ENH: Scale LWs based on # leaves; rename numleafs

I think there is still more work that should be done on biocore#144,
but this is probably sufficient for a PR for now.

empress/support_files/js/bp-tree.js

@@ -219,11 +219,11 @@ define(["ByteArray"], function (ByteArray) {
 
  /**
  *
- * The number of leaf noes in tree
+ * The number of leaf nodes in tree
  *
  * @return {Number}
  */
- BPTree.prototype.numleafs = function () {
+ BPTree.prototype.numleaves = function () {
  var total = 0;
  for (var i = 0; i < this.b_.length - 1; i++) {
  total = this.isleaf(i) ? total + 1 : total;

empress/support_files/js/empress.js

@@ -169,18 +169,10 @@ define([
  */
  this.layoutAvgPoint = {};
 
- /**
- * type {Number}
- * A constant value that defines how "extra line width" is scaled
- * relative to the area of a given tree layout.
- * The user-entered "extra line width" value will be converted to units
- * of (tree area) multiplied by this constant.
- */
- this.EXTRA_LW_AREA_COEFFICIENT = 1 / 100000000;
-
  /**
  * @type{Number}
- * The line width used for drawing "thick" lines.
+ * The (not-yet-scaled) line width used for drawing "thick" lines.
+ * Can be passed as input to this.thickenSameSampleLines().
  */
  this._currentLineWidth = 0;
 
@@ -253,7 +245,7 @@ define([
  // | +-
  // |
  // +--------
- var leafAndRootCt = this._tree.numleafs() + 1;
+ var leafAndRootCt = this._tree.numleaves() + 1;
  numLines = leafAndRootCt + 2 * (this._tree.size - leafAndRootCt);
  } else if (this._currentLayout === "Circular") {
  // All internal nodes (except root which is just a point) have an
@@ -264,7 +256,7 @@ define([
  // i.e. 3 lines for the leaves and 16 * (5 - 3 - 1) lines for the
  // internal nodes. The -1 is there because we do not draw a line
  // for the root.
- var leafCt = this._tree.numleafs();
+ var leafCt = this._tree.numleaves();
  numLines = leafCt + 16 * (this._tree.size - leafCt - 1);
  } else {
  // the root is not drawn in the unrooted layout
@@ -601,15 +593,12 @@ define([
  }
  }
  this._currentLineWidth = lw;
- // Scale the line width by (tree area) * EXTRA_LW_AREA_COEFFICIENT,
- // and divide the resulting scaled line width by 2. (The division by 2
- // makes coordinate computation easier.)
- var coeff =
- (this.computeTreeArea() * this.EXTRA_LW_AREA_COEFFICIENT) / 2;
- var lwScaled = lw * coeff;
- console.log("input LW: " + lw);
- console.log("tree area: " + this.computeTreeArea());
- console.log("scaled LW: " + lwScaled);
+ // Scale the line width in such a way that trees with more leaves have
+ // "smaller" line width values than trees with less leaves. This is a
+ // pretty arbitrary equation based on messing around and seeing what
+ // looked nice on mid- and small-sized trees; as a TODO for the future,
+ // there is almost certainly a better way to do this.
+ var lwScaled = (2 * lw) / Math.pow(Math.log10(this._tree.numleaves()), 2);
  var tree = this._tree;
 
  // the coordinates of the tree

tests/test-bp-tree.js

@@ -100,8 +100,8 @@ require(["jquery", "ByteArray", "BPTree"], function ($, ByteArray, BPTree) {
  }
  });
 
- test("Test number of leafs", function () {
- equal(this.bpObj.numleafs(), 6);
+ test("Test number of leaves", function () {
+ equal(this.bpObj.numleaves(), 6);
  });
 
  test("Test rank property", function () {