tests pass

Makefile

@@ -1,5 +1,6 @@
 NODE_PATH = ./node_modules
 JS_COMPILER = $(NODE_PATH)/uglify-js/bin/uglifyjs
+#JS_TESTER = $(NODE_PATH)/vows/bin/vows --nocolor -v
 
 all: \
 	reorder.v1.js \

TODO

@@ -14,5 +14,12 @@ Reordering:
 		Correspondence analysis
 	Chun-Hou Chen methods: http://gap.stat.sinica.edu.tw/Papers/GAP_2002.pdf
 		 Elliptical
-	Barycenter method: http://www.informatica.si/PDF/29-3/13_Makinen-The%20Barycenter%20Heuristic....pdf
-
+
+Reordering done:
+	Barycenter method:
+		   http://www.informatica.si/PDF/29-3/13_Makinen-The%20Barycenter%20Heuristic....pdf
+	Optimal Leaf Ordering
+		Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommy S. Jaakkola and Nathan Srebro
+		K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.
+		Bioinformatics, 19(9), pp 1070-8, 2003
+		http://www.cs.cmu.edu/~zivbj/compBio/k-aryBio.pdf

reorder.v1.js

@@ -1,5 +1,5 @@
 (function(exports){
-reorder = {version: "0.0.2"}; // semver
+reorder = {version: "0.0.3"}; // semver
 
 reorder.dot = science.lin.dot;
 reorder.length = science.lin.length;
@@ -644,6 +644,16 @@ function count_crossings(graph, north, south) {
 	firstIndex, treeSize, tree, index, weightSum,
 	invert = false, crosscount;
 
+    if (north==undefined) {
+	var comp = reorder.permutation(graph.nodes().length);
+	north = comp.filter(function(n) {
+	    return graph.outEdges(n).length!=0;
+	}),
+	south = comp.filter(function(n) {
+	    return graph.inEdges(n).length!=0;
+	});
+    }
+
     // Choose the smaller axis
     if (north.length < south.length) {
 	var tmp = north;
@@ -693,14 +703,18 @@ function count_crossings(graph, north, south) {
 }
 reorder.count_crossings = count_crossings;
 reorder.barycenter = function(graph, iter, comps) {
-    var perm = [];
+    var perms = [[], [], 0];
     // Compute the barycenter heuristic on each connected component
     if (! comps) {
 	comps = graph.components();
     }
-    for (var i = 0; i < comps.length; i++)
-	perm = perm.concat(reorder.barycenter1(graph, comps[i], iter));
-    return perm;
+    for (var i = 0; i < comps.length; i++) {
+	var p = reorder.barycenter1(graph, comps[i], iter);
+	perms = [ perms[0].concat(p[0]),
+		  perms[1].concat(p[1]),
+		  perms[2]+p[2] ];
+    }
+    return perms;
 };
 
 // Take the list of neighbor indexes and return the median according to 
@@ -733,8 +747,16 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	layer, 
 	i, v, neighbors;
 
-    if (comp.length < 3)
-	return comp;
+    layer1 = comp.filter(function(n) {
+	return graph.outEdges(n).length!=0;
+    });
+    layer2 = comp.filter(function(n) {
+	return graph.inEdges(n).length!=0;
+    });
+    if (comp.length < 3) {
+	return [layer1, layer2,
+		count_crossings(graph, layer1, layer2)];
+    }
 
     if (! max_iter)
 	max_iter = 24;
@@ -786,7 +808,7 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	    else if (d > 0) return 1;
 	    return 0;
 	});
-	for (i = 0; i < layer2.length; i++)
+	for (i = 0; i < layer.length; i++)
 	    nodes[layer[i]].pos = i;
 	crossings = count_crossings(graph, layer1, layer2);
 	if (crossings < best_crossings) {
@@ -796,7 +818,7 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	    best_iter = iter;
 	}
     }
-    console.log('Best iter: '+best_iter);
+    //console.log('Best iter: '+best_iter);
     return [best_layer1, best_layer2, best_crossings];
 };
 reorder.dijkstra = function(graph) {

src/barycenter.js

@@ -1,12 +1,16 @@
 reorder.barycenter = function(graph, iter, comps) {
-    var perm = [];
+    var perms = [[], [], 0];
     // Compute the barycenter heuristic on each connected component
     if (! comps) {
 	comps = graph.components();
     }
-    for (var i = 0; i < comps.length; i++)
-	perm = perm.concat(reorder.barycenter1(graph, comps[i], iter));
-    return perm;
+    for (var i = 0; i < comps.length; i++) {
+	var p = reorder.barycenter1(graph, comps[i], iter);
+	perms = [ perms[0].concat(p[0]),
+		  perms[1].concat(p[1]),
+		  perms[2]+p[2] ];
+    }
+    return perms;
 };
 
 // Take the list of neighbor indexes and return the median according to 
@@ -39,8 +43,16 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	layer, 
 	i, v, neighbors;
 
-    if (comp.length < 3)
-	return comp;
+    layer1 = comp.filter(function(n) {
+	return graph.outEdges(n).length!=0;
+    });
+    layer2 = comp.filter(function(n) {
+	return graph.inEdges(n).length!=0;
+    });
+    if (comp.length < 3) {
+	return [layer1, layer2,
+		count_crossings(graph, layer1, layer2)];
+    }
 
     if (! max_iter)
 	max_iter = 24;
@@ -92,7 +104,7 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	    else if (d > 0) return 1;
 	    return 0;
 	});
-	for (i = 0; i < layer2.length; i++)
+	for (i = 0; i < layer.length; i++)
 	    nodes[layer[i]].pos = i;
 	crossings = count_crossings(graph, layer1, layer2);
 	if (crossings < best_crossings) {
@@ -102,6 +114,6 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	    best_iter = iter;
 	}
     }
-    console.log('Best iter: '+best_iter);
+    //console.log('Best iter: '+best_iter);
     return [best_layer1, best_layer2, best_crossings];
 };

src/core.js

@@ -1,2 +1,2 @@
-reorder = {version: "0.0.2"}; // semver
+reorder = {version: "0.0.3"}; // semver
 

src/count_crossings.js

@@ -6,6 +6,16 @@ function count_crossings(graph, north, south) {
 	firstIndex, treeSize, tree, index, weightSum,
 	invert = false, crosscount;
 
+    if (north==undefined) {
+	var comp = reorder.permutation(graph.nodes().length);
+	north = comp.filter(function(n) {
+	    return graph.outEdges(n).length!=0;
+	}),
+	south = comp.filter(function(n) {
+	    return graph.inEdges(n).length!=0;
+	});
+    }
+
     // Choose the smaller axis
     if (north.length < south.length) {
 	var tmp = north;

test/barycenter-test.js

@@ -7,22 +7,34 @@ var vows = require("vows"),
 
 var suite = vows.describe("reorder.barycenter");
 
+function dotest(mat) {
+    var graph = reorder.mat2graph(mat, true);
+    //reorder.printmat(mat);
+    var initial_crossings = reorder.count_crossings(graph);
+    var perms = reorder.barycenter(graph);
+    //console.log('VOrder: %j, HOrder: %j, Crossings: %d',
+    //perms[1], perms[0], perms[2]);
+    //reorder.printmat(mat, perms[1], perms[0]);
+    assert.isTrue(initial_crossings > perms[2]);
+}
+
 suite.addBatch({
     "barycenter": {
 	"simple": function() {
 	    var mat = [
 		[0, 1, 0, 1, 0],
 		[1, 0, 1, 0, 1],
 		[0, 1, 0, 1, 1],
-		[1, 1, 1, 0, 0]],
-		graph = reorder.mat2graph(mat, true),
-		expect = [0, 1, 3, 2, 4];
-	    reorder.printmat(mat);
-	    perm = reorder.barycenter(graph);
-	    console.log('VOrder: %j, HOrder: %j, Crossings: %d',
-			perm[1], perm[0], perm[2]);
-	    reorder.printmat(mat, perm[1], perm[0]);
-	    //assert.deepEqual(perm, expect);
+		[1, 1, 1, 0, 0]];
+	    dotest(mat);
+	},
+	"hard": function() {
+	    for (var i = 10; i < 100; i += 20) {
+		for (var j = 10; j < 100; j += 20) {
+		    var mat = reorder.randomMatrix(0.2, i, j, false);
+		    dotest(mat);
+		}
+	    }
 	}
     }
 });

test/ca-test.js

@@ -9,6 +9,19 @@ Math.seedrandom('reorder');
 
 var suite = vows.describe("reorder.ca");
 
+function inDeltaArray(actual, expected, delta) {
+  var n = expected.length, i = -1;
+  if (actual.length !== n) return false;
+  while (++i < n) if (!inDeltaNumber(actual[i], expected[i], delta)) return false;
+  return true;
+}
+
+function inDeltaNumber(actual, expected, delta) {
+    var d = Math.abs(actual-expected);
+    //console.log("d="+d+": "+((d < delta) ? "pass" : "fail"));
+    return d < delta;
+}
+
 suite.addBatch({
     "ca": {
 	"simple": function() {
@@ -20,7 +33,10 @@ suite.addBatch({
 		res = reorder.ca(mat, 0.0001);
 
 	    //assert.isTrue(true);
-	    assert.inDeltaArray(res, [-0.5354605, -0.2626774, 0.8026722], 0.001);
+	    if (!inDeltaArray(res, [-0.5354605, -0.2626774, 0.8026722], 0.001)
+		&&  !inDeltaArray(res, [0.5354605, 0.2626774, -0.8026722], 0.001)) {
+		assert.fail(actual, expected, message || "expected {actual} to be in within *" + delta + "* of {expected}", null, assert.inDelta);
+	    }
 	}
     }
 });

test/count_crossings-test.js

@@ -34,7 +34,7 @@ function naive_count_crossings(graph, north, south) {
     return count;
 }
 
-function dohard(mat) {
+function dotest(mat) {
     var graph = reorder.mat2graph(mat, true),
 	comps = graph.components(),
 	comp = comps.reduce(function(a, b) {
@@ -95,7 +95,7 @@ suite.addBatch({
 			 12);
 	},
 	"bug": function() {
-	    dohard([
+	    dotest([
     [0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0],
     [0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
     [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
@@ -132,7 +132,7 @@ suite.addBatch({
 	    for (var i = 10; i < 100; i += 20) {
 		for (var j = 10; j < 100; j += 20) {
 		    var mat = reorder.randomMatrix(0.2, i, j, false);
-		    dohard(mat);
+		    dotest(mat);
 		}
 	    }
 	}

test/graph2mat-test.js

@@ -9,6 +9,29 @@ Math.seedrandom('reorder');
 
 var suite = vows.describe("reorder.graph2mat");
 
+function remove_zeroes(mat) {
+    var i, j;
+    for (i = mat.length-1; i >= 0; i--) {
+	var row = mat[i];
+	if (row.some(function(a) { return a > 0; })) {
+	    //console.log('remove row %d', i);
+	    break;
+	}
+	mat.pop();
+    }
+    for (j = mat[0].length-1; j >= 0; j--) {
+	if (mat.some(function(row) {
+	    return row[j] != 0;
+	})) {
+	    //console.log('remove column %d', j);
+	    break;
+	}
+	for (i = 0; i < mat.length; i++)
+	    mat[i].pop();
+    }
+
+    return mat;
+}
 
 suite.addBatch({
     "graph2mat": {
@@ -33,7 +56,7 @@ suite.addBatch({
 	"hard": function() {
 	    for (var i = 10; i < 100; i += 20) {
 		for (var j = 10; j < 100; j += 20) {
-		    var mat = reorder.randomMatrix(0.2, i, j, false),
+		    var mat = remove_zeroes(reorder.randomMatrix(0.2, i, j, false)),
 			graph = reorder.mat2graph(mat, true),
 			m2 = reorder.graph2mat(graph);
 		    assert.deepEqual(m2, mat);