Shear UI

empress/support_files/css/empress.css

@@ -585,6 +585,13 @@ p.side-header button:hover,
     white-space: nowrap;
 }
 
+.shear-layer-legend div {
+    max-height: 15em;
+    /* The side panel width is 450px */
+    max-width: 430px;
+    overflow: auto;
+}
+
 .barplot-layer-legend {
     max-height: 15em;
     /* The side panel width is 450px */

empress/support_files/js/empress.js

@@ -391,21 +391,32 @@ define([
         );
         // Rectangular
         if (this._currentLayout === "Rectangular") {
-            data = LayoutsUtil.rectangularLayout(
-                this._tree.getTree(),
-                4020,
-                4020,
-                // since lengths for "ignoreLengths" are set by `lengthGetter`,
-                // we don't need (and should likely deprecate) the ignoreLengths
-                // option for the Layout functions since the layout function only
-                // needs to know lengths in order to layout a tree, it doesn't
-                // really need encapsulate all of the logic for determining
-                // what lengths it should lay out.
-                this.leafSorting,
-                undefined,
-                lengthGetter,
-                checkLengthsChange
-            );
+            // tree is just root
+            if (this._tree.currentSize == 1) {
+                data = {
+                    xCoord: [null, 0],
+                    yCoord: [null, 0],
+                    highestChildYr: [null, 0],
+                    lowestChildYr: [null, 0],
+                    yScalingFactor: [null, 0],
+                };
+            } else {
+                data = LayoutsUtil.rectangularLayout(
+                    this._tree.getTree(),
+                    4020,
+                    4020,
+                    // since lengths for "ignoreLengths" are set by `lengthGetter`,
+                    // we don't need (and should likely deprecate) the ignoreLengths
+                    // option for the Layout functions since the layout function only
+                    // needs to know lengths in order to layout a tree, it doesn't
+                    // really need encapsulate all of the logic for determining
+                    // what lengths it should lay out.
+                    this.leafSorting,
+                    undefined,
+                    lengthGetter,
+                    checkLengthsChange
+                );
+            }
             this._yrscf = data.yScalingFactor;
             for (i of this._tree.postorderTraversal((includeRoot = true))) {
                 // remove old layout information
@@ -421,15 +432,30 @@ define([
                 j += 1;
             }
         } else if (this._currentLayout === "Circular") {
-            data = LayoutsUtil.circularLayout(
-                this._tree.getTree(),
-                4020,
-                4020,
-                this.leafSorting,
-                undefined,
-                lengthGetter,
-                checkLengthsChange
-            );
+            if (this._tree.currentSize == 1) {
+                data = {
+                    // store new layout information
+                    x0: [null, 0],
+                    y0: [null, 0],
+                    x1: [null, 0],
+                    y1: [null, 0],
+                    angle: [null, 0],
+                    arcx0: [null, 0],
+                    arcy0: [null, 0],
+                    arcStartAngle: [null, 0],
+                    arcEndAngle: [null, 0],
+                };
+            } else {
+                data = LayoutsUtil.circularLayout(
+                    this._tree.getTree(),
+                    4020,
+                    4020,
+                    this.leafSorting,
+                    undefined,
+                    lengthGetter,
+                    checkLengthsChange
+                );
+            }
             for (i of this._tree.postorderTraversal((includeRoot = true))) {
                 // remove old layout information
                 this._treeData[i].length = this._numOfNonLayoutParams;
@@ -449,14 +475,22 @@ define([
                 j += 1;
             }
         } else {
-            data = LayoutsUtil.unrootedLayout(
-                this._tree.getTree(),
-                4020,
-                4020,
-                undefined,
-                lengthGetter,
-                checkLengthsChange
-            );
+            if (this._tree.currentSize == 1) {
+                data = {
+                    // store new layout information
+                    xCoord: [null, 0],
+                    yCoord: [null, 0],
+                };
+            } else {
+                data = LayoutsUtil.unrootedLayout(
+                    this._tree.getTree(),
+                    4020,
+                    4020,
+                    undefined,
+                    lengthGetter,
+                    checkLengthsChange
+                );
+            }
             for (i of this._tree.postorderTraversal((includeRoot = true))) {
                 // remove old layout information
                 this._treeData[i].length = this._numOfNonLayoutParams;
@@ -2142,6 +2176,18 @@ define([
         this.drawTree();
     };
 
+    /**
+     *
+     */
+    Empress.prototype.getUniqueSampleMetadataInfo = function (cat) {
+        var obs = this._biom.getObsBy(cat);
+        var nodes = new Set([...this._tree.postorderTraversal()]);
+        _.each(obs, function (observations, key) {
+            obs[key] = observations.filter((x) => nodes.has(x));
+        });
+        return obs;
+    };
+
     /**
      * Color the tree using sample metadata
      *
@@ -2162,7 +2208,8 @@ define([
         reverse = false
     ) {
         var tree = this._tree;
-        var obs = this._biom.getObsBy(cat);
+        // var obs = this._biom.getObsBy(cat);
+        var obs = this.getUniqueSampleMetadataInfo(cat);
         var categories = Object.keys(obs);
 
         // Assign colors to categories
@@ -2177,6 +2224,11 @@ define([
         var cm = colorer.getMapRGB();
         // colors for the legend
         var keyInfo = colorer.getMapHex();
+        for (var key in keyInfo) {
+            if (obs[key].length === 0) {
+                delete keyInfo[key];
+            }
+        }
 
         // shared by the following for loops
         var i, j, category;
@@ -2232,6 +2284,9 @@ define([
      *                   an array of the node name(s) with each value.
      */
     Empress.prototype.getUniqueFeatureMetadataInfo = function (cat, method) {
+        // get nodes in tree
+        var nodes = new Set([...this._tree.postorderTraversal()]);
+
         // In order to access feature metadata for a given node, we need to
         // find the 0-based index in this._featureMetadataColumns that the
         // specified f.m. column corresponds to. (We *could* get around this by
@@ -2258,15 +2313,16 @@ define([
         var uniqueValueToFeatures = {};
         _.each(fmObjs, function (mObj) {
             _.mapObject(mObj, function (fmRow, node) {
+                var fmVal = fmRow[fmIdx];
+                if (!_.has(uniqueValueToFeatures, fmVal)) {
+                    uniqueValueToFeatures[fmVal] = [];
+                }
                 // need to convert to integer
                 node = parseInt(node);
-                // This is loosely based on how BIOMTable.getObsBy() works.
-                var fmVal = fmRow[fmIdx];
-                if (_.has(uniqueValueToFeatures, fmVal)) {
-                    uniqueValueToFeatures[fmVal].push(node);
-                } else {
-                    uniqueValueToFeatures[fmVal] = [node];
+                if (!nodes.has(node)) {
+                    return;
                 }
+                uniqueValueToFeatures[fmVal].push(node);
             });
         });
 
@@ -2329,9 +2385,14 @@ define([
         );
         // colors for drawing the tree
         var cm = colorer.getMapRGB();
+
         // colors for the legend
         var keyInfo = colorer.getMapHex();
-
+        for (var key in keyInfo) {
+            if (uniqueValueToFeatures[key].length === 0) {
+                delete keyInfo[key];
+            }
+        }
         // Do upwards propagation only if the coloring method is "tip"
         if (method === "tip") {
             obs = this._projectObservations(obs, false);
@@ -3565,5 +3626,63 @@ define([
         }
     };
 
+    /**
+     * This will shear/unshear
+     */
+    Empress.prototype.shear = function (shearMap) {
+        this._tree.unshear();
+        var scope = this;
+        var removeNodes = new Set();
+
+        shearMap.forEach(function (values, cat) {
+            var fmInfo = scope.getUniqueFeatureMetadataInfo(cat, "tip");
+            var uniqueValueToFeatures = fmInfo.uniqueValueToFeatures;
+            _.each(values, function (val) {
+                var obs = uniqueValueToFeatures[val];
+                for (var node of obs) {
+                    removeNodes.add(node);
+                }
+            });
+        });
+
+        // remove removeNodes
+        var allNodes = Array.from(Array(this._tree.size + 1).keys());
+        allNodes.shift();
+
+        allNodes = new Set(allNodes);
+        var keepNodes = new Set(
+            [...allNodes].filter((x) => !removeNodes.has(x))
+        );
+
+        var keepNames = [];
+        for (var node of keepNodes) {
+            var name = this._tree.name(this._tree.postorderselect(node));
+            keepNames.push(name);
+        }
+
+        this._tree.shear(new Set(keepNames));
+        var nodeNames = this._tree.getAllNames();
+        // Don't include nodes with the name null (i.e. nodes without a
+        // specified name in the Newick file) in the auto-complete.
+        nodeNames = nodeNames.filter((n) => n !== null);
+        this._events.autocomplete(nodeNames);
+
+        this.getLayoutInfo();
+
+        // Undraw or redraw barplots as needed (assuming barplots are supported
+        // in the first place, of course; if no feature or sample metadata at
+        // all was passed then barplots are not available :()
+        if (!_.isNull(this._barplotPanel)) {
+            var supported = this._barplotPanel.updateLayoutAvailability(
+                this._currentLayout
+            );
+            if (!supported && this._barplotsDrawn) {
+                this.undrawBarplots();
+            } else if (supported && this._barplotPanel.enabled) {
+                this.drawBarplots();
+            }
+        }
+    };
+
     return Empress;
 });

empress/support_files/js/legend.js

@@ -218,17 +218,8 @@ define(["jquery", "underscore", "util"], function ($, _, util) {
      * @param {Object} info Color key information. This should map unique
      *                      values (e.g. in sample or feature metadata) to
      *                      their assigned color, expressed in hex format.
-     *
-     * @throws {Error} If info has no keys. This check is done before anything
-     *                 else is done in this function.
      */
     Legend.prototype.addCategoricalKey = function (name, info) {
-        if (_.isEmpty(info)) {
-            throw new Error(
-                "Can't create a categorical legend when there are no " +
-                    "categories in the info"
-            );
-        }
         this.clear();
         this.addTitle(name);
         this._sortedCategories = util.naturalSort(_.keys(info));