Zoom to visible nodes

This commit re-implements the "zoom to selected" function in the tree panel to emphasize visible nodes by expanding their "yValues" to take up 80% of the vertical span of the panel. Notes on implementation details:

- I mirrored redux dataflow of "distanceMeasure" and "layout" to create a new redux variable of "treeZoom". This is defaults to "even" but is updated to "zoom" when clicking the "zoom to selected" tab. Further clicks increment the redux variable to "zoom-2", "zoom-3", etc... and clicking "reset layout" restores it to "even".
- A PhyloTree redraw is triggered when redux treeZoom variable is updated. This allows filters to change, etc... without triggering immediate changes to layout, but then clicking "zoom to selected" will redraw layout to emphasize currently selected nodes.
- phylotree.layouts contains the actual logic in the calcYValues function. This dynamically sets node.n.yValue based on node.visibility, so that calls to other layout functions like rectangularLayout will have updated node.n.yValue from which to construct node.y.

src/actions/recomputeReduxState.js

@@ -58,6 +58,9 @@ const modifyStateViaURLQuery = (state, query) => {
   if (query.m && state.branchLengthsToDisplay === "divAndDate") {
     state["distanceMeasure"] = query.m;
   }
+  if (query.z) {
+    state["treeZoom"] = query.z;
+  }
   if (query.c) {
     state["colorBy"] = query.c;
   }

src/actions/types.js

@@ -11,6 +11,7 @@ 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 CHANGE_TREE_ZOOM = "CHANGE_TREE_ZOOM";
 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/tree/index.js

@@ -13,6 +13,7 @@ const Tree = connect((state) => ({
   scatterVariables: state.controls.scatterVariables,
   temporalConfidence: state.controls.temporalConfidence,
   distanceMeasure: state.controls.distanceMeasure,
+  treeZoom: state.controls.treeZoom,
   mutType: state.controls.mutType,
   colorScale: state.controls.colorScale,
   metadata: state.metadata,

src/components/tree/phyloTree/change.js

@@ -256,6 +256,7 @@ export const change = function change({
   /* change these things to provided value (unless undefined) */
   newDistance = undefined,
   newLayout = undefined,
+  newTreeZoom = undefined,
   updateLayout = undefined, // todo - this seems identical to `newLayout`
   newBranchLabellingKey = undefined,
   newTipLabelKey = undefined,
@@ -310,7 +311,7 @@ export const change = function change({
     svgPropsToUpdate.add("stroke-width");
     nodePropsToModify["stroke-width"] = branchThickness;
   }
-  if (newDistance || newLayout || updateLayout || zoomIntoClade || svgHasChangedDimensions) {
+  if (newDistance || newLayout || newTreeZoom || updateLayout || zoomIntoClade || svgHasChangedDimensions) {
     elemsToUpdate.add(".tip").add(".branch.S").add(".branch.T").add(".branch");
     elemsToUpdate.add(".vaccineCross").add(".vaccineDottedLine").add(".conf");
     elemsToUpdate.add('.branchLabel').add('.tipLabel');
@@ -344,8 +345,10 @@ 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) */
-  if (newDistance || newLayout || updateLayout) {
+  /* treeZoom */
+  if (newTreeZoom || updateLayout) this.setTreeZoom(newTreeZoom);
+  /* layout (must run after distance and treeZoom) */
+  if (newDistance || newLayout || newTreeZoom || updateLayout) {
     this.setLayout(newLayout || this.layout, scatterVariables);
   }
   /* show confidences - set this param which actually adds the svg paths for
@@ -356,6 +359,7 @@ export const change = function change({
     svgPropsToUpdate.has(["stroke-width"]) ||
     newDistance ||
     newLayout ||
+    newTreeZoom ||
     updateLayout ||
     zoomIntoClade ||
     svgHasChangedDimensions ||

src/components/tree/phyloTree/layouts.js

@@ -3,10 +3,11 @@
 import { min, max } from "d3-array";
 import scaleLinear from "d3-scale/src/linear";
 import {point as scalePoint} from "d3-scale/src/band";
-import { addLeafCount} from "./helpers";
+import { addLeafCount } from "./helpers";
 import { calculateRegressionThroughRoot, calculateRegressionWithFreeIntercept } from "./regression";
 import { timerStart, timerEnd } from "../../../util/perf";
 import { getTraitFromNode, getDivFromNode } from "../../../util/treeMiscHelpers";
+import { NODE_VISIBLE } from "../../../util/globals";
 
 /**
  * assigns the attribute this.layout and calls the function that
@@ -265,6 +266,64 @@ export const setDistance = function setDistance(distanceAttribute) {
   timerEnd("setDistance");
 };
 
+/**
+ * given nodes add y values (node.yvalue) to every node
+ * Nodes are the phyloTree nodes (i.e. node.n is the redux node)
+ * Nodes must have parent child links established (via createChildrenAndParents)
+ * PhyloTree can subsequently use this information. Accessed by prototypes
+ * rectangularLayout, radialLayout, createChildrenAndParents
+ * side effects: node.n.yvalue (i.e. in the redux node) and node.yRange (i.e. in the phyloTree node)
+ */
+export const calcYValues = (nodes, spacing = "even") => {
+  // console.log("calcYValues started with ", spacing);
+  let total = 0; /* cumulative counter of y value at tip */
+  let calcY; /* fn called calcY(node) to return some amount of y value at a tip */
+  if (spacing.includes("zoom") && 'visibility' in nodes[0]) {
+    const numberOfTips = nodes.length;
+    const numTipsVisible = nodes.map((d) => d.terminal && d.visibility === NODE_VISIBLE).filter((x) => x).length;
+    const yPerVisible = (0.8 * numberOfTips) / numTipsVisible;
+    const yPerNotVisible = (0.2 * numberOfTips) / (numberOfTips - numTipsVisible);
+    calcY = (node) => {
+      total += node.visibility === NODE_VISIBLE ? yPerVisible : yPerNotVisible;
+      return total;
+    };
+  } else { /* fall back to even spacing */
+    if (spacing !== "even") console.warn("falling back to even spacing of y values. Unknown arg:", spacing);
+    calcY = () => ++total;
+  }
+
+  const recurse = (node) => {
+    if (node.children) {
+      for (let i = node.children.length - 1; i >= 0; i--) {
+        recurse(node.children[i]);
+      }
+    } else {
+      node.n.yvalue = calcY(node);
+      node.yRange = [node.n.yvalue, node.n.yvalue];
+      return;
+    }
+    /* if here, then all children have yvalues, but we dont. */
+    node.n.yvalue = node.children.reduce((acc, d) => acc + d.n.yvalue, 0) / node.children.length;
+    node.yRange = [node.n.children[0].yvalue, node.n.children[node.n.children.length - 1].yvalue];
+  };
+  recurse(nodes[0]);
+};
+
+/**
+ * assigns the attribute this.treeZoom and calls the function that
+ * recalculates yvalues based on treeZoom setting
+ * @param treeZoom -- how to zoom nodes, eg ["even", "zoom"]
+ */
+export const setTreeZoom = function setTreeZoom(treeZoom) {
+  timerStart("setTreeZoom");
+  if (typeof treeZoom === "undefined") {
+    this.treeZoom = "even";
+  } else {
+    this.treeZoom = treeZoom;
+  }
+  calcYValues(this.nodes, this.treeZoom);
+  timerEnd("setTreeZoom");
+};
 
 /**
  * Initializes and sets the range of the scales (this.xScale, this.yScale)

src/components/tree/phyloTree/phyloTree.js

@@ -65,6 +65,7 @@ PhyloTree.prototype.updateColorBy = renderers.updateColorBy;
 /* C A L C U L A T E    G E O M E T R I E S  E T C   ( M O D I F I E S    N O D E S ,    N O T    S V G ) */
 PhyloTree.prototype.setDistance = layouts.setDistance;
 PhyloTree.prototype.setLayout = layouts.setLayout;
+PhyloTree.prototype.setTreeZoom = layouts.setTreeZoom;
 PhyloTree.prototype.rectangularLayout = layouts.rectangularLayout;
 PhyloTree.prototype.scatterplotLayout = layouts.scatterplotLayout;
 PhyloTree.prototype.unrootedLayout = layouts.unrootedLayout;

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} treeZoom       -- how to to treat spread of yValues, e.g. "even" or "zoom"
  * @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, treeZoom, 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);
@@ -31,6 +32,7 @@ export const render = function render(svg, layout, distance, parameters, callbac
 
   /* set x, y values & scale them to the screen */
   this.setDistance(distance);
+  this.setTreeZoom(treeZoom);
   this.setLayout(layout, scatterVariables);
   this.mapToScreen();
 

src/components/tree/reactD3Interface/change.js

@@ -51,6 +51,12 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
     args.newDistance = newProps.distanceMeasure;
   }
 
+  /* change treeZoom behavior */
+  if (oldProps.treeZoom !== newProps.treeZoom) {
+    args.newTreeZoom = newProps.treeZoom;
+    args.updateLayout = true;
+  }
+
   /* change in key used to define branch labels, tip labels */
   if (oldProps.canRenderBranchLabels===true && newProps.canRenderBranchLabels===false) {
     args.newBranchLabellingKey = "none";

src/components/tree/reactD3Interface/initialRender.js

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

src/components/tree/tree.js

@@ -1,6 +1,7 @@
 import React from "react";
 import { withTranslation } from "react-i18next";
 import { updateVisibleTipsAndBranchThicknesses } from "../../actions/tree";
+import { CHANGE_TREE_ZOOM } from "../../actions/types";
 import Card from "../framework/card";
 import Legend from "./legend/legend";
 import PhyloTree from "./phyloTree/phyloTree";
@@ -36,6 +37,7 @@ class Tree extends React.Component {
     this.clearSelectedTip = callbacks.clearSelectedTip.bind(this);
     // this.handleIconClickHOF = callbacks.handleIconClickHOF.bind(this);
     this.redrawTree = () => {
+      this.props.dispatch({ type: CHANGE_TREE_ZOOM, data: "even" });
       this.props.dispatch(updateVisibleTipsAndBranchThicknesses({
         root: [0, 0]
       }));
@@ -95,15 +97,8 @@ class Tree extends React.Component {
   }
 
   getStyles = () => {
-    const activeResetTreeButton = this.props.tree.idxOfInViewRootNode !== 0 ||
-      this.props.treeToo.idxOfInViewRootNode !== 0;
-
-    const filteredTree = !!this.props.tree.idxOfFilteredRoot &&
-      this.props.tree.idxOfInViewRootNode !== this.props.tree.idxOfFilteredRoot;
-    const filteredTreeToo = !!this.props.treeToo.idxOfFilteredRoot &&
-      this.props.treeToo.idxOfInViewRootNode !== this.props.treeToo.idxOfFilteredRoot;
-    const activeZoomButton = filteredTree || filteredTreeToo;
-
+    const activeResetTreeButton = true;
+    const activeZoomButton = true;
     return {
       treeButtonsDiv: {
         zIndex: 100,
@@ -141,6 +136,19 @@ class Tree extends React.Component {
   }
 
   zoomToSelected = () => {
+    // if currently set to "even", start at "zoom"
+    let treeZoomData = "zoom";
+    if (this.props.treeZoom.includes("zoom")) {
+      // if currently at "zoom", increment to "zoom-2"
+      if (!this.props.treeZoom.includes("-")) {
+        treeZoomData = "zoom-2";
+      } else {
+      // if currently at "zoom-2", increment to "zoom-3", etc...
+        const increment = parseInt(this.props.treeZoom.split('-')[1], 10) + 1;
+        treeZoomData = "zoom-" + increment.toString();
+      }
+    }
+    this.props.dispatch({ type: CHANGE_TREE_ZOOM, data: treeZoomData });
     this.props.dispatch(updateVisibleTipsAndBranchThicknesses({
       root: [this.props.tree.idxOfFilteredRoot, this.props.treeToo.idxOfFilteredRoot]
     }));

src/middleware/changeURL.js

@@ -112,6 +112,10 @@ export const changeURLMiddleware = (store) => (next) => (action) => {
       query.p = action.notInURLState === true ? undefined : action.data;
       break;
     }
+    case types.CHANGE_TREE_ZOOM: {
+      query.z = action.data === state.controls.defaults.treeZoom ? undefined : action.data;
+      break;
+    }
     case types.TOGGLE_SIDEBAR: {
       // we never add this to the URL on purpose -- it should be manually set as it specifies a world
       // where resizes can not open / close the sidebar. The exception is if it's toggled, we

src/reducers/controls.js

@@ -4,6 +4,7 @@ import { defaultGeoResolution,
   defaultDateRange,
   defaultDistanceMeasure,
   defaultLayout,
+  defaultTreeZoom,
   defaultMutType,
   controlsHiddenWidth,
   strainSymbol,
@@ -19,6 +20,7 @@ export const getDefaultControlsState = () => {
   const defaults = {
     distanceMeasure: defaultDistanceMeasure,
     layout: defaultLayout,
+    treeZoom: defaultTreeZoom,
     geoResolution: defaultGeoResolution,
     filters: {},
     colorBy: defaultColorBy,
@@ -51,6 +53,7 @@ export const getDefaultControlsState = () => {
     layout: defaults.layout,
     scatterVariables: {},
     distanceMeasure: defaults.distanceMeasure,
+    treeZoom: defaults.treeZoom,
     dateMin,
     dateMinNumeric,
     dateMax,
@@ -153,6 +156,10 @@ const Controls = (state = getDefaultControlsState(), action) => {
         });
       }
       return Object.assign({}, state, updatesToState);
+    case types.CHANGE_TREE_ZOOM:
+      return Object.assign({}, state, {
+        treeZoom: action.data
+      });
     case types.CHANGE_DATES_VISIBILITY_THICKNESS: {
       const newDates = { quickdraw: action.quickdraw };
       if (action.dateMin) {

src/util/globals.js

@@ -27,6 +27,7 @@ export const defaultColorBy = "country";
 export const defaultGeoResolution = "country";
 export const defaultLayout = "rect";
 export const defaultDistanceMeasure = "num_date";
+export const defaultTreeZoom = "even";
 export const defaultDateRange = 6;
 export const date_select = true;
 export const file_prefix = "Zika_";