diff --git a/Makefile b/Makefile
index e68e7f7..ba78086 100644
--- a/Makefile
+++ b/Makefile
@@ -51,7 +51,8 @@ reorder.v1.js: \
 	src/pca_order.js \
 	src/ca.js \
 	src/cuthill_mckee_order.js \
-	src/condition.js
+	src/condition.js \
+	src/pcp.js
 
 test: all
 	@npm test
diff --git a/examples/pcp/index.html b/examples/pcp/index.html
index b55cb04..44f0427 100644
--- a/examples/pcp/index.html
+++ b/examples/pcp/index.html
@@ -1,8 +1,12 @@
 <meta charset="UTF8">
 <script src="../../lib/d3.v3.js"></script>
 <script src="../../lib/d3.parcoords.js"></script>
+<script src="../../lib/science.v1.js"></script>
+<script src="../../lib/tiny-queue.js"></script>
+<script src="../../reorder.v1.js"></script>
 <link rel="stylesheet" type="text/css" href="../../lib/d3.parcoords.css">
 <div id="example" class="parcoords" style="width:360px;height:150px"></div>
+<div id="example2" class="parcoords" style="width:360px;height:150px"></div>
 
 <script>
 var data = [
@@ -11,11 +15,26 @@
   [2,-2,4,4,0.5,2],
   [3,-3,9,6,0.33,4],
   [4,-4,16,8,0.25,9]
-];
+],
+  dimensions = reorder.range(6),
+  axes = ['a', 'b', 'c', 'd', 'e', 'f'];
 
 var pc = d3.parcoords()("#example")
-  .data(data)
+  .data(reorder.array_to_dicts(data, axes))
   .render()
   .ticks(3)
   .createAxes();
+
+var pcp = reorder.pcp(data, axes),
+   ndata = pcp[0],
+   perm = pcp[1],
+   naxes = pcp[2];
+
+var pc2 = d3.parcoords()("#example2")
+  .data(reorder.array_to_dicts(ndata, naxes))
+  .render()
+  .ticks(3)
+  .dimensions(naxes)
+  .createAxes();
+
 </script>
diff --git a/reorder.v1.js b/reorder.v1.js
index 63ba08c..755e2fe 100644
--- a/reorder.v1.js
+++ b/reorder.v1.js
@@ -2689,4 +2689,84 @@ reorder.condition = function(matrix) {
     }
     return ret;
 };
+function array_to_dicts(data, axes) {
+    if (arguments.length < 2) 
+	axes = reorder.range(data[0].length);
+    var ret = [], row, dict, i, j;
+    for (i = 0; i < data.length; i++) {
+	row = data[i];
+	dict = {};
+	for (j = 0; j < row.length; j++) {
+	    dict[axes[j]] = row[j];
+	}
+	ret.push(dict);
+    }
+    return ret;
+}
+
+reorder.array_to_dicts = array_to_dicts;
+
+function dicts_to_array(dicts, keys) {
+    if (arguments.length < 2)
+	keys = Object.keys(dicts[0]);
+    var n = keys.length,
+	m = dicts.length,
+	array = Array(m), i, j, row;
+
+    for (i = 0; i < m; i++) {
+	row = Array(n);
+	array[i] = row;
+	for (j = 0; j < n; j++)
+	    row[j] = dicts[i][keys[j]];
+    }
+    return array;
+}
+
+reorder.dicts_to_array = dicts_to_array;
+
+function abs_matrix(x) {
+    return x.map(function(y) { return y.map(Math.abs); });
+}
+
+function pcp(data, axes) {
+    if (arguments.length < 2) 
+	axes = reorder.range(data[0].length);
+    var tdata = reorder.transpose(data),
+	pcor = reorder.correlation.pearsonMatrix(tdata),
+	abs_pcor = abs_matrix(pcor),
+	h1 = science.stats.hcluster()
+	    .linkage("complete")
+	    .distanceMatrix(abs_pcor)(tdata),
+	perm = reorder.optimal_leaf_order()
+	    .distanceMatrix(abs_pcor)(tdata),
+	naxes = reorder.permute(axes, perm);
+    tdata = reorder.permute(tdata, perm);
+
+    var i, c, sign = 1, signs = [], negs=0;
+    
+    console.log('Permutation is '+perm);
+    
+    for (i = 1; i < tdata.length; i++) {
+	c = pcor[perm[i-1]][perm[i]];
+	if (c < 0)
+	    sign = -sign;
+	if (sign < 0) {
+	    signs.push(-1);
+	    negs++;
+	}
+	else
+	    signs.push(1);
+    }
+    sign = (negs > (tdata.length-negs)) ? -1 : 1;
+    for (i = 0; i < (tdata.length-1); i++) {
+	if (signs[i]*sign < 0) {
+	    naxes[i] = '-'+naxes[i];
+	    tdata[i] = tdata[i].map(function(x) { return -x; });
+	}
+    }
+    var  ndata = reorder.transpose(tdata);
+    return [ndata, perm, naxes];
+}
+
+reorder.pcp = pcp;
 })(this);
diff --git a/reorder.v1.min.js b/reorder.v1.min.js
index 1f90d3f..d1d0f1c 100644
--- a/reorder.v1.min.js
+++ b/reorder.v1.min.js
@@ -1,3 +1,3 @@
 (function(exports){reorder={version:"0.1.0"};reorder.cmp_number_asc=function(a,b){return a-b};reorder.cmp_number=reorder.cmp_number_asc;reorder.cmp_number_desc=function(a,b){return b-a};reorder.flatten=function(a,b){return a.concat(b)};reorder.infinities=function(n){var i=-1,a=[];if(arguments.length===1)while(++i<n)a[i]=Infinity;else while(++i<n)a[i]=reorder.infinities.apply(this,Array.prototype.slice.call(arguments,1));return a};reorder.array1d=function(n,v){var i=-1,a=Array(n);while(++i<n)a[i]=v;return a};reorder.dot=science.lin.dot;reorder.length=science.lin.length;reorder.normalize=science.lin.normalize;reorder.zeroes=science.zeroes;reorder.displaymat=function(mat,rowperm,colperm){var i,j,row,col,str;if(!rowperm){rowperm=reorder.permutation(mat.length)}if(!colperm){colperm=reorder.permutation(mat[0].length)}console.log("Matrix:");for(i=0;i<mat.length;i++){row=rowperm?mat[rowperm[i]]:mat[i];str="";for(j=0;j<row.length;j++){col=colperm?row[colperm[j]]:row[j];str+=col?"*":" "}console.log(str)}};reorder.printmat=function(m,prec){var i,j,row,line;if(!prec)prec=4;for(i=0;i<m.length;i++){row=m[i];line="";for(j=0;j<row.length;j++){if(line.length!==0)line+=", ";line+=row[j].toFixed(prec)}console.log(i+": "+line)}};reorder.assert=function(v,msg){if(!v){console.log(msg);throw msg||"Assertion failed"}};reorder.printhcluster=function(cluster,indent){if(cluster.left===null)return Array(indent+1).join(" ")+"id: "+cluster.id;return Array(indent+1).join(" ")+"id: "+cluster.id+", dist: "+cluster.dist+"\n"+reorder.printhcluster(cluster.left,indent+1)+"\n"+reorder.printhcluster(cluster.right,indent+1)};reorder.mean=science.stats.mean;reorder.meantranspose=function(v,j){var n=v.length;if(n===0)return NaN;var o=v[0].length,m=0,i=-1,row;while(++i<n)m+=(v[i][j]-m)/(i+1);return m};reorder.meancolumns=function(v){var n=v.length;if(n===0)return NaN;var o=v[0].length,m=v[0].slice(0),i=0,j,row;while(++i<n){row=v[i];for(j=0;j<o;j++)m[j]+=(row[j]-m[j])/(i+1)}return m};reorder.sum=function(v){var i=v.length,s=v[0];while(i-->1)s+=v[i];return s};function isNum(a,b){return!(isNaN(a)||isNaN(b)||a==Infinity||b==Infinity)}reorder.distance={euclidean:function(a,b){var i=a.length,s=0,x;while(i-->0){if(isNum(a[i],b[i])){x=a[i]-b[i];s+=x*x}}return Math.sqrt(s)},manhattan:function(a,b){var i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){s+=Math.abs(a[i]-b[i])}}return s},minkowski:function(p){return function(a,b){var i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){s+=Math.pow(Math.abs(a[i]-b[i]),p)}}return Math.pow(s,1/p)}},chebyshev:function(a,b){var i=a.length,max=0,x;while(i-->0){if(isNum(a[i],b[i])){x=Math.abs(a[i]-b[i]);if(x>max)max=x}}return max},hamming:function(a,b){var i=a.length,d=0;while(i-->0){if(isNum(a[i],b[i])){if(a[i]!==b[i])d++}}return d},jaccard:function(a,b){var n=0,i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){if(a[i]===b[i])s++;n++}}if(n===0)return 0;return s/n},braycurtis:function(a,b){var i=a.length,s0=0,s1=0,ai,bi;while(i-->0){ai=a[i];bi=b[i];if(isNum(ai,bi)){s0+=Math.abs(ai-bi);s1+=Math.abs(ai+bi)}}if(s1===0)return 0;return s0/s1}};reorder.range=function(start,stop,step){if(arguments.length<3){step=1;if(arguments.length<2){stop=start;start=0}}var range=[],i=start;if(step<0)for(;i>stop;i+=step)range.push(i);else for(;i<stop;i+=step)range.push(i);return range};reorder.transpose=science.lin.transpose;reorder.transposeSlice=function(a,start,end){if(arguments.length<3){end=a[0].length;if(arguments.length<2){start=0}}var m=a.length,n=end,i=start-1,j,b=new Array(end-start);while(++i<n){b[i]=new Array(m);j=-1;while(++j<m)b[i-start][j]=a[j][i]}return b};reorder.correlation={pearson:function(a,b){var ma=science.stats.mean(a),mb=science.stats.mean(b),s1=0,s2=0,s3=0,i,dx,dy,n=Math.min(a.length,b.length);if(n===0)return NaN;for(i=0;i<n;i++){dx=a[i]-ma;dy=b[i]-mb;s1+=dx*dy;s2+=dx*dx;s3+=dy*dy}return s1/Math.sqrt(s2*s3)},pearsonMatrix:function(matrix){var a,ma,i,j,dx,cor=reorder.correlation.pearson,n=matrix.length,ret,mx,sx,sx2;if(n===0)return NaN;ret=reorder.zeroes(n,n);for(i=0;i<n-1;i++){for(j=i+1;j<n;j++){var p=cor(matrix[i],matrix[j]);ret[i][j]=ret[j][i]=p}}return ret}};reorder.bandwidth=function(graph,order){if(!order)order=reorder.range(graph.nodes().length);var inv=inverse_permutation(order),links=graph.links(),i,e,d,max=0;for(i=0;i<links.length;i++){e=links[i];d=Math.abs(inv[e.source.index]-inv[e.target.index]);max=Math.max(max,d)}return max};reorder.edgesum=function(graph,order){if(!order)order=reorder.range(graph.nodes().length);var inv=inverse_permutation(order),links=graph.links(),i,e,d,sum=0;for(i=0;i<links.length;i++){e=links[i];d=Math.abs(inv[e.source.index]-inv[e.target.index]);sum+=d}return sum};reorder.permutation=reorder.range;function inverse_permutation(perm,dense){var inv=dense?Array(perm.length):{};for(var i=0;i<perm.length;i++){inv[perm[i]]=i}return inv}reorder.inverse_permutation=inverse_permutation;reorder.graph=function(nodes,links,directed){var graph={},linkDistance=1,edges,inEdges,outEdges,components;graph.nodes=function(x){if(!arguments.length)return nodes;nodes=x;return graph};graph.nodes_indices=function(){return nodes.map(function(n){return n.index})};graph.generate_nodes=function(n){nodes=[];for(var i=0;i<n;i++)nodes.push({id:i});return graph};graph.links=function(x){if(!arguments.length)return links;links=x;return graph};graph.links_indices=function(){return links.map(function(l){return{source:l.source.index,target:l.target.index}})};graph.linkDistance=function(x){if(!arguments.length)return linkDistance;linkDistance=typeof x==="function"?x:+x;return graph};graph.directed=function(x){if(!arguments.length)return directed;directed=x;return graph};function init(){var i,o,n=nodes.length,m=links.length;components=undefined;for(i=0;i<n;++i){(o=nodes[i]).index=i;o.weight=0}for(i=0;i<m;++i){(o=links[i]).index=i;if(typeof o.source=="number")o.source=nodes[o.source];if(typeof o.target=="number")o.target=nodes[o.target];if(!("value"in o))o.value=1;++o.source.weight;++o.target.weight}if(typeof linkDistance==="function")for(i=0;i<m;++i)links[i].distance=+linkDistance.call(this,links[i],i);else for(i=0;i<m;++i)links[i].distance=linkDistance;edges=Array(nodes.length);for(i=0;i<nodes.length;++i){edges[i]=[]}if(directed){inEdges=Array(nodes.length);outEdges=Array(nodes.length);for(i=0;i<nodes.length;++i){inEdges[i]=[];outEdges[i]=[]}}else{inEdges=outEdges=edges}for(i=0;i<links.length;++i){o=links[i];edges[o.source.index].push(o);if(o.source.index!=o.target.index)edges[o.target.index].push(o);if(directed)inEdges[o.source.index].push(o);if(directed)outEdges[o.target.index].push(o)}return graph}graph.init=init;graph.edges=function(node){if(typeof node!="number"){node=node.index;console.log("received node %d",node)}return edges[node]};graph.degree=function(node){if(typeof node!="number")node=node.index;return edges[node].length};graph.inEdges=function(node){if(typeof node!="number")node=node.index;return inEdges[node]};graph.inDegree=function(node){if(typeof node!="number")node=node.index;return inEdges[node].length};graph.outEdges=function(node){if(typeof node!="number")node=node.index;return outEdges[node]};graph.outDegree=function(node){if(typeof node!="number")node=node.index;return outEdges[node].length};graph.sinks=function(){var sinks=[],i;for(i=0;i<nodes.length;i++){if(graph.outEdges(i).length===0)sinks.push(i)}return sinks};graph.sources=function(){var sources=[],i;for(i=0;i<nodes.length;i++){if(graph.inEdges(i).length===0)sources.push(i)}return sources};function distance(i){return links[i].distance}graph.distance=distance;function neighbors(node){var e=edges[node],ret=[];for(var i=0;i<e.length;++i){var o=e[i];if(o.source.index==node)ret.push(o.target);else ret.push(o.source)}return ret}graph.neighbors=neighbors;graph.other=function(o,node){if(typeof o=="number")o=links[o];if(o.source.index==node)return o.target;else return o.source};function compute_components(){var stack=[],comp=0,comps=[],ccomp,n=nodes.length,i,j,v,l,o,e;for(i=0;i<n;i++)nodes[i].comp=0;for(j=0;j<n;j++){if(nodes[j].comp!==0)continue;comp=comp+1;nodes[j].comp=comp;stack.push(j);ccomp=[j];while(stack.length){v=stack.shift();l=edges[v];for(i=0;i<l.length;i++){e=l[i];o=e.source;if(o.index==v)o=e.target;if(o.index==v)continue;if(o.comp===0){o.comp=comp;ccomp.push(o.index);stack.push(o.index)}}}if(ccomp.length){ccomp.sort(reorder.cmp_number);comps.push(ccomp)}}comps.sort(function(a,b){return b.length-a.length});return comps}graph.components=function(){if(!components)components=compute_components();return components};return graph};reorder.graph_random_erdos_renyi=function(n,p,directed){if(p<=0)return reorder.graph_empty(n,directed);else if(p>=1)return reorder.graph_complete(n,directed);var nodes=graph_empty_nodes(n),links=[],v,w,i,lr,lp;w=-1;lp=Math.log(1-p);if(directed){for(v=0;v<n;){lr=Math.log(1-Math.random());w=w+1+Math.floor(lr/lp);if(v==w)w=w+1;while(w>=n&&v<n){w=w-n;v=v+1;if(v==w)w=w+1}if(v<n)links.push({source:v,target:w})}}else{for(v=1;v<n;){lr=Math.log(1-Math.random());w=w+1+Math.floor(lr/lp);while(w>=v&&v<n){w=w-v;v=v+1}if(v<n)links.push({source:v,target:w})}}return reorder.graph(nodes,links,directed).init()};reorder.graph_random=reorder.graph_random_erdos_renyi;function graph_empty_nodes(n){var nodes=Array(n),i;for(i=0;i<n;i++)nodes[i]={id:i};return nodes}reorder.graph_empty_nodes=graph_empty_nodes;reorder.graph_empty=function(n,directed){return graph(graph_empty_nodes(n),[],directed)};reorder.complete_graph=function(n,directed){var nodes=graph_empty_nodes(n),links=[],i,j;if(directed){for(i=0;i<n;i++){for(j=0;j<n;j++){if(i!=j)links.push({source:i,target:j})}}}else{for(i=0;i<n-1;i++){for(j=i+1;j<n;j++)links.push({source:i,target:j})}}return reorder.graph(nodes,links,directed).init()};reorder.graph_connect=function(graph,comps){var i,j,links=graph.links();if(!comps)comps=graph.components();for(i=0;i<comps.length-1;i++){for(j=i+1;j<comps.length;j++){links.push({source:comps[i][0],target:comps[j][0]})}}graph.links(links);return graph.init()};reorder.bfs=function(graph,v,fn){var q=new Queue,discovered={},i,e,v2,edges;q.push(v);discovered[v]=true;fn(v,undefined);while(q.length){v=q.shift();fn(v,v);edges=graph.edges(v);for(i=0;i<edges.length;i++){e=edges[i];v2=graph.other(e,v).index;if(!discovered[v2]){q.push(v2);discovered[v2]=true;fn(v,v2)}}fn(v,-1)}};reorder.bfs_distances=function(graph,v){var dist={};dist[v]=0;reorder.bfs(graph,v,function(v,c){if(c>=0&&v!=c)dist[c]=dist[v]+1});return dist};reorder.all_pairs_distance_bfs=function(graph,comps){if(!comps)comps=[graph.nodes_indices()];var nodes=comps.reduce(reorder.flatten).sort(reorder.cmp_number),mat=Array(nodes.length),i,j,dist;for(i=0;i<nodes.length;i++)mat[i]=Array(nodes.length);for(i=0;i<nodes.length;i++){dist=reorder.bfs_distances(graph,i);for(j in dist){mat[i][j]=dist[j];mat[j][i]=dist[j]}}return mat};bfs_order=function(graph,comps){if(!comps)comps=graph.components();var i,comp,order=[];for(i=0;i<comps.length;i++){comp=comps[i];reorder.bfs(graph,comp[0],function(v,c){if(c>=0&&v!=c)order.push(v)})}return order};reorder.mat2graph=function(mat,directed){var n=mat.length,nodes=[],links=[],max_value=Number.NEGATIVE_INFINITY,i,j,v,m;for(i=0;i<n;i++)nodes.push({id:i});for(i=0;i<n;i++){v=mat[i];m=directed?0:i;for(j=m;j<v.length;j++){if(j==nodes.length)nodes.push({id:j});if(v[j]!==0){if(v[j]>max_value)max_value=v[j];links.push({source:i,target:j,value:v[j]})}}}return reorder.graph(nodes,links,directed).linkDistance(function(l,i){return 1+max_value-l.value}).init()};reorder.graph2mat=function(graph,directed){var nodes=graph.nodes(),links=graph.links(),n=nodes.length,i,l,mat;if(!directed)directed=graph.directed();if(directed){var rows=n,cols=n;for(i=n-1;i>=0;i--){if(graph.inEdges(i).length!==0)break;else rows--}for(i=n-1;i>=0;i--){if(graph.outEdges(i).length!==0)break;else cols--}mat=reorder.zeroes(rows,cols);for(i=0;i<links.length;i++){l=links[i];mat[l.source.index][l.target.index]=l.value?l.value:1}}else{mat=reorder.zeroes(n,n);for(i=0;i<links.length;i++){l=links[i];mat[l.source.index][l.target.index]=l.value?l.value:1;mat[l.target.index][l.source.index]=l.value?l.value:1}}return mat};function count_crossings(graph,north,south){var i,j,n,firstIndex,treeSize,tree,index,weightSum,invert=false,crosscount;var comp=reorder.permutation(graph.nodes().length);if(north===undefined){north=comp.filter(function(n){return graph.outDegree(n)!==0});south=comp.filter(function(n){return graph.inDegree(n)!==0})}if(north.length<south.length){var tmp=north;north=south;south=tmp;invert=true}var south_inv=inverse_permutation(south),southsequence=[];for(i=0;i<north.length;i++){if(invert){n=graph.inEdges(north[i]).map(function(e){return south_inv[e.target.index]})}else{n=graph.outEdges(north[i]).map(function(e){return south_inv[e.source.index]})}n.sort(reorder.cmp_number);southsequence=southsequence.concat(n)}firstIndex=1;while(firstIndex<south.length)firstIndex<<=1;treeSize=2*firstIndex-1;firstIndex-=1;tree=reorder.zeroes(treeSize);crosscount=0;for(i=0;i<southsequence.length;i++){index=southsequence[i]+firstIndex;tree[index]++;while(index>0){if(index%2)crosscount+=tree[index+1];index=index-1>>1;tree[index]++}}return crosscount}reorder.count_crossings=count_crossings;function count_in_crossings(graph,v,w,inv){var v_edges=graph.inEdges(v),w_edges=graph.inEdges(w),iv,iw,p0,cross=0;for(iw=0;iw<w_edges.length;iw++){p0=inv[w_edges[iw].target.index];for(iv=0;iv<v_edges.length;iv++){if(inv[v_edges[iv].target.index]>p0)cross++}}return cross}function count_out_crossings(graph,v,w,inv){var v_edges=graph.outEdges(v),w_edges=graph.outEdges(w),iv,iw,p0,cross=0;for(iw=0;iw<w_edges.length;iw++){p0=inv[w_edges[iw].source.index];for(iv=0;iv<v_edges.length;iv++){if(inv[v_edges[iv].source.index]>p0)cross++}}return cross}function adjacent_exchange(graph,layer1,layer2){layer1=layer1.slice();layer2=layer2.slice();var i,v,w,c0,c1,inv_layer1=inverse_permutation(layer1),inv_layer2=inverse_permutation(layer2),swapped=true,improved=0;while(swapped){swapped=false;for(i=0;i<layer1.length-1;i++){v=layer1[i];w=layer1[i+1];c0=count_out_crossings(graph,v,w,inv_layer2);c1=count_out_crossings(graph,w,v,inv_layer2);if(c0>c1){layer1[i]=w;layer1[i+1]=v;inv_layer1[w]=i;inv_layer1[v]=i+1;swapped=true;improved+=c0-c1}}for(i=0;i<layer2.length-1;i++){v=layer2[i];w=layer2[i+1];c0=count_in_crossings(graph,v,w,inv_layer1);c1=count_in_crossings(graph,w,v,inv_layer1);if(c0>c1){layer2[i]=w;layer2[i+1]=v;inv_layer2[w]=i;inv_layer2[v]=i+1;swapped=true;improved+=c0-c1}}}return[layer1,layer2,improved]}reorder.adjacent_exchange=adjacent_exchange;reorder.barycenter_order=function(graph,comps,max_iter){var orders=[[],[],0];if(!comps){comps=graph.components()}for(var i=0;i<comps.length;i++){var o=reorder.barycenter(graph,comps[i],max_iter);orders=[orders[0].concat(o[0]),orders[1].concat(o[1]),orders[2]+o[2]]}return orders};function median(neighbors){if(neighbors.length===0)return-1;if(neighbors.length===1)return neighbors[0];if(neighbors.length===2)return(neighbors[0]+neighbors[1])/2;neighbors.sort(reorder.cmp_number);if(neighbors.length%2)return neighbors[(neighbors.length-1)/2];var rm=neighbors.length/2,lm=rm-1,rspan=neighbors[neighbors.length-1]-neighbors[rm],lspan=neighbors[lm]-neighbors[0];if(lspan==rspan)return(neighbors[lm]+neighbors[rm])/2;else return(neighbors[lm]*rspan+neighbors[rm]*lspan)/(lspan+rspan)}reorder.barycenter=function(graph,comp,max_iter){var nodes=graph.nodes(),layer1,layer2,crossings,iter,best_layer1,best_layer2,best_crossings,best_iter,layer,inv_layer={},i,v,neighbors,med;layer1=comp.filter(function(n){return graph.outDegree(n)!==0});layer2=comp.filter(function(n){return graph.inDegree(n)!==0});if(comp.length<3){return[layer1,layer2,count_crossings(graph,layer1,layer2)]}if(!max_iter)max_iter=24;else if(max_iter%2==1)max_iter++;inv_layer=inverse_permutation(layer2);best_crossings=count_crossings(graph,layer1,layer2);best_layer1=layer1.slice();best_layer2=layer2.slice();best_iter=0;var inv_neighbor=function(e){var n=e.source==v?e.target:e.source;return inv_layer[n.index]},barycenter_sort=function(a,b){var d=med[a]-med[b];if(d===0){d=graph.edges(b).length%2-graph.edges(a).length%2}if(d<0)return-1;else if(d>0)return 1;return 0};for(layer=layer1,iter=0;iter<max_iter;iter++,layer=layer==layer1?layer2:layer1){med={};for(i=0;i<layer.length;i++){v=nodes[layer[i]];if(layer==layer1)neighbors=graph.outEdges(v.index);else neighbors=graph.inEdges(v.index);neighbors=neighbors.map(inv_neighbor);med[v.index]=+median(neighbors)}layer.sort(barycenter_sort);for(i=0;i<layer.length;i++)inv_layer=inverse_permutation(layer);crossings=count_crossings(graph,layer1,layer2);if(crossings<best_crossings){best_crossings=crossings;best_layer1=layer1.slice();best_layer2=layer2.slice();best_iter=iter;max_iter=Math.max(max_iter,iter+2)}}return[best_layer1,best_layer2,best_crossings]};reorder.all_pairs_distance=function(graph,comps){var distances=[];if(!comps)comps=graph.components();for(var i=0;i<comps.length;i++)distances.push(all_pairs_distance_floyd_warshall(graph,comps[i]));return distances};function all_pairs_distance_floyd_warshall(graph,comp){var dist=reorder.infinities(comp.length,comp.length),i,j,k,inv;inv=inverse_permutation(comp);for(i=0;i<comp.length;i++)dist[i][i]=0;var build_dist=function(e){if(e.source==e.target)return;if(!(e.source.index in inv)||!(e.target.index in inv))return;var u=inv[e.source.index],v=inv[e.target.index];dist[v][u]=dist[u][v]=graph.distance(e.index)};for(i=0;i<comp.length;i++){graph.edges(comp[i]).forEach(build_dist)}for(k=0;k<comp.length;k++){for(i=0;i<comp.length;i++)if(dist[i][k]!=Infinity){for(j=0;j<comp.length;j++)if(dist[k][j]!=Infinity&&dist[i][j]>dist[i][k]+dist[k][j]){dist[i][j]=dist[i][k]+dist[k][j];dist[j][i]=dist[i][j]}}}return dist}reorder.all_pairs_distance_floyd_warshall=all_pairs_distance_floyd_warshall;function floyd_warshall_with_path(graph,comp){if(!comp)comp=graph.components()[0];var dist=reorder.infinities(comp.length,comp.length),next=Array(comp.length),directed=graph.directed(),i,j,k,inv;inv=inverse_permutation(comp);for(i=0;i<comp.length;i++){dist[i][i]=0;next[i]=Array(comp.length)}var build_dist=function(e){if(e.source==e.target)return;var u=inv[e.source.index],v=inv[e.target.index];dist[u][v]=graph.distance(e);next[u][v]=v;if(!directed){dist[v][u]=graph.distance(e);next[v][u]=u}};for(i=0;i<comp.length;i++){graph.edges(comp[i]).forEach(build_dist)}for(k=0;k<comp.length;k++){for(i=0;i<comp.length;i++){for(j=0;j<comp.length;j++){if(dist[i][j]>dist[i][k]+dist[k][j]){dist[i][j]=dist[i][k]+dist[k][j];next[i][j]=next[i][k];if(!directed){dist[j][i]=dist[i][j];next[j][i]=next[k][j]}}}}}return[dist,next]}reorder.floyd_warshall_with_path=floyd_warshall_with_path;function floyd_warshall_path(next,u,v){if(next[u][v]===undefined)return[];var path=[u];while(u!=v){u=next[u][v];path.push(u)}return path}reorder.floyd_warshall_path=floyd_warshall_path;function distmat2valuemat(distmat){var n=distmat.length,valuemat=reorder.zeroes(n,n),max_dist=reorder.distmax(distmat),i,j;for(i=0;i<n;i++){for(j=i;j<n;j++){valuemat[j][i]=valuemat[i][j]=1+max_dist-distmat[i][j]}}return valuemat}reorder.distmat2valuemat=distmat2valuemat;reorder.graph2valuemats=function(graph,comps){if(!comps)comps=graph.components();var dists=reorder.all_pairs_distance(graph,comps);return dists.map(distmat2valuemat)};reorder.valuemats_reorder=function(valuemats,leaforder,comps){var orders=valuemats.map(leaforder);if(comps){orders=orders.map(function(d,i){return reorder.permute(comps[i],d)})}return orders.reduce(reorder.flatten)};reorder.dist=function(){var distance=reorder.distance.euclidean;function dist(vectors){var n=vectors.length,distMatrix=[];for(var i=0;i<n;i++){var d=[];distMatrix[i]=d;for(var j=0;j<n;j++){if(j<i){d.push(distMatrix[j][i])}else if(i===j){d.push(0)}else{d.push(distance(vectors[i],vectors[j]))}}}return distMatrix}dist.distance=function(x){if(!arguments.length)return distance;distance=x;return dist};return dist};reorder.distmax=function(distMatrix){var max=0,n=distMatrix.length,i,j,row;for(i=0;i<n;i++){row=distMatrix[i];for(j=i+1;j<n;j++)if(row[j]>max)max=row[j]}return max};reorder.distmin=function(distMatrix){var min=Infinity,n=distMatrix.length,i,j,row;for(i=0;i<n;i++){row=distMatrix[i];for(j=i+1;j<n;j++)if(row[j]<min)min=row[j]}return min};reorder.dist_remove=function(dist,n,m){if(arguments.length<3)m=n+1;var i;dist.splice(n,m-n);for(i=dist.length;i-->0;)dist[i].splice(n,m-n);return dist};reorder.randomPermute=function(array,i,j){if(arguments.length<3){j=array.length;if(arguments.length<2){i=0}}var m=j-i,t,k;while(m>0){k=i+Math.floor(Math.random()*m--);t=array[i+m];array[i+m]=array[k];array[k]=t}return array};reorder.randomPermutation=function(n){return reorder.randomPermute(reorder.permutation(n))};reorder.random_array=function(n,min,max){var ret=Array(n);if(arguments.length==1){while(n)ret[--n]=Math.random()}else if(arguments.length==2){while(n)ret[--n]=Math.random()*min}else{while(n)ret[--n]=min+Math.random()*(max-min)}return ret};reorder.random_matrix=function(p,n,m,sym){if(!m)m=n;if(n!=m)sym=false;else if(!sym)sym=true;var mat=reorder.zeroes(n,m),i,j,cnt;if(sym){for(i=0;i<n;i++){cnt=0;for(j=0;j<i+1;j++){if(Math.random()<p){mat[i][j]=mat[j][i]=1;cnt++}}if(cnt===0){j=Math.floor(Math.random()*n/2);mat[i][j]=mat[j][i]=1}}}else{for(i=0;i<n;i++){cnt=0;for(j=0;j<m;j++){if(Math.random()<p){mat[i][j]=1;cnt++}}if(cnt===0)mat[i][Math.floor(Math.random()*m)]=1}}return mat};function permute_copy(list,perm){var m=perm.length;var copy=list.slice();while(m--)copy[m]=list[perm[m]];return copy}reorder.permute=permute_copy;function permute_inplace(list,perm){var i,j,v,tmp;for(i=0;i<list.length;i++){j=perm[i];if(j<0){perm[i]=-1-j;continue}v=i;while(j!=i){tmp=list[j];list[j]=list[v];list[v]=tmp;v=j;tmp=perm[j];perm[j]=-1-tmp;j=tmp}}return list}reorder.permute_inplace=permute_inplace;reorder.permutetranspose=function(array,indexes){var m=array.length;while(m-->0)array[m]=reorder.permute(array[m],indexes);return array};reorder.stablepermute=function(list,indexes){var p=reorder.permute(list,indexes);if(p[0]>p[p.length-1]){p.reverse()}return p};reorder.sort_order=function(v){return reorder.permutation(0,v.length).sort(function(a,b){return v[a]-v[b]})};if(typeof science=="undefined"){science={version:"1.9.1"};science.stats={}}science.stats.hcluster=function(){var distance=reorder.distance.euclidean,linkage="single",distMatrix=null;function hcluster(vectors){var n=vectors.length,dMin=[],cSize=[],clusters=[],c1,c2,c1Cluster,c2Cluster,p,root,i,j,id=0;if(distMatrix===null){distMatrix=[];i=-1;while(++i<n){dMin[i]=0;distMatrix[i]=[];j=-1;while(++j<n){distMatrix[i][j]=i===j?Infinity:distance(vectors[i],vectors[j]);if(distMatrix[i][dMin[i]]>distMatrix[i][j])dMin[i]=j}}}else{if(distMatrix.length<n||distMatrix[0].length<n)throw{error:"Provided distance matrix length "+distMatrix.length+" instead of "+n};i=-1;while(++i<n){dMin[i]=0;j=-1;while(++j<n){if(i===j)distMatrix[i][j]=Infinity;if(distMatrix[i][dMin[i]]>distMatrix[i][j])dMin[i]=j}}}i=-1;while(++i<n){if(i!=id)console.log("i = %d, id = %d",i,id);clusters[i]=[];clusters[i][0]={left:null,right:null,dist:0,centroid:vectors[i],id:id++,size:1,depth:0};cSize[i]=1}for(p=0;p<n-1;p++){c1=0;for(i=0;i<n;i++){if(distMatrix[i][dMin[i]]<distMatrix[c1][dMin[c1]])c1=i}c2=dMin[c1];c1Cluster=clusters[c1][0];c2Cluster=clusters[c2][0];var newCluster={left:c1Cluster,right:c2Cluster,dist:distMatrix[c1][c2],centroid:calculateCentroid(c1Cluster.size,c1Cluster.centroid,c2Cluster.size,c2Cluster.centroid),id:id++,size:c1Cluster.size+c2Cluster.size,depth:1+Math.max(c1Cluster.depth,c2Cluster.depth)};clusters[c1].splice(0,0,newCluster);cSize[c1]+=cSize[c2];for(j=0;j<n;j++){switch(linkage){case"single":if(distMatrix[c1][j]>distMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"complete":if(distMatrix[c1][j]<distMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"average":distMatrix[j][c1]=distMatrix[c1][j]=(cSize[c1]*distMatrix[c1][j]+cSize[c2]*distMatrix[c2][j])/(cSize[c1]+cSize[j]);break}}distMatrix[c1][c1]=Infinity;for(i=0;i<n;i++)distMatrix[i][c2]=distMatrix[c2][i]=Infinity;for(j=0;j<n;j++){if(dMin[j]==c2)dMin[j]=c1;if(distMatrix[c1][j]<distMatrix[c1][dMin[c1]])dMin[c1]=j}root=newCluster}return root}hcluster.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return hcluster};hcluster.distance=function(x){if(!arguments.length)return distance;distance=x;return hcluster};hcluster.distanceMatrix=function(x){if(!arguments.length)return distMatrix;distMatrix=x.map(function(y){return y.slice(0)});return hcluster};return hcluster};function calculateCentroid(c1Size,c1Centroid,c2Size,c2Centroid){var newCentroid=[],newSize=c1Size+c2Size,n=c1Centroid.length,i=-1;while(++i<n){newCentroid[i]=(c1Size*c1Centroid[i]+c2Size*c2Centroid[i])/newSize}return newCentroid}reorder.optimal_leaf_order=function(){var distanceMatrix=null,distance=reorder.distance.euclidean,linkage="complete",debug=0,leavesMap={},orderMap={};function isLeaf(n){return n.depth===0}function leaves(n){if(n===null)return[];if(n.id in leavesMap)return leavesMap[n.id];return leavesMap[n.id]=_leaves(n)}function _leaves(n){if(n===null)return[];if(n.depth===0)return[n.id];return leaves(n.left).concat(leaves(n.right))}function order(v,i,j){var key="k"+v.id+"-"+i+"-"+j;if(key in orderMap)return orderMap[key];return orderMap[key]=_order(v,i,j)}function _order(v,i,j){if(v.depth===0)return[0,[v.id]];var l=v.left,r=v.right;var L=leaves(l),R=leaves(r);var w,x;if(L.indexOf(i)!==-1&&R.indexOf(j)!==-1){w=l;x=r}else if(R.indexOf(i)!==-1&&L.indexOf(j)!==-1){w=r;x=l}else throw{error:"Node is not common ancestor of "+i+", "+j};var Wl=leaves(w.left),Wr=leaves(w.right);var Ks=Wr.indexOf(i)!=-1?Wl:Wr;if(Ks.length===0)Ks=[i];var Xl=leaves(x.left),Xr=leaves(x.right);var Ls=Xr.indexOf(j)!=-1?Xl:Xr;if(Ls.length===0)Ls=[j];var min=Infinity,optimal_order=[];for(var k=0;k<Ks.length;k++){var w_min=order(w,i,Ks[k]);for(var m=0;m<Ls.length;m++){var x_min=order(x,Ls[m],j);var dist=w_min[0]+distanceMatrix[Ks[k]][Ls[m]]+x_min[0];if(dist<min){min=dist;optimal_order=w_min[1].concat(x_min[1])}}}return[min,optimal_order]}function orderFull(v){leavesMap={};orderMap={};var min=Infinity,optimal_order=[],left=leaves(v.left),right=leaves(v.right);if(debug)console.log(reorder.printhcluster(v,0));for(var i=0;i<left.length;i++){for(var j=0;j<right.length;j++){var so=order(v,left[i],right[j]);if(so[0]<min){min=so[0];optimal_order=so[1]}}}distanceMatrix=null;return optimal_order}optimal_leaf_order.order=orderFull;function optimal_leaf_order(matrix){if(distanceMatrix===null)distanceMatrix=reorder.dist().distance(distance)(matrix);var hcluster=science.stats.hcluster().linkage(linkage).distanceMatrix(distanceMatrix);return orderFull(hcluster(matrix))}optimal_leaf_order.debug=function(x){if(!arguments.length)return debug;debug=x;return optimal_leaf_order};optimal_leaf_order.distance=function(x){if(!arguments.length)return distance;distance=x;distanceMatrix=null;return optimal_leaf_order};optimal_leaf_order.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return optimal_leaf_order};optimal_leaf_order.distance_matrix=function(x){if(!arguments.length)return distanceMatrix;distanceMatrix=x.map(function(y){return y.slice(0)});return optimal_leaf_order};optimal_leaf_order.distanceMatrix=optimal_leaf_order.distance_matrix;return optimal_leaf_order};reorder.order=function(){var distance=reorder.distance.euclidean,ordering=reorder.optimal_leaf_order,linkage="complete",distanceMatrix=null,vector,except=[],debug=0,i=0,j=Infinity;function _reset(){distance=reorder.distance.euclidean;ordering=reorder.optimal_leaf_order;linkage="complete";distanceMatrix=null;vector=null;except=[];debug=0;i=0;j=Infinity}function order(v){vector=v;j=Math.min(j,v.length);var i0=i>0?i-1:0,j0=j<vector.length?j+1:j,k,low,high;for(k=except.length-1;k>0;k-=2){low=except[k-1];high=except[k];if(high>=j0){if(j0>j){j0=Math.min(j0,low+1);except.splice(k-1,2)}else{high=j0}}else if(low<=i0){if(i0<i){i0=Math.max(i0,high-1);except.splice(k-1,2)}else{low=i0}}else if(high-low<3)except.splice(k-1,2)}try{return _order_limits(i0,j0)}finally{_reset()}}function _order_limits(i0,j0){var orig=vector,perm,row,k,l;vector=vector.slice(i0,j0);if(i===0&&j==vector.length)return _order_except();if(debug)console.log("i0="+i0+" j0="+j0);if(distanceMatrix!==null){if(j0!==vector.length)reorder.dist_remove(distanceMatrix,j0,vector.length);if(i0>0)reorder.dist_remove(distanceMatrix,0,i0)}else{_compute_dist()}var max=reorder.distmax(distanceMatrix);if(i0<i){row=distanceMatrix[0];for(k=row.length;k-->1;)row[k]+=max;for(k=distanceMatrix.length;k-->1;)distanceMatrix[k][0]+=max;max+=max;if(i0!==0){for(k=0;k<except.length;k++)except[k]-=i0}}if(j0>j){l=distanceMatrix.length-1;row=distanceMatrix[l];for(k=l;k-->0;){row[k]+=max;distanceMatrix[k][l]+=max}}perm=_order_except();if(i0<i){if(perm[0]!==0)perm.reverse();if(j0>j){reorder.assert(perm[0]===0&&perm[perm.length-1]==perm.length-1,"Invalid constrained permutation endpoints")}else{reorder.assert(perm[0]===0,"Invalid constrained permutation start")}}else if(j0>j){if(perm[perm.length-1]!==perm.length-1)perm=perm.reverse();reorder.assert(perm[perm.length-1]==perm.length-1,"Invalid constrained permutation end")}if(i0!==0){perm=reorder.permutation(i0).concat(perm.map(function(v){return v+i0}))}if(orig.length>j0){perm=perm.concat(reorder.range(j0,orig.length))}return perm}function _order_except(){var perm,k,l,low,high,pos;if(except.length===0)return _order_equiv();_compute_dist();for(k=except.length-1;k>0;k-=2){low=except[k-1];high=except[k];distanceMatrix=reorder.dist_remove(distanceMatrix,low+1,high-1);vector.splice(low+1,high-low-2);if(debug)console.log("Except["+low+", "+high+"]");if(distanceMatrix[low][low+1]!==0){distanceMatrix[low][low+1]=distanceMatrix[low+1][low]=-1}}perm=_order_equiv();for(k=0;k<except.length;k+=2){low=except[k];high=except[k+1];for(l=0;l<perm.length;l++){if(perm[l]>low)perm[l]+=high-low-2;else if(perm[l]==low)pos=l}if(pos>0&&perm[pos-1]==high-1){Array.prototype.splice.apply(perm,[pos,0].concat(reorder.range(high-2,low,-1)))}else if(perm[pos+1]==high-1){Array.prototype.splice.apply(perm,[pos+1,0].concat(reorder.range(low+1,high-1)))}else{throw"Range not respected"}}return perm}function _order_equiv(){var perm,row,e,j,k,l,m,n,has_1=false,equiv=[],fix_except={};_compute_dist();for(k=0;k<distanceMatrix.length-1;k++){row=distanceMatrix[k];e=[];j=row.indexOf(-1);if(j!==-1){fix_except[k]=[k,j];has_1=true}for(l=row.length;--l>k;){if(row[l]===0){j=distanceMatrix[l].indexOf(-1);if(j!==-1){fix_except[k]=[l,j];distanceMatrix[j][k]=row[j]=-1;has_1=true}e.unshift(l);distanceMatrix=reorder.dist_remove(distanceMatrix,l);vector.splice(l,1)}else if(row[l]<0)has_1=true}if(e.length!==0){e.unshift(k);equiv.push(e)}}if(has_1){for(k=0;k<distanceMatrix.length-1;k++){row=distanceMatrix[k];for(l=k+1;l<row.length-1;l++){if(distanceMatrix[l][l+1]==-1){distanceMatrix[l+1][l]=distanceMatrix[l][l+1]=0}}}}perm=_order();for(k=equiv.length;k-->0;){e=equiv[k];l=perm.indexOf(e[0]);m=fix_except[e[0]];if(m&&m[0]==e[0]){l=_fix_exception(perm,l,m[0],m[1],0);m=undefined}for(n=1;n<e.length;n++){perm=_perm_insert(perm,l,e[n]);if(m&&m[0]==e[n]){l=_fix_exception(perm,l,m[0],m[1],n);m=undefined}}}return perm}function _fix_exception(perm,l,m,next,len){var i,j,k;if(l>0&&perm[l-1]==next){_swap(perm,l,perm.indexOf(m));return l+1}else if(perm[l+len+1]==next){_swap(perm,l+len,perm.indexOf(m));return l}else throw"Index not found"}function _swap(perm,a,b){if(a==b)return;var c=perm[a];perm[a]=perm[b];perm[b]=c}function _order(){if(debug>1)reorder.printmat(distanceMatrix);if(debug>2)reorder.printmat(vector);var perm=ordering().debug(debug).linkage(linkage).distanceMatrix(distanceMatrix)(vector);if(debug)console.log("Permutation: "+perm);return perm}function _perm_insert(perm,i,nv){perm=perm.map(function(v){return v<nv?v:v+1});perm.splice(i,0,nv);return perm}order.debug=function(x){if(!arguments.length)return debug;
 
-debug=x;return order};function _compute_dist(){if(distanceMatrix===null)distanceMatrix=reorder.dist().distance(distance)(vector);return distanceMatrix}order.distance=function(x){if(!arguments.length)return distance;distance=x;return order};order.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return order};order.limits=function(x,y){if(!arguments.length)return[i,j];i=x;j=y;return order};order.except=function(list){if(!arguments.length)return except.slice(0);except=list.sort(function(a,b){if(a>=b)throw"Invalid list, indices not sorted";return a-b});return order};function _orderExcept(vector,i,j){var distanceMatrix=reorder.dist().distance(distance)(vector);var row,k,l,rev=false,args,pos=-1;distanceMatrix[i][i+1]=0;distanceMatrix[i+1][i]=0;var perm=ordering().distanceMatrix(distanceMatrix)(vector);pos=perm.indexOf(i);for(k=0;k<perm.length;k++){l=perm[k];if(l>i)perm[k]+=j-i-2}if(pos!==0&&perm[pos-1]===j-1)rev=true;if(rev){perm.reverse();pos=perm.length-pos-1}args=[pos+1,0].concat(reorder.range(i+1,j-1));Array.prototype.splice.apply(perm,args);return perm}order.orderrowsexcept=order.orderexcept;return order};reorder.covariance=reorder.dot;reorder.covariancetranspose=function(v,a,b){var n=v.length,cov=0,i;for(i=0;i<n;i++){cov+=v[i][a]*v[i][b]}return cov};reorder.variancecovariance=function(v){var o=v[0].length,cov=Array(o),i,j;for(i=0;i<o;i++){cov[i]=Array(o)}for(i=0;i<o;i++){for(j=i;j<o;j++)cov[i][j]=cov[j][i]=reorder.covariancetranspose(v,i,j)}return cov};reorder.laplacian=function(graph,comp){var n=comp.length,lap=reorder.zeroes(n,n),inv=inverse_permutation(comp),i,j,k,row,sum,edges,v,e,other;reorder.assert(!graph.directed(),"Laplacian only for undirected graphs");for(i=0;i<n;i++){v=comp[i];row=lap[i];sum=0;edges=graph.edges(v);for(j=0;j<edges.length;j++){e=edges[j];other=inv[graph.other(e,v).index];if(other!=i){sum+=e.value;row[other]=-e.value}}row[i]=sum}return lap};function normalize(v){var norm=science.lin.length(v),i=v.length;if(norm===0||Math.abs(norm-1)<1e-7)return v;while(i-->0)v[i]/=norm;return v}reorder.poweriteration=function(v,eps,init){if(!eps)eps=1e-9;var n=v.length,b,i,j,tmp=Array(n),norm,s=100,e;reorder.assert(n==v[0].length,"poweriteration needs a square matrix");if(!init){b=reorder.random_array(n)}else b=init.slice();normalize(b);while(s-->0){for(i=0;i<n;i++){tmp[i]=0;for(j=0;j<n;j++)tmp[i]+=v[i][j]*b[j]}normalize(tmp);if(reorder.dot(tmp,b)>1-eps)break;var t=tmp;tmp=b;b=t}return tmp};reorder.poweriteration_n=function(v,p,init,eps,start){if(!eps)eps=1e-9;var n=v.length,b=Array(p),i,j,k,l,bk,dot,row,tmp=Array(n),s=100;reorder.assert(n==v[0].length,"poweriteration needs a square matrix");if(!init){for(i=0;i<p;i++){row=b[i]=reorder.random_array(n);normalize(row)}}else{for(i=0;i<p;i++){b[i]=init[i].slice();normalize(b[i])}}if(!start)start=0;for(k=start;k<p;k++){bk=b[k];while(s-->0){for(l=0;l<k;l++){row=b[l];dot=reorder.dot(bk,row);for(i=0;i<n;i++)bk[i]-=dot*row[i]}for(i=0;i<n;i++){tmp[i]=0;for(j=0;j<n;j++)tmp[i]+=v[i][j]*bk[j]}normalize(tmp);if(reorder.dot(tmp,bk)>1-eps)break;bk=tmp;tmp=b[k];b[k]=bk}}return b};function gershgorin_bound(B){var i,j,max=0,n=B.length,t,row;for(i=0;i<n;i++){row=B[i];t=row[i];for(j=0;j<n;j++)if(j!=i)t+=Math.abs(row[j]);if(t>max)max=t}return max}function fiedler_vector(B,eps){var g=gershgorin_bound(B),n=B.length,Bhat=B.map(function(row){return row.slice()}),i,j,row;for(i=0;i<n;i++){row=Bhat[i];for(j=0;j<n;j++){if(i==j)row[j]=g-row[j];else row[j]=-row[j]}}var init=[reorder.array1d(n,1),reorder.random_array(n)],eig=reorder.poweriteration_n(Bhat,2,init,eps,1);return eig[1]}reorder.fiedler_vector=fiedler_vector;function spectral_order(graph,comps){var i,vec,comp,perm,order=[];if(!comps)comps=graph.components();for(i=0;i<comps.length;i++){comp=comps[i];vec=reorder.fiedler_vector(reorder.laplacian(graph,comp));perm=reorder.sort_order(vec);order=order.concat(reorder.permute(comp,perm))}return order}reorder.spectral_order=spectral_order;function center(v){var n=v.length;if(n===0)return null;var mean=reorder.meancolumns(v),o=mean.length,v1=Array(n),i,j,row;for(i=0;i<n;i++){row=v[i].slice(0);for(j=0;j<o;j++){row[j]-=mean[j]}v1[i]=row}return v1}reorder.pca1d=function(v,eps){var n=v.length;if(v.length===0)return null;v=center(v);var cov=reorder.variancecovariance(v);return reorder.poweriteration(cov,eps)};reorder.pca_order=function(v,eps){return reorder.sort_order(pca1d(v,eps))};reorder.sumlines=function(v){var n=v.length,o=v[0].length,sumline=Array(n),i,j,row,s;for(i=0;i<n;i++){row=v[i];s=0;for(j=0;j<o;j++)s+=row[j];sumline[i]=s}return sumline};reorder.sumcols=function(v){var n=v.length,o=v[0].length,sumcol=reorder.zeroes(o),i,j,row;for(i=0;i<n;i++){row=v[i];for(j=0;j<o;j++)sumcol[j]+=row[j]}return sumcol};reorder.ca=function(v,eps){var n=v.length,o=v[0].length,sumline=reorder.sumlines(v),sumcol=reorder.sumcols(v),s=reorder.sum(sumcol),i,j,row;for(i=0;i<n;i++){row=v[i];for(j=0;j<row.length;j++)row[j]/=s}sumline=reorder.sumlines(v);sumcol=reorder.sumcols(v);var v2=Array(n),ep;for(i=0;i<n;i++){v2[i]=Array(o);for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v2[i][j]=(v[i][j]-ep)/Math.sqrt(ep)}}for(i=0;i<n;i++){for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v[i][j]=(v[i][j]-ep)/(sumcol[j]*Math.sqrt(sumline[i]))}}var cov=Array(n);for(i=0;i<n;i++)cov[i]=Array(n);for(i=0;i<n;i++)for(j=i;j<n;j++)cov[i][j]=cov[j][i]=reorder.covariance(v2[i],v2[j]);var eigenvector1=reorder.poweriteration(cov,eps),eigenvalue1=0;for(i=0;i<n;i++)eigenvalue1+=eigenvector1[i]*cov[i][0];eigenvalue1/=eigenvector1[0];return eigenvector1};reorder.cuthill_mckee=function(graph,comp){if(comp.length<3)return comp;var nodes=graph.nodes(),start=comp[0],min_deg=graph.degree(start),i,n,edges,e,visited={},queue=new Queue,inv=inverse_permutation(comp),perm=[];for(i=0;i<comp.length;i++){n=comp[i];if(graph.degree(n)<min_deg){min_deg=graph.degree(n);start=n;if(min_deg==1)break}}queue.push(start);while(queue.length!==0){n=queue.shift();if(visited[n])continue;visited[n]=true;perm.push(n);e=graph.edges(n).map(function(edge){return graph.other(edge,n).index}).filter(function(n){return!visited[n]&&n in inv}).sort(function(a,b){return graph.degree(a)-graph.degree(b)});e.forEach(queue.push,queue)}return perm};reorder.reverse_cuthill_mckee=function(graph,comp){return reorder.cuthill_mckee(graph,comp).reverse()};reorder.cuthill_mckee_order=function(graph,comps){var i,comp,order=[];if(!comps){comps=graph.components()}for(i=0;i<comps.length;i++){comp=comps[i];order=order.concat(reorder.cuthill_mckee(graph,comp))}return order};reorder.reverse_cuthill_mckee_order=function(graph,comps){var i,comp,order=[];if(!comps){comps=graph.components()}for(i=0;i<comps.length;i++){comp=comps[i];order=order.concat(reorder.reverse_cuthill_mckee(graph,comp))}return order};reorder.condition=function(matrix){var i,j,min,max,v,s,row,ret=[];for(i=0;0<matrix.length;i++){row=matrix[i].slice();row.push(ret);for(j=0;j<ret.length;j++){v=row[j];if(v!==null&&b>=b){min=max=row[j];break}}for(;j<ret.length;j++){v=row[j];if(v<min)min=v;else if(v>max)max=v}s=max!=min?1/(max-min):0;for(j=1;j<ret.length;j++){v=row[j];if(v!=null&&v>=v)row[j]=row[j]*s-min;else v=NaN}}return ret}})(this);
\ No newline at end of file
+debug=x;return order};function _compute_dist(){if(distanceMatrix===null)distanceMatrix=reorder.dist().distance(distance)(vector);return distanceMatrix}order.distance=function(x){if(!arguments.length)return distance;distance=x;return order};order.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return order};order.limits=function(x,y){if(!arguments.length)return[i,j];i=x;j=y;return order};order.except=function(list){if(!arguments.length)return except.slice(0);except=list.sort(function(a,b){if(a>=b)throw"Invalid list, indices not sorted";return a-b});return order};function _orderExcept(vector,i,j){var distanceMatrix=reorder.dist().distance(distance)(vector);var row,k,l,rev=false,args,pos=-1;distanceMatrix[i][i+1]=0;distanceMatrix[i+1][i]=0;var perm=ordering().distanceMatrix(distanceMatrix)(vector);pos=perm.indexOf(i);for(k=0;k<perm.length;k++){l=perm[k];if(l>i)perm[k]+=j-i-2}if(pos!==0&&perm[pos-1]===j-1)rev=true;if(rev){perm.reverse();pos=perm.length-pos-1}args=[pos+1,0].concat(reorder.range(i+1,j-1));Array.prototype.splice.apply(perm,args);return perm}order.orderrowsexcept=order.orderexcept;return order};reorder.covariance=reorder.dot;reorder.covariancetranspose=function(v,a,b){var n=v.length,cov=0,i;for(i=0;i<n;i++){cov+=v[i][a]*v[i][b]}return cov};reorder.variancecovariance=function(v){var o=v[0].length,cov=Array(o),i,j;for(i=0;i<o;i++){cov[i]=Array(o)}for(i=0;i<o;i++){for(j=i;j<o;j++)cov[i][j]=cov[j][i]=reorder.covariancetranspose(v,i,j)}return cov};reorder.laplacian=function(graph,comp){var n=comp.length,lap=reorder.zeroes(n,n),inv=inverse_permutation(comp),i,j,k,row,sum,edges,v,e,other;reorder.assert(!graph.directed(),"Laplacian only for undirected graphs");for(i=0;i<n;i++){v=comp[i];row=lap[i];sum=0;edges=graph.edges(v);for(j=0;j<edges.length;j++){e=edges[j];other=inv[graph.other(e,v).index];if(other!=i){sum+=e.value;row[other]=-e.value}}row[i]=sum}return lap};function normalize(v){var norm=science.lin.length(v),i=v.length;if(norm===0||Math.abs(norm-1)<1e-7)return v;while(i-->0)v[i]/=norm;return v}reorder.poweriteration=function(v,eps,init){if(!eps)eps=1e-9;var n=v.length,b,i,j,tmp=Array(n),norm,s=100,e;reorder.assert(n==v[0].length,"poweriteration needs a square matrix");if(!init){b=reorder.random_array(n)}else b=init.slice();normalize(b);while(s-->0){for(i=0;i<n;i++){tmp[i]=0;for(j=0;j<n;j++)tmp[i]+=v[i][j]*b[j]}normalize(tmp);if(reorder.dot(tmp,b)>1-eps)break;var t=tmp;tmp=b;b=t}return tmp};reorder.poweriteration_n=function(v,p,init,eps,start){if(!eps)eps=1e-9;var n=v.length,b=Array(p),i,j,k,l,bk,dot,row,tmp=Array(n),s=100;reorder.assert(n==v[0].length,"poweriteration needs a square matrix");if(!init){for(i=0;i<p;i++){row=b[i]=reorder.random_array(n);normalize(row)}}else{for(i=0;i<p;i++){b[i]=init[i].slice();normalize(b[i])}}if(!start)start=0;for(k=start;k<p;k++){bk=b[k];while(s-->0){for(l=0;l<k;l++){row=b[l];dot=reorder.dot(bk,row);for(i=0;i<n;i++)bk[i]-=dot*row[i]}for(i=0;i<n;i++){tmp[i]=0;for(j=0;j<n;j++)tmp[i]+=v[i][j]*bk[j]}normalize(tmp);if(reorder.dot(tmp,bk)>1-eps)break;bk=tmp;tmp=b[k];b[k]=bk}}return b};function gershgorin_bound(B){var i,j,max=0,n=B.length,t,row;for(i=0;i<n;i++){row=B[i];t=row[i];for(j=0;j<n;j++)if(j!=i)t+=Math.abs(row[j]);if(t>max)max=t}return max}function fiedler_vector(B,eps){var g=gershgorin_bound(B),n=B.length,Bhat=B.map(function(row){return row.slice()}),i,j,row;for(i=0;i<n;i++){row=Bhat[i];for(j=0;j<n;j++){if(i==j)row[j]=g-row[j];else row[j]=-row[j]}}var init=[reorder.array1d(n,1),reorder.random_array(n)],eig=reorder.poweriteration_n(Bhat,2,init,eps,1);return eig[1]}reorder.fiedler_vector=fiedler_vector;function spectral_order(graph,comps){var i,vec,comp,perm,order=[];if(!comps)comps=graph.components();for(i=0;i<comps.length;i++){comp=comps[i];vec=reorder.fiedler_vector(reorder.laplacian(graph,comp));perm=reorder.sort_order(vec);order=order.concat(reorder.permute(comp,perm))}return order}reorder.spectral_order=spectral_order;function center(v){var n=v.length;if(n===0)return null;var mean=reorder.meancolumns(v),o=mean.length,v1=Array(n),i,j,row;for(i=0;i<n;i++){row=v[i].slice(0);for(j=0;j<o;j++){row[j]-=mean[j]}v1[i]=row}return v1}reorder.pca1d=function(v,eps){var n=v.length;if(v.length===0)return null;v=center(v);var cov=reorder.variancecovariance(v);return reorder.poweriteration(cov,eps)};reorder.pca_order=function(v,eps){return reorder.sort_order(pca1d(v,eps))};reorder.sumlines=function(v){var n=v.length,o=v[0].length,sumline=Array(n),i,j,row,s;for(i=0;i<n;i++){row=v[i];s=0;for(j=0;j<o;j++)s+=row[j];sumline[i]=s}return sumline};reorder.sumcols=function(v){var n=v.length,o=v[0].length,sumcol=reorder.zeroes(o),i,j,row;for(i=0;i<n;i++){row=v[i];for(j=0;j<o;j++)sumcol[j]+=row[j]}return sumcol};reorder.ca=function(v,eps){var n=v.length,o=v[0].length,sumline=reorder.sumlines(v),sumcol=reorder.sumcols(v),s=reorder.sum(sumcol),i,j,row;for(i=0;i<n;i++){row=v[i];for(j=0;j<row.length;j++)row[j]/=s}sumline=reorder.sumlines(v);sumcol=reorder.sumcols(v);var v2=Array(n),ep;for(i=0;i<n;i++){v2[i]=Array(o);for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v2[i][j]=(v[i][j]-ep)/Math.sqrt(ep)}}for(i=0;i<n;i++){for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v[i][j]=(v[i][j]-ep)/(sumcol[j]*Math.sqrt(sumline[i]))}}var cov=Array(n);for(i=0;i<n;i++)cov[i]=Array(n);for(i=0;i<n;i++)for(j=i;j<n;j++)cov[i][j]=cov[j][i]=reorder.covariance(v2[i],v2[j]);var eigenvector1=reorder.poweriteration(cov,eps),eigenvalue1=0;for(i=0;i<n;i++)eigenvalue1+=eigenvector1[i]*cov[i][0];eigenvalue1/=eigenvector1[0];return eigenvector1};reorder.cuthill_mckee=function(graph,comp){if(comp.length<3)return comp;var nodes=graph.nodes(),start=comp[0],min_deg=graph.degree(start),i,n,edges,e,visited={},queue=new Queue,inv=inverse_permutation(comp),perm=[];for(i=0;i<comp.length;i++){n=comp[i];if(graph.degree(n)<min_deg){min_deg=graph.degree(n);start=n;if(min_deg==1)break}}queue.push(start);while(queue.length!==0){n=queue.shift();if(visited[n])continue;visited[n]=true;perm.push(n);e=graph.edges(n).map(function(edge){return graph.other(edge,n).index}).filter(function(n){return!visited[n]&&n in inv}).sort(function(a,b){return graph.degree(a)-graph.degree(b)});e.forEach(queue.push,queue)}return perm};reorder.reverse_cuthill_mckee=function(graph,comp){return reorder.cuthill_mckee(graph,comp).reverse()};reorder.cuthill_mckee_order=function(graph,comps){var i,comp,order=[];if(!comps){comps=graph.components()}for(i=0;i<comps.length;i++){comp=comps[i];order=order.concat(reorder.cuthill_mckee(graph,comp))}return order};reorder.reverse_cuthill_mckee_order=function(graph,comps){var i,comp,order=[];if(!comps){comps=graph.components()}for(i=0;i<comps.length;i++){comp=comps[i];order=order.concat(reorder.reverse_cuthill_mckee(graph,comp))}return order};reorder.condition=function(matrix){var i,j,min,max,v,s,row,ret=[];for(i=0;0<matrix.length;i++){row=matrix[i].slice();row.push(ret);for(j=0;j<ret.length;j++){v=row[j];if(v!==null&&b>=b){min=max=row[j];break}}for(;j<ret.length;j++){v=row[j];if(v<min)min=v;else if(v>max)max=v}s=max!=min?1/(max-min):0;for(j=1;j<ret.length;j++){v=row[j];if(v!=null&&v>=v)row[j]=row[j]*s-min;else v=NaN}}return ret};function array_to_dicts(data,axes){if(arguments.length<2)axes=reorder.range(data[0].length);var ret=[],row,dict,i,j;for(i=0;i<data.length;i++){row=data[i];dict={};for(j=0;j<row.length;j++){dict[axes[j]]=row[j]}ret.push(dict)}return ret}reorder.array_to_dicts=array_to_dicts;function dicts_to_array(dicts,keys){if(arguments.length<2)keys=Object.keys(dicts[0]);var n=keys.length,m=dicts.length,array=Array(m),i,j,row;for(i=0;i<m;i++){row=Array(n);array[i]=row;for(j=0;j<n;j++)row[j]=dicts[i][keys[j]]}return array}reorder.dicts_to_array=dicts_to_array;function abs_matrix(x){return x.map(function(y){return y.map(Math.abs)})}function pcp(data,axes){if(arguments.length<2)axes=reorder.range(data[0].length);var tdata=reorder.transpose(data),pcor=reorder.correlation.pearsonMatrix(tdata),abs_pcor=abs_matrix(pcor),h1=science.stats.hcluster().linkage("complete").distanceMatrix(abs_pcor)(tdata),perm=reorder.optimal_leaf_order().distanceMatrix(abs_pcor)(tdata),naxes=reorder.permute(axes,perm);tdata=reorder.permute(tdata,perm);var i,c,sign=1,signs=[],negs=0;console.log("Permutation is "+perm);for(i=1;i<tdata.length;i++){c=pcor[perm[i-1]][perm[i]];if(c<0)sign=-sign;if(sign<0){signs.push(-1);negs++}else signs.push(1)}sign=negs>tdata.length-negs?-1:1;for(i=0;i<tdata.length-1;i++){if(signs[i]*sign<0){naxes[i]="-"+naxes[i];tdata[i]=tdata[i].map(function(x){return-x})}}var ndata=reorder.transpose(tdata);return[ndata,perm,naxes]}reorder.pcp=pcp})(this);
\ No newline at end of file
diff --git a/src/pcp.js b/src/pcp.js
new file mode 100644
index 0000000..742ddb0
--- /dev/null
+++ b/src/pcp.js
@@ -0,0 +1,80 @@
+function array_to_dicts(data, axes) {
+    if (arguments.length < 2) 
+	axes = reorder.range(data[0].length);
+    var ret = [], row, dict, i, j;
+    for (i = 0; i < data.length; i++) {
+	row = data[i];
+	dict = {};
+	for (j = 0; j < row.length; j++) {
+	    dict[axes[j]] = row[j];
+	}
+	ret.push(dict);
+    }
+    return ret;
+}
+
+reorder.array_to_dicts = array_to_dicts;
+
+function dicts_to_array(dicts, keys) {
+    if (arguments.length < 2)
+	keys = Object.keys(dicts[0]);
+    var n = keys.length,
+	m = dicts.length,
+	array = Array(m), i, j, row;
+
+    for (i = 0; i < m; i++) {
+	row = Array(n);
+	array[i] = row;
+	for (j = 0; j < n; j++)
+	    row[j] = dicts[i][keys[j]];
+    }
+    return array;
+}
+
+reorder.dicts_to_array = dicts_to_array;
+
+function abs_matrix(x) {
+    return x.map(function(y) { return y.map(Math.abs); });
+}
+
+function pcp(data, axes) {
+    if (arguments.length < 2) 
+	axes = reorder.range(data[0].length);
+    var tdata = reorder.transpose(data),
+	pcor = reorder.correlation.pearsonMatrix(tdata),
+	abs_pcor = abs_matrix(pcor),
+	h1 = science.stats.hcluster()
+	    .linkage("complete")
+	    .distanceMatrix(abs_pcor)(tdata),
+	perm = reorder.optimal_leaf_order()
+	    .distanceMatrix(abs_pcor)(tdata),
+	naxes = reorder.permute(axes, perm);
+    tdata = reorder.permute(tdata, perm);
+
+    var i, c, sign = 1, signs = [], negs=0;
+    
+    console.log('Permutation is '+perm);
+    
+    for (i = 1; i < tdata.length; i++) {
+	c = pcor[perm[i-1]][perm[i]];
+	if (c < 0)
+	    sign = -sign;
+	if (sign < 0) {
+	    signs.push(-1);
+	    negs++;
+	}
+	else
+	    signs.push(1);
+    }
+    sign = (negs > (tdata.length-negs)) ? -1 : 1;
+    for (i = 0; i < (tdata.length-1); i++) {
+	if (signs[i]*sign < 0) {
+	    naxes[i] = '-'+naxes[i];
+	    tdata[i] = tdata[i].map(function(x) { return -x; });
+	}
+    }
+    var  ndata = reorder.transpose(tdata);
+    return [ndata, perm, naxes];
+}
+
+reorder.pcp = pcp;
diff --git a/test/pcp-test.js b/test/pcp-test.js
new file mode 100644
index 0000000..bba8288
--- /dev/null
+++ b/test/pcp-test.js
@@ -0,0 +1,23 @@
+require("science");
+require("../reorder.v1");
+
+var vows = require("vows"),
+    assert = require("assert");
+
+var suite = vows.describe("reorder.pcp");
+
+suite.addBatch({
+    "pcp": {
+	"simple": function() {
+	    var earray = [[0, 1, 2], [3, 4, 5]],
+		dicts = reorder.array_to_dicts(earray);
+	    assert.equal(dicts.length, earray.length);
+	    var array = reorder.dicts_to_array(dicts);
+	    assert.deepEqual(earray,array);
+	}
+    }
+});
+
+suite.export(module);
+
+