diff --git a/Makefile b/Makefile index 6fa03b2..08e39da 100644 --- a/Makefile +++ b/Makefile @@ -49,7 +49,8 @@ reorder.v1.js: \ src/spectral_order.js \ src/pca_order.js \ src/ca.js \ - src/cuthill_mckee_order.js + src/cuthill_mckee_order.js \ + src/condition.js test: all @npm test diff --git a/TODO b/TODO index 6c43dfe..12ac67a 100644 --- a/TODO +++ b/TODO @@ -5,10 +5,26 @@ Interaction: zoom in/out MatLink +Conditioning: + min-max conditioning + average/std-dev conditioning + +Documentation: + Finish documenting functions + Continue documenting high-level concepts in the Wiki + +Examples: + Finish simple D3-based graph visualization module + Create simple canvas-based graph visualization module + Finish simple D3-based table visualization module + Finish simple canvas-based table visualization module + Create example(s) with tables and conditioning + Create example(s) with parallel coordinates and axes ordering + Reordering: Sloan ordering Biclustering - Contingency tables methods: + Contingency tables methods (check): PCA ordering Correspondence analysis Chun-Hou Chen methods: http://gap.stat.sinica.edu.tw/Papers/GAP_2002.pdf diff --git a/examples/tables/index_canvas.html b/examples/tables/index_canvas.html index 48670b5..e86acf9 100644 --- a/examples/tables/index_canvas.html +++ b/examples/tables/index_canvas.html @@ -3,7 +3,6 @@ Heatmap Canvas - diff --git a/reorder.v1.js b/reorder.v1.js index ff8f008..cb58623 100644 --- a/reorder.v1.js +++ b/reorder.v1.js @@ -39,10 +39,10 @@ reorder.zeroes = science.zeroes; reorder.displaymat = function(mat, rowperm, colperm) { var i, j, row, col, str; if (! rowperm) { - rowperm = reorder.range(mat.length); + rowperm = reorder.permutation(mat.length); } if (! colperm) { - colperm = reorder.range(mat[0].length); + colperm = reorder.permutation(mat[0].length); } console.log('Matrix:'); for (i = 0; i < mat.length; i++) { @@ -1346,39 +1346,6 @@ reorder.dist_remove = function(dist, n, m) { dist[i].splice(n, m-n); return dist; }; -reorder.disttranspose = 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[j] , vectors[i])); - } - } - } - return distMatrix; - } - - dist.distance = function(x) { - if (!arguments.length) return distance; - distance = x; - return dist; - }; - - return dist; -}; /* Fisher-Yates shuffle. See http://bost.ocks.org/mike/shuffle/ */ @@ -1506,7 +1473,7 @@ reorder.stablepermute = function(list, indexes) { return p; }; reorder.sort_order = function(v) { - return reorder.range(0, v.length).sort( + return reorder.permutation(0, v.length).sort( function(a,b) { return v[a] - v[b]; }); }; if (typeof science == "undefined") { @@ -1533,7 +1500,7 @@ science.stats.hcluster = function() { root, i, j, - id = 0; + id = 0; // Initialise distance matrix and vector of closest clusters. if (distMatrix === null) { @@ -1561,6 +1528,7 @@ science.stats.hcluster = function() { } // create leaves of the tree i = -1; while (++i < n) { + if (i != id) console.log("i = %d, id = %d", i, id); clusters[i] = []; clusters[i][0] = { left: null, @@ -2666,4 +2634,35 @@ reorder.reverse_cuthill_mckee_order = function(graph, comps) { 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 ? 1.0 / (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); diff --git a/reorder.v1.min.js b/reorder.v1.min.js index 6c22d79..7f08b17 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(++i1)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=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&&v=v&&v=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=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;imax_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;i0){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;iwp0)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;iwp0)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;ic1){layer1[i]=w;layer1[i+1]=v;inv_layer1[w]=i;inv_layer1[v]=i+1;swapped=true;improved+=c0-c1}}for(i=0;ic1){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;i0)return 1;return 0};for(layer=layer1,iter=0;iterdist[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;idist[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;imax)max=row[j]}return max};reorder.distmin=function(distMatrix){var min=Infinity,n=distMatrix.length,i,j,row;for(i=0;i0;)dist[i].splice(n,m-n);return dist};reorder.disttranspose=function(){var distance=reorder.distance.euclidean;function dist(vectors){var n=vectors.length,distMatrix=[];for(var i=0;i0){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;i0)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.range(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(++idistMatrix[i][j])dMin[i]=j}}}else{if(distMatrix.lengthdistMatrix[i][j])dMin[i]=j}}}i=-1;while(++idistMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"complete":if(distMatrix[c1][j]0?i-1:0,j0=j0;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(i0j){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;klow)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;kk;){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;k0;){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;n0&&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); +(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(++i1)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=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&&v=v&&v=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=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;imax_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;i0){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;iwp0)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;iwp0)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;ic1){layer1[i]=w;layer1[i+1]=v;inv_layer1[w]=i;inv_layer1[v]=i+1;swapped=true;improved+=c0-c1}}for(i=0;ic1){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;i0)return 1;return 0};for(layer=layer1,iter=0;iterdist[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;idist[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;imax)max=row[j]}return max};reorder.distmin=function(distMatrix){var min=Infinity,n=distMatrix.length,i,j,row;for(i=0;i0;)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;i0)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(++idistMatrix[i][j])dMin[i]=j}}}else{if(distMatrix.lengthdistMatrix[i][j])dMin[i]=j}}}i=-1;while(++idistMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"complete":if(distMatrix[c1][j]0?i-1:0,j0=j0;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(i0j){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;klow)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;kk;){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;k0;){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;n0&&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=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;ki)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;i0)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;i1-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;i0){for(l=0;l1-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;imax)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=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;ki)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;i0)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;i1-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;i0){for(l=0;l1-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;imax)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=b){min=max=row[j];break}}for(;jmax)max=v}s=max!=min?1/(max-min):0;for(j=1;j=v)row[j]=row[j]*s-min;else v=NaN}}return ret}})(this); \ No newline at end of file diff --git a/src/condition.js b/src/condition.js new file mode 100644 index 0000000..2de8608 --- /dev/null +++ b/src/condition.js @@ -0,0 +1,31 @@ +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 ? 1.0 / (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; +}; diff --git a/src/debug.js b/src/debug.js index d971929..b64f6ae 100644 --- a/src/debug.js +++ b/src/debug.js @@ -1,10 +1,10 @@ reorder.displaymat = function(mat, rowperm, colperm) { var i, j, row, col, str; if (! rowperm) { - rowperm = reorder.range(mat.length); + rowperm = reorder.permutation(mat.length); } if (! colperm) { - colperm = reorder.range(mat[0].length); + colperm = reorder.permutation(mat[0].length); } console.log('Matrix:'); for (i = 0; i < mat.length; i++) { diff --git a/src/hcluster.js b/src/hcluster.js index 1375126..c774c1b 100644 --- a/src/hcluster.js +++ b/src/hcluster.js @@ -22,7 +22,7 @@ science.stats.hcluster = function() { root, i, j, - id = 0; + id = 0; // Initialise distance matrix and vector of closest clusters. if (distMatrix === null) { @@ -50,6 +50,7 @@ science.stats.hcluster = function() { } // create leaves of the tree i = -1; while (++i < n) { + if (i != id) console.log("i = %d, id = %d", i, id); clusters[i] = []; clusters[i][0] = { left: null, diff --git a/src/sort_order.js b/src/sort_order.js index a65cadb..c39c556 100644 --- a/src/sort_order.js +++ b/src/sort_order.js @@ -1,4 +1,4 @@ reorder.sort_order = function(v) { - return reorder.range(0, v.length).sort( + return reorder.permutation(0, v.length).sort( function(a,b) { return v[a] - v[b]; }); };