util/globals";
+import { isValueValid, strainSymbol } from "../../../util/globals";
 import { formatDivergence, getIdxOfInViewRootNode } from "../phyloTree/helpers";
 import { parseIntervalsOfNsOrGaps } from "./MutationTable";
+import { nodeDisplayName } from "./helpers";
 
 export const InfoLine = ({name, value, padBelow=false}) => {
   const renderValues = () => {
@@ -32,12 +33,6 @@ export const InfoLine = ({name, value, padBelow=false}) => {
   );
 };
 
-const StrainName = ({name}) => (
-  <div style={infoPanelStyles.tooltipHeading}>
-    {name}
-  </div>
-);
-
 /**
  * A React component to display information about the branch's time & divergence (where applicable)
  * @param  {Object} props
@@ -267,14 +262,13 @@ const BranchMutations = ({node, geneSortFn, observedMutations, t}) => {
  * @param  {Object} props
  * @param  {Object} props.node  branch node which is currently highlighted
  */
-const BranchDescendents = ({node, t}) => {
+const BranchDescendants = ({node, t, tipLabelKey}) => {
   const [name, value] = node.fullTipCount === 1 ?
-    [t("Branch leading to"), node.name] :
+    [nodeDisplayName(t, node, tipLabelKey, true), ""] :
     [t("Number of descendants")+":", node.fullTipCount];
   return <InfoLine name={name} value={value} padBelow/>;
 };
 
-
 /**
  * A React component to show vaccine information, if present
  * @param  {Object} props
@@ -399,17 +393,20 @@ const HoverInfoPanel = ({
   colorings,
   geneSortFn,
   observedMutations,
+  tipLabelKey,
   t
 }) => {
   if (!selectedNode) return null
   const node = selectedNode.node.n; // want the redux node, not the phylo node
   const idxOfInViewRootNode = getIdxOfInViewRootNode(node);
-
   return (
     <Container node={node} panelDims={panelDims}>
       {selectedNode.isBranch===false ? (
         <>
-          <StrainName name={node.name}/>
+          <div style={infoPanelStyles.tooltipHeading}>
+            {nodeDisplayName(t, node, tipLabelKey, false)}
+          </div>
+          {tipLabelKey!==strainSymbol && <InfoLine name="Node name:" value={node.name}/>}
           <VaccineInfo node={node} t={t}/>
           <TipMutations node={node} t={t}/>
           <BranchLength node={node} t={t}/>
@@ -419,7 +416,7 @@ const HoverInfoPanel = ({
         </>
       ) : (
         <>
-          <BranchDescendents node={node} t={t}/>
+          <BranchDescendants node={node} t={t} tipLabelKey={tipLabelKey}/>
           <BranchMutations node={node} geneSortFn={geneSortFn} observedMutations={observedMutations} t={t}/>
           <BranchLength node={node} t={t}/>
           <ColorBy node={node} colorBy={colorBy} colorByConfidence={colorByConfidence} colorScale={colorScale} colorings={colorings}/>

src/components/tree/tree.js

@@ -206,6 +206,7 @@ class Tree extends React.Component {
           geneSortFn={this.state.geneSortFn}
           observedMutations={this.props.tree.observedMutations}
           panelDims={{width: this.props.width, height: this.props.height, spaceBetweenTrees}}
+          tipLabelKey={this.props.tipLabelKey}
           t={t}
         />
         <NodeClickedPanel
@@ -216,6 +217,7 @@ class Tree extends React.Component {
           observedMutations={this.props.tree.observedMutations}
           colorings={this.props.colorings}
           geneSortFn={this.state.geneSortFn}
+          tipLabelKey={this.props.tipLabelKey}
           t={t}
         />
         {this.props.showTangle && this.state.tree && this.state.treeToo ? (

src/util/treeJsonProcessing.js

@@ -10,11 +10,15 @@ const pseudoRandomName = () => (Math.random()*1e32).toString(36).slice(0, 6);
  * node.hasChildren {bool}
  * node.arrayIdx  {integer} - the index of the node in the nodes array
  * @param  {array} nodes redux tree nodes
- * @return {array} input array (kinda unnecessary)
+ * @return {Object} ret 
+ * @return {Set} ret.nodeAttrKeys collection of all `node_attr` keys whose values are Objects
+ * @return {Array} ret.nodes input array (kinda unnecessary)
+ * 
  * side-effects: node.hasChildren (bool) and node.arrayIdx (INT) for each node in nodes
  */
 const processNodes = (nodes) => {
   const nodeNamesSeen = new Set();
+  const nodeAttrKeys = new Set();
   calcFullTipCounts(nodes[0]); /* recursive. Uses d.children */
   nodes.forEach((d, idx) => {
     d.arrayIdx = idx; /* set an index so that we can access visibility / nodeColors if needed */
@@ -32,8 +36,15 @@ const processNodes = (nodes) => {
       console.warn(`Tree node detected with a duplicate name. Changing '${prev}' to '${d.name}' and continuing...`);
     }
     nodeNamesSeen.add(d.name);
+
+    for (const [attrKey, attrValue] of Object.entries(d.node_attrs || {})) {
+      if (typeof attrValue === 'object' && 'value' in attrValue) {
+        nodeAttrKeys.add(attrKey)
+      }
+    }
+
   });
-  return nodes;
+  return {nodeAttrKeys, nodes};
 };
 
 /**
@@ -165,7 +176,7 @@ export const treeJsonToState = (treeJSON) => {
     nodesArray.push(...flattenTree(treeRootNode));
   }
   nodesArray.unshift(makeSubtreeRootNode(nodesArray, subtreeIndicies));
-  const nodes = processNodes(nodesArray);
+  const {nodeAttrKeys, nodes} = processNodes(nodesArray);
   addParentInfo(nodesArray);
   const vaccines = nodes.filter((d) => {
     const v = getVaccineFromNode(d);
@@ -174,6 +185,6 @@ export const treeJsonToState = (treeJSON) => {
   const availableBranchLabels = processBranchLabelsInPlace(nodesArray);
   const observedMutations = collectObservedMutations(nodesArray);
   return Object.assign({}, getDefaultTreeState(), {
-    nodes, vaccines, observedMutations, availableBranchLabels, loaded: true
+    nodes, nodeAttrKeys, vaccines, observedMutations, availableBranchLabels, loaded: true
   });
 };