Merge pull request #1373: tree: Add toggle to focus on selected

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+* Added an experimental "Focus on Selected" toggle in the sidebar.
+  When focusing on selected nodes, nodes that do not match the filter will occupy less vertical space on the tree.
+  Only applicable to rectangular and radial layouts.
+  ([#1373](https://github.com/nextstrain/auspice/pull/1373))
+
 ## version 2.58.0 - 2024/09/12
 
 

src/actions/types.js

@@ -7,6 +7,7 @@ export const SEARCH_INPUT_CHANGE = "SEARCH_INPUT_CHANGE";
 export const CHANGE_LAYOUT = "CHANGE_LAYOUT";
 export const CHANGE_BRANCH_LABEL = "CHANGE_BRANCH_LABEL";
 export const CHANGE_DISTANCE_MEASURE = "CHANGE_DISTANCE_MEASURE";
+export const TOGGLE_FOCUS = "TOGGLE_FOCUS";
 export const CHANGE_DATES_VISIBILITY_THICKNESS = "CHANGE_DATES_VISIBILITY_THICKNESS";
 export const CHANGE_ABSOLUTE_DATE_MIN = "CHANGE_ABSOLUTE_DATE_MIN";
 export const CHANGE_ABSOLUTE_DATE_MAX = "CHANGE_ABSOLUTE_DATE_MAX";

src/components/controls/controls.tsx

@@ -18,12 +18,14 @@ import TransmissionLines from './transmission-lines';
 import NormalizeFrequencies from "./frequency-normalization";
 import AnimationOptions from "./animation-options";
 import { PanelSection } from "./panelSection";
+import ToggleFocus from "./toggle-focus";
 import ToggleTangle from "./toggle-tangle";
 import Language from "./language";
 import { ControlsContainer } from "./styles";
 import FilterData, {FilterInfo} from "./filter";
 import {TreeInfo, MapInfo, AnimationOptionsInfo, PanelLayoutInfo,
-  ExplodeTreeInfo, EntropyInfo, FrequencyInfo, MeasurementsInfo} from "./miscInfoText";
+  ExplodeTreeInfo, EntropyInfo, FrequencyInfo, MeasurementsInfo,
+  ToggleFocusInfo} from "./miscInfoText";
 import { ControlHeader } from "./controlHeader";
 import MeasurementsOptions from "./measurementsOptions";
 import { RootState } from "../../store";
@@ -64,6 +66,7 @@ function Controls() {
           tooltip={TreeInfo}
           options={<>
             <ChooseLayout />
+            <ToggleFocus tooltip={ToggleFocusInfo} />
             <ChooseMetric />
             <ChooseBranchLabelling />
             <ChooseTipLabel />

src/components/controls/miscInfoText.js

@@ -64,3 +64,11 @@ export const ExplodeTreeInfo = (
     It works best when the trait doesn't change value too frequently.
   </>
 );
+
+export const ToggleFocusInfo = (
+  <>This functionality is experimental and should be treated with caution!
+    <br/>When focusing on selected nodes, nodes that do not match the
+    filter will occupy less vertical space on the tree. Only applicable to
+    rectangular and radial layouts.
+  </>
+);

src/components/controls/toggle-focus.tsx

@@ -0,0 +1,54 @@
+import React from "react";
+import { connect } from "react-redux";
+import { FaInfoCircle } from "react-icons/fa";
+import { Dispatch } from "@reduxjs/toolkit";
+import Toggle from "./toggle";
+import { SidebarIconContainer, StyledTooltip } from "./styles";
+import { TOGGLE_FOCUS } from "../../actions/types";
+import { RootState } from "../../store";
+
+
+function ToggleFocus({ tooltip, focus, layout, dispatch, mobileDisplay }: {
+  tooltip: React.ReactElement;
+  focus: boolean;
+  layout: "rect" | "radial" | "unrooted" | "clock" | "scatter";
+  dispatch: Dispatch;
+  mobileDisplay: boolean;
+}) {
+  // Focus functionality is only available to layouts that have the concept of a unitless y-axis
+  const validLayouts = new Set(["rect", "radial"]);
+  if (!validLayouts.has(layout)) return <></>;
+
+  const label = (
+    <div style={{ display: "flex", alignItems: "center" }}>
+      <span style={{ marginRight: "5px" }}>Focus on Selected</span>
+      {tooltip && !mobileDisplay && (
+        <>
+          <SidebarIconContainer style={{ display: "inline-flex" }} data-tip data-for="toggle-focus">
+            <FaInfoCircle />
+          </SidebarIconContainer>
+          <StyledTooltip place="bottom" type="dark" effect="solid" id="toggle-focus">
+            {tooltip}
+          </StyledTooltip>
+        </>
+      )}
+    </div>
+  );
+
+  return (
+    <Toggle
+      display
+      isExperimental={true}
+      on={focus}
+      callback={() => dispatch({ type: TOGGLE_FOCUS })}
+      label={label}
+      style={{ paddingBottom: "10px" }}
+    />
+  );
+}
+
+export default connect((state: RootState) => ({
+  focus: state.controls.focus,
+  layout: state.controls.layout,
+  mobileDisplay: state.general.mobileDisplay,
+}))(ToggleFocus);

src/components/controls/toggle.js

@@ -1,4 +1,5 @@
 import React from "react";
+import { ImLab } from "react-icons/im";
 import styled from 'styled-components';
 import { SidebarSubtitle } from "./styles";
 
@@ -28,6 +29,11 @@ const ToggleSubtitle = styled(SidebarSubtitle)`
   width: 200px;
 `;
 
+const ExperimentalIcon = styled.span`
+  color: ${(props) => props.theme.color};
+  margin-right: 5px;
+`
+
 const Slider = styled.div`
   & {
     position: absolute;
@@ -73,11 +79,16 @@ const Input = styled.input`
 `;
 
 
-const Toggle = ({display, on, callback, label, style={}}) => {
+const Toggle = ({display, isExperimental = false, on, callback, label, style={}}) => {
   if (!display) return null;
 
   return (
     <ToggleContainer style={style}>
+      {isExperimental &&
+        <ExperimentalIcon>
+          <ImLab />
+        </ExperimentalIcon>
+      }
       <ToggleBackground>
         <Input type="checkbox" checked={on} onChange={callback}/>
         <Slider/>

src/components/tree/index.ts

@@ -8,6 +8,7 @@ const Tree = connect((state: RootState) => ({
   selectedNode: state.controls.selectedNode,
   dateMinNumeric: state.controls.dateMinNumeric,
   dateMaxNumeric: state.controls.dateMaxNumeric,
+  filters: state.controls.filters,
   quickdraw: state.controls.quickdraw,
   colorBy: state.controls.colorBy,
   colorByConfidence: state.controls.colorByConfidence,
@@ -16,6 +17,7 @@ const Tree = connect((state: RootState) => ({
   temporalConfidence: state.controls.temporalConfidence,
   distanceMeasure: state.controls.distanceMeasure,
   explodeAttr: state.controls.explodeAttr,
+  focus: state.controls.focus,
   colorScale: state.controls.colorScale,
   colorings: state.metadata.colorings,
   genomeMap: state.entropy.genomeMap,

src/components/tree/phyloTree/change.js

@@ -270,6 +270,7 @@ export const change = function change({
   tipRadii = undefined,
   branchThickness = undefined,
   /* other data */
+  focus = undefined,
   scatterVariables = undefined
 }) {
   // console.log("\n** phylotree.change() (time since last run:", Date.now() - this.timeLastRenderRequested, "ms) **\n\n");
@@ -323,7 +324,7 @@ export const change = function change({
   }
 
   if (changeNodeOrder) {
-    setDisplayOrder(this.nodes);
+    setDisplayOrder({nodes: this.nodes, focus});
     this.setDistance();
   }
 
@@ -359,7 +360,9 @@ export const change = function change({
   /* run calculations as needed - these update properties on the phylotreeNodes (similar to updateNodesWithNewData) */
   /* distance */
   if (newDistance || updateLayout) this.setDistance(newDistance);
-  /* layout (must run after distance) */
+  /* focus */
+  if (updateLayout) setDisplayOrder({nodes: this.nodes, focus});
+  /* layout (must run after distance and focus) */
   if (newDistance || newLayout || updateLayout || changeNodeOrder) {
     this.setLayout(newLayout || this.layout, scatterVariables);
   }

src/components/tree/phyloTree/helpers.js

@@ -1,6 +1,8 @@
 /* eslint-disable no-param-reassign */
 import { max } from "d3-array";
 import {getTraitFromNode, getDivFromNode, getBranchMutations} from "../../../util/treeMiscHelpers";
+import { NODE_VISIBLE } from "../../../util/globals";
+import { timerStart, timerEnd } from "../../../util/perf";
 
 /** get a string to be used as the DOM element ID
  * Note that this cannot have any "special" characters
@@ -33,18 +35,22 @@ export const applyToChildren = (phyloNode, func) => {
  * of nodes in a rectangular tree.
  * If `yCounter` is undefined then we wish to hide the node and all descendants of it
  * @param {PhyloNode} node
+ * @param {function} incrementer
  * @param {int|undefined} yCounter
  * @sideeffect modifies node.displayOrder and node.displayOrderRange
  * @returns {int|undefined} current yCounter after assignment to the tree originating from `node`
  */
-export const setDisplayOrderRecursively = (node, yCounter) => {
+export const setDisplayOrderRecursively = (node, incrementer, yCounter) => {
   const children = node.n.children; // (redux) tree node
   if (children && children.length) {
     for (let i = children.length - 1; i >= 0; i--) {
-      yCounter = setDisplayOrderRecursively(children[i].shell, yCounter);
+      yCounter = setDisplayOrderRecursively(children[i].shell, incrementer, yCounter);
     }
   } else {
-    node.displayOrder = (node.n.fullTipCount===0 || yCounter===undefined) ? yCounter : ++yCounter;
+    if (node.n.fullTipCount !== 0 && yCounter !== undefined) {
+      yCounter += incrementer(node);
+    }
+    node.displayOrder = yCounter;
     node.displayOrderRange = [yCounter, yCounter];
     return yCounter;
   }
@@ -77,26 +83,63 @@ function _getSpaceBetweenSubtrees(numSubtrees, numTips) {
  * PhyloTree can subsequently use this information. Accessed by prototypes
  * rectangularLayout, radialLayout, createChildrenAndParents
  * side effects: <phyloNode>.displayOrder (i.e. in the redux node) and <phyloNode>.displayOrderRange
- * @param {Array<PhyloNode>} nodes
+ * @param {Object} props
+ * @param {Array<PhyloNode>} props.nodes
+ * @param {boolean} props.focus
  * @returns {undefined}
  */
-export const setDisplayOrder = (nodes) => {
+export const setDisplayOrder = ({nodes, focus}) => {
+  timerStart("setDisplayOrder");
+
   const numSubtrees = nodes[0].n.children.filter((n) => n.fullTipCount!==0).length;
-  const numTips = nodes[0].n.fullTipCount;
+  const numTips = focus ? nodes[0].n.tipCount : nodes[0].n.fullTipCount;
   const spaceBetweenSubtrees = _getSpaceBetweenSubtrees(numSubtrees, numTips);
+
+  // No focus: 1 unit per node
+  let incrementer = (_node) => 1;
+
+  if (focus) {
+    const nVisible = nodes[0].n.tipCount;
+    const nTotal = nodes[0].n.fullTipCount;
+
+    let yProportionFocused = 0.8;
+    // Adjust for a small number of visible tips (n<4)
+    yProportionFocused = Math.min(yProportionFocused, nVisible / 5);
+    // Adjust for a large number of visible tips (>80% of all tips)
+    yProportionFocused = Math.max(yProportionFocused, nVisible / nTotal);
+
+    const yPerFocused = (yProportionFocused * nTotal) / nVisible;
+    const yPerUnfocused = ((1 - yProportionFocused) * nTotal) / (nTotal - nVisible);
+
+    incrementer = (() => {
+      let previousWasVisible = false;
+      return (node) => {
+        // Focus if the current node is visible or if the previous node was visible (for symmetric padding)
+        const y = (node.visibility === NODE_VISIBLE || previousWasVisible) ? yPerFocused : yPerUnfocused;
+
+        // Update for the next node
+        previousWasVisible = node.visibility === NODE_VISIBLE;
+
+        return y;
+      }
+    })();
+  }
+
   let yCounter = 0;
   /* iterate through each subtree, and add padding between each */
   for (const subtree of nodes[0].n.children) {
     if (subtree.fullTipCount===0) { // don't use screen space for this subtree
-      setDisplayOrderRecursively(nodes[subtree.arrayIdx], undefined);
+      setDisplayOrderRecursively(nodes[subtree.arrayIdx], incrementer, undefined);
     } else {
-      yCounter = setDisplayOrderRecursively(nodes[subtree.arrayIdx], yCounter);
+      yCounter = setDisplayOrderRecursively(nodes[subtree.arrayIdx], incrementer, yCounter);
       yCounter+=spaceBetweenSubtrees;
     }
   }
   /* note that nodes[0] is a dummy node holding each subtree */
   nodes[0].displayOrder = undefined;
   nodes[0].displayOrderRange = [undefined, undefined];
+
+  timerEnd("setDisplayOrder");
 };
 
 

src/components/tree/phyloTree/renderers.js

@@ -7,6 +7,7 @@ import { getEmphasizedColor } from "../../../util/colorHelpers";
  * @param {d3 selection} svg      -- the svg into which the tree is drawn
  * @param {string} layout         -- the layout to be used, e.g. "rect"
  * @param {string} distance       -- the property used as branch length, e.g. div or num_date
+ * @param {string} focus          -- whether to focus on filtered nodes
  * @param {object} parameters     -- an object that contains options that will be added to this.params
  * @param {object} callbacks      -- an object with call back function defining mouse behavior
  * @param {array} branchThickness -- array of branch thicknesses (same ordering as tree nodes)
@@ -21,7 +22,7 @@ import { getEmphasizedColor } from "../../../util/colorHelpers";
  * @param {object} scatterVariables  -- {x, y} properties to map nodes => scatterplot (only used if layout="scatter")
  * @return {null}
  */
-export const render = function render(svg, layout, distance, parameters, callbacks, branchThickness, visibility, drawConfidence, vaccines, branchStroke, tipStroke, tipFill, tipRadii, dateRange, scatterVariables) {
+export const render = function render(svg, layout, distance, focus, parameters, callbacks, branchThickness, visibility, drawConfidence, vaccines, branchStroke, tipStroke, tipFill, tipRadii, dateRange, scatterVariables) {
   timerStart("phyloTree render()");
   this.svg = svg;
   this.params = Object.assign(this.params, parameters);
@@ -40,7 +41,7 @@ export const render = function render(svg, layout, distance, parameters, callbac
   });
 
   /* set x, y values & scale them to the screen */
-  setDisplayOrder(this.nodes);
+  setDisplayOrder({nodes: this.nodes, focus});
   this.setDistance(distance);
   this.setLayout(layout, scatterVariables);
   this.mapToScreen();

src/components/tree/reactD3Interface/change.js

@@ -7,6 +7,14 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
   const oldTreeRedux = mainTree ? oldProps.tree : oldProps.treeToo;
   const newTreeRedux = mainTree ? newProps.tree : newProps.treeToo;
 
+  /* zoom to a clade / reset zoom to entire tree */
+  const zoomChange = oldTreeRedux.idxOfInViewRootNode !== newTreeRedux.idxOfInViewRootNode;
+
+  const dateRangeChange = oldProps.dateMinNumeric !== newProps.dateMinNumeric ||
+                          oldProps.dateMaxNumeric !== newProps.dateMaxNumeric;
+
+  const filterChange = oldProps.filters !== newProps.filters;
+
   /* do any properties on the tree object need to be updated?
   Note that updating properties itself won't trigger any visual changes */
   phylotree.dateRange = [newProps.dateMinNumeric, newProps.dateMaxNumeric];
@@ -47,6 +55,20 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
   /* explode! */
   if (oldProps.explodeAttr !== newProps.explodeAttr) {
     args.changeNodeOrder = true;
+    args.focus = newProps.focus;
+  }
+
+  /* enable/disable focus */
+  if (oldProps.focus !== newProps.focus) {
+    args.focus = newProps.focus;
+    args.updateLayout = true;
+  }
+  /* re-focus on changes */
+  else if (oldProps.focus === true &&
+           newProps.focus === true &&
+           (zoomChange || dateRangeChange || filterChange)) {
+    args.focus = true;
+    args.updateLayout = true;
   }
 
   /* change in key used to define branch labels, tip labels */
@@ -86,8 +108,7 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
   }
 
 
-  /* zoom to a clade / reset zoom to entire tree */
-  if (oldTreeRedux.idxOfInViewRootNode !== newTreeRedux.idxOfInViewRootNode) {
+  if (zoomChange) {
     const rootNode = phylotree.nodes[newTreeRedux.idxOfInViewRootNode];
     args.zoomIntoClade = rootNode;
     newState.selectedNode = {};

src/components/tree/reactD3Interface/initialRender.js

@@ -22,6 +22,7 @@ export const renderTree = (that, main, phylotree, props) => {
     select(ref),
     props.layout,
     props.distanceMeasure,
+    props.focus,
     { /* parameters (modifies PhyloTree's defaults) */
       grid: true,
       confidence: props.temporalConfidence.display,

src/components/tree/tangle/untangling.js

@@ -78,6 +78,7 @@ export const untangleTreeToo = (phylotree1, phylotree2) => {
   // const init_corr = calculatePearsonCorrelationCoefficient(phylotree1, phylotree2);
   flipChildrenPostorder(phylotree1, phylotree2);
   // console.log(`Untangling ${init_corr} -> ${calculatePearsonCorrelationCoefficient(phylotree1, phylotree2)}`);
-  setDisplayOrder(phylotree2.nodes);
+  // TODO: check the value of focus
+  setDisplayOrder({nodes: phylotree2.nodes, focus: false});
   // console.timeEnd("untangle");
 };