Group nuc mutations on-hover

Grouping nucleotide mutations (as per previous commits) while hovering on branches is really helpful for understanding the tree. The penalty is the use of more space, and so I've chosen to not group AA mutations here; one can shift+click on the branch to see these grouped if needed.
nextstrain · Feb 14, 2022 · 69b53a0 · 69b53a0
1 parent 9971471
commit 69b53a0
Show file tree

Hide file tree

Showing 2 changed files with 28 additions and 27 deletions.
diff --git a/src/components/tree/infoPanels/hover.js b/src/components/tree/infoPanels/hover.js
@@ -4,9 +4,10 @@ import { numericToCalendar } from "../../../util/dateHelpers";
 import { getTipColorAttribute } from "../../../util/colorHelpers";
 import { isColorByGenotype, decodeColorByGenotype } from "../../../util/getGenotype";
 import { getTraitFromNode, getDivFromNode, getVaccineFromNode,
-  getFullAuthorInfoFromNode, getTipChanges } from "../../../util/treeMiscHelpers";
+  getFullAuthorInfoFromNode, getTipChanges, getBranchMutations } from "../../../util/treeMiscHelpers";
 import { isValueValid } from "../../../util/globals";
 import { formatDivergence, getIdxOfInViewRootNode } from "../phyloTree/helpers";
+import { parseIntervalsOfNsOrGaps } from "./MutationTable";
 
 const InfoLine = ({name, value, padBelow=false}) => {
   const renderValues = () => {
@@ -173,41 +174,39 @@ const TipMutations = ({node, t}) => {
  * @param  {Object} props
  * @param  {Object} props.node     branch node which is currently highlighted
  * @param  {Object} props.geneSortFn function to sort a list of genes
+ * @param  {Object} props.observedMutations counts of all observed mutations across the tree
+
  */
-const BranchMutations = ({node, geneSortFn, t}) => {
+const BranchMutations = ({node, geneSortFn, observedMutations, t}) => {
   if (!node.branch_attrs || !node.branch_attrs.mutations) return null;
   const elements = []; // elements to render
   const mutations = node.branch_attrs.mutations;
 
-  /* --------- NUCLEOTIDE MUTATIONS --------------- */
-  /* Nt mutations are found at `mutations.nuc` -> Array of strings */
-  if (mutations.nuc && mutations.nuc.length) {
-    const nDisplay = 9; // max number of mutations to display
-
-    const isMutGap = (mut) => mut.slice(-1) === "-" || mut.slice(0, 1) === "-";
-    const isMutUnknown = (mut) => mut.slice(-1) === "N" || mut.slice(0, 1) === "N";
+  const categorisedMutations = getBranchMutations(node, observedMutations);
 
-    // gather muts which aren't to/from a gap or a "N"
-    const nucs = mutations.nuc.filter((mut) => (!isMutGap(mut) && !(isMutUnknown(mut))));
-    const nucLen = nucs.length; // number of mutations that exist without N/-
+  const subset = (muts, maxNum) =>
+    muts.slice(0, Math.min(maxNum, muts.length)).join(", ") +
+    (muts.length > maxNum ? ` + ${muts.length-maxNum} more` : '');
 
-    let m = nucs.slice(0, Math.min(nDisplay, nucLen)).join(", ");
-    if (nucLen > nDisplay) {
-      m += " + " + t("{{x}} more", {x: nucLen - nDisplay});
+  /* --------- NUCLEOTIDE MUTATIONS --------------- */
+  if (categorisedMutations.nuc) {
+    const nDisplay = 5; // max number of mutations to display per category
+    if (categorisedMutations.nuc.unique.length) {
+      elements.push(<InfoLine name='Unique Nucleotide mutations:' value={subset(categorisedMutations.nuc.unique, nDisplay)} key="nuc_unique"/>);
     }
-
-    if (nucLen !== 0) {
-      elements.push(<InfoLine name={t("Nucleotide mutations")+":"} value={m} key="nuc"/>);
+    if (categorisedMutations.nuc.homoplasies.length) {
+      elements.push(<InfoLine name='Homoplasic mutations:' value={subset(categorisedMutations.nuc.homoplasies, nDisplay)} key="nuc_homoplasies"/>);
     }
-
-    const nGapMutations = mutations.nuc.filter((mut) => isMutGap(mut)).length;
-    if (nGapMutations) {
-      elements.push(<InfoLine name={`${t("Gaps")} ("-"):`} value={nGapMutations} key="gaps"/>);
+    if (categorisedMutations.nuc.reversionsToRoot.length) {
+      elements.push(<InfoLine name='Reversions to Root:' value={categorisedMutations.nuc.reversionsToRoot.length} key="nuc_rtr"/>);
     }
-
-    const nUnknownMutations = mutations.nuc.filter((mut) => isMutUnknown(mut)).length;
-    if (nUnknownMutations) {
-      elements.push(<InfoLine name='Ns:' value={nUnknownMutations} key="Ns"/>);
+    if (categorisedMutations.nuc.gaps.length) {
+      const value = `${parseIntervalsOfNsOrGaps(categorisedMutations.nuc.gaps).length} regions, ${categorisedMutations.nuc.gaps.length}bp.`;
+      elements.push(<InfoLine name='Gaps:' value={value} key="nuc_gaps"/>);
+    }
+    if (categorisedMutations.nuc.ns.length) {
+      const value = `${parseIntervalsOfNsOrGaps(categorisedMutations.nuc.ns).length} regions, ${categorisedMutations.nuc.ns.length}bp.`;
+      elements.push(<InfoLine name='Ns:' value={value} key="nuc_ns"/>);
     }
   } else {
     elements.push(<InfoLine name={t("No nucleotide mutations")} value="" key="nuc"/>);
@@ -390,6 +389,7 @@ const HoverInfoPanel = ({
   panelDims,
   colorings,
   geneSortFn,
+  observedMutations,
   t
 }) => {
   if (selectedNode.event !== "hover") return null;
@@ -411,7 +411,7 @@ const HoverInfoPanel = ({
       ) : (
         <>
           <BranchDescendents node={node} t={t}/>
-          <BranchMutations node={node} geneSortFn={geneSortFn} t={t}/>
+          <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}/>
           <Comment>

diff --git a/src/components/tree/tree.js b/src/components/tree/tree.js
@@ -191,6 +191,7 @@ class Tree extends React.Component {
           colorScale={this.props.colorScale}
           colorings={this.props.metadata.colorings}
           geneSortFn={this.state.geneSortFn}
+          observedMutations={this.props.tree.observedMutations}
           panelDims={{width: this.props.width, height: this.props.height, spaceBetweenTrees}}
           t={t}
         />