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fixed a lot of issues

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master
Angelos Chatzimparmpas 5 years ago
parent 3357daab80
commit 19472c9fa4
2 changed files with 296 additions and 83 deletions
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  1. 14
      index.html
  2. 365
      js/tsne_vis.js

14
index.html
Unescape View File

@ -55,8 +55,8 @@
<div id="control-panel">
<div class="param">
<label for="param-lim">Points radius scaling factor</label>
<input id="param-lim" type="range" min="4" max="20" value="10", step="4">
<output for="param-lim" id="param-lim-value">10</output>
<input id="param-lim" type="range" min="0.25" max="4" value="2", step="0.25">
<output for="param-lim" id="param-lim-value">2</output>
</div>
</div>
</div>
@ -71,15 +71,13 @@
<div class="col-md-2">
<div id="ThumbNailsList">
<label for="male">Neighborhood Preservation</label>
<select id="param-neighborhoodMapping" name ="param-neighborhoodMapping">
<select id="param-neighborHood" name ="param-neighborHood">
<option selected="selected" value="color">Color</option>
<option value="size">Size</option>
</select>
<output for="param-neighborHood" id="param-neighborHood-value"></output>
<label for="male">Final Cost (Kullback-Leibler)</label>
<select id="param-divergenceMapping" name ="param-divergenceMapping">
<option value="color">Color</option>
<option selected="selected" value="size">Size</option>
</select>
<label>Vice versa</label>
<div id="param-correlation">
<div class="param">
<label for="param-corr">Correlation threshold</label>
@ -187,8 +185,6 @@
</div>
</div>
<script>
$('#param-neighborHood').bind('input', function () { $('#param-neighborhoodMapping-value').text($('#param-neighborhoodMapping').val()); });
$('#param-divergence').bind('input', function () { $('#param-divergenceMapping-value').text($('#param-divergenceMapping').val()); });
$('#param-lim').bind('input', function () { $('#param-lim-value').text($('#param-lim').val()); });
$('#param-corr').bind('input', function () { $('#param-corr-value').text($('#param-corr').val()); });
$('#param-perplexity').bind('input', function () { $('#param-perplexity-value').text($('#param-perplexity').val()); });

365
js/tsne_vis.js
Unescape View File

@ -8,7 +8,7 @@ var dimensions = document.getElementById('modtSNEcanvas').offsetWidth;
var dim = document.getElementById('tSNEcanvas').offsetWidth;
var format; var new_file; var opt; var step_counter; var final_dataset; var max_counter; var dists; var dists2d; var all_labels; var runner; var tsne; var count_canvas = 0; var x_position = []; var y_position = []; var x_position2 = []; var y_position2 = []; var cost_each; var beta_all = [];
var points2d = []; var ArrayContainsDataFeatures = [];
var points2d = []; var ArrayContainsDataFeatures = []; var ArrayContainsDataFeaturesCleared = [];
function getfile(file){
new_file = file; //uploaded file data
@ -88,10 +88,18 @@ function init(data, results_all, fields) {
tsne = new tsnejs.tSNE(opt);
final_dataset = data;
dataFeatures = results_all;
var temp, object;
for (let k = 0; k < dataFeatures.length; k++){
ArrayContainsDataFeatures.push(Object.values(dataFeatures[k]).concat(k));
object = [];
Object.values(dataFeatures[k]).forEach(function(dataFeature){
if(typeof(dataFeature) == "number"){
object.push(dataFeature);
}
});
ArrayContainsDataFeaturesCleared.push(object);
}
dists = computeDistances(data, document.getElementById("param-distance").value, document.getElementById("param-transform").value);
tsne.initDataDist(dists);
all_labels = [];
@ -123,7 +131,6 @@ function initDist(data) {
// calculate euclidean distance
function euclideanDist(data) {
dist = initDist(data);
for(var i = 0; i < data.length; i++) {
for(var j = i + 1; j < data.length; j++) {
@ -242,8 +249,9 @@ function updateEmbedding() {
for(var i = 0; i < final_dataset.length; i++) {
x_position[i] = x(Y[i][0]);
y_position[i] = y(Y[i][1]);
points[i] = {id: i, x: x_position[i], y: y_position[i], beta: final_dataset[i].beta, cost: final_dataset[i].cost, selected: true};
points[i] = {id: i, x: x_position[i], y: y_position[i], beta: final_dataset[i].beta, cost: final_dataset[i].cost, selected: true, DimON: null};
points2d[i] = {id: i, x: x_position[i], y: y_position[i], selected: true};
points[i] = extend(points[i], ArrayContainsDataFeaturesCleared[i]);
points[i] = extend(points[i], dataFeatures[i]);
}
function extend(obj, src) {
@ -588,7 +596,6 @@ function OverviewtSNE(points){
// vertex shader source code
var vertCode = 'attribute vec3 coordinates;'+
'attribute vec3 limitdist;'+
'attribute vec3 color;'+
'varying vec3 vColor;'+
'void main(void) {' +
@ -961,10 +968,10 @@ function click(){
}
if (SignStore[i][1] == correlationResults[j][1]) {
correlationResults[j][1] = parseInt(correlationResults[j][1] * 100);
correlationResults[j].push(j);
}
}
}
/////////////////////////////////////////////////////////////
///////////////// Set-up SVG and wrappers ///////////////////
/////////////////////////////////////////////////////////////
@ -1070,7 +1077,8 @@ function click(){
/////////////////////////////////////////////////////////////
///////////////////////// Create brush //////////////////////
/////////////////////////////////////////////////////////////
var brushExtent = parseInt(Math.max( 2, Math.min( 20, Math.round(correlationResults.length*0.2 ) ) ));
var brushExtent = parseInt(Math.max( 1, Math.min( 20, Math.round(correlationResults.length * 0.75) ) ));
//What should the first extent of the brush become - a bit arbitrary this
//var brushExtent = Math.max( 1, Math.min( 20, Math.round(correlationResults.length*0.2) ) );
// console.log(brushExtent);
@ -1110,8 +1118,8 @@ function click(){
defs = svg.append("defs")
//Create two separate gradients for the main and mini bar - just because it looks fun
createGradient("gradient-main", "65%");
createGradient("gradient-mini", "14%");
createGradient("gradient-main", "60%");
createGradient("gradient-mini", "13%");
//Add the clip path for the main bar chart
defs.append("clipPath")
@ -1128,7 +1136,7 @@ function click(){
//The mini brushable bar
//DATA JOIN
var mini_bar = d3v3.select(".miniGroup").selectAll(".bar")
.data(correlationResults, function(d) { return d[2]; });
.data(correlationResults, function(d) { return +d[2]; });
//UDPATE
mini_bar
@ -1165,7 +1173,7 @@ function updateBarChart() {
/////////////////////////////////////////////////////////////
var bar = d3v3.select(".mainGroup").selectAll(".bar")
.data(correlationResults, function(d) { return d[2]; })
.data(correlationResults, function(d) { return +d[2]; })
//, function(d) { return d.key; });
bar
@ -1173,7 +1181,7 @@ function updateBarChart() {
.attr("width", function(d) { return Math.abs(main_xScale(d[1]) - main_xScale(0)); })
.attr("y", function(d,i) { return main_yScale(d[0]); })
.attr("height", main_yScale.rangeBand());
//ENTER
bar.enter().append("rect")
.attr("class", "bar")
@ -1181,7 +1189,25 @@ function updateBarChart() {
.attr("x", function (d) { return main_xScale(Math.min(0, d[1])); })
.attr("width", function(d) { return Math.abs(main_xScale(d[1]) - main_xScale(0)); })
.attr("y", function(d,i) { return main_yScale(d[0]); })
.attr("height", main_yScale.rangeBand());
.attr("height", main_yScale.rangeBand())
.on("mouseover", () => {
svg.select('.tooltip').style('display', 'none');
})
.on("mouseout", function(d){
points.forEach(function (p) {
p.DimON = null
})
BetatSNE(points);
svg.select('.tooltip').style('display', 'none');
})
.on("mousemove", function(d) {
points.forEach(function (p) {
if (p.selected == true) {
p.DimON = d[0];
}
})
BetatSNE(points);
});
//EXIT
bar.exit()
@ -1398,7 +1424,6 @@ function mapOrder(array, order, key) {
best = [best.x, best.y];
best.distance = Math.sqrt(bestDistance);
best.id = point[2];
//console.log(best);
return best;
function distance2(p) {
@ -1443,6 +1468,23 @@ function dragmove(d) {
}
*/
function abbreviateNumber(value) {
var newValue = value;
if (value >= 1000) {
var suffixes = ["", "k", "m", "b","t"];
var suffixNum = Math.floor( (""+value).length/3 );
var shortValue = '';
for (var precision = 2; precision >= 1; precision--) {
shortValue = parseFloat( (suffixNum != 0 ? (value / Math.pow(1000,suffixNum) ) : value).toPrecision(precision));
var dotLessShortValue = (shortValue + '').replace(/[^a-zA-Z 0-9]+/g,'');
if (dotLessShortValue.length <= 2) { break; }
}
if (shortValue % 1 != 0) shortNum = shortValue.toFixed(1);
newValue = shortValue+suffixes[suffixNum];
}
return newValue;
}
function BetatSNE(points){
if(step_counter == max_counter || step_counter == 1){
@ -1474,64 +1516,117 @@ function BetatSNE(points){
return;
}
max = (d3.max(final_dataset,function(d){ return d.beta; }));
min = (d3.min(final_dataset,function(d){ return d.beta; }));
// colors
let colorbrewer = ["#ffffcc","#ffeda0","#fed976","#feb24c","#fd8d3c","#fc4e2a","#e31a1c","#bd0026","#800026"];
let calcStep = (max-min)/7;
let colorScale = d3.scaleLinear()
.domain(d3.range(0, max+calcStep, calcStep))
.range(colorbrewer);
points = points.sort(function(a, b) {
return a.beta - b.beta;
})
function abbreviateNumber(value) {
var newValue = value;
if (value >= 1000) {
var suffixes = ["", "k", "m", "b","t"];
var suffixNum = Math.floor( (""+value).length/3 );
var shortValue = '';
for (var precision = 2; precision >= 1; precision--) {
shortValue = parseFloat( (suffixNum != 0 ? (value / Math.pow(1000,suffixNum) ) : value).toPrecision(precision));
var dotLessShortValue = (shortValue + '').replace(/[^a-zA-Z 0-9]+/g,'');
if (dotLessShortValue.length <= 2) { break; }
}
if (shortValue % 1 != 0) shortNum = shortValue.toFixed(1);
newValue = shortValue+suffixes[suffixNum];
}
return newValue;
}
var labels_beta = [];
var abbr_labels_beta = [];
labels_beta = d3.range(0, max+calcStep, calcStep);
for (var i=0; i<9; i++){
labels_beta[i] = parseInt(labels_beta[i]);
abbr_labels_beta[i] = abbreviateNumber(labels_beta[i]);
}
if(step_counter == 1){
var svg = d3.select("#legend1");
var ColSizeSelector = document.getElementById("param-neighborHood").value;
if (ColSizeSelector == "color") {
var max = (d3.max(final_dataset,function(d){ return d.beta; }));
var min = (d3.min(final_dataset,function(d){ return d.beta; }));
// colors
var colorbrewer = ["#ffffcc","#ffeda0","#fed976","#feb24c","#fd8d3c","#fc4e2a","#e31a1c","#bd0026","#800026"];
var calcStep = (max-min)/7;
var colorScale = d3.scaleLinear()
.domain(d3.range(0, max+calcStep, calcStep))
.range(colorbrewer);
var maxSize1 = (d3.max(final_dataset,function(d){ return d.cost; }));
var minSize1 = (d3.min(final_dataset,function(d){ return d.cost; }));
var rscale1 = d3.scaleLinear()
.domain([minSize1, maxSize1])
.range([5,10]);
var colorScale = d3.scaleLinear()
.domain(d3.range(0, max+calcStep, calcStep))
.range(colorbrewer);
points = points.sort(function(a, b) {
return a.beta - b.beta;
})
var labels_beta = [];
var abbr_labels_beta = [];
labels_beta = d3.range(0, max+calcStep, calcStep);
for (var i=0; i<9; i++){
labels_beta[i] = parseInt(labels_beta[i]);
abbr_labels_beta[i] = abbreviateNumber(labels_beta[i]);
}
var svg = d3.select("#legend1");
svg.append("g")
.attr("class", "legendLinear")
.attr("transform", "translate(10,15)");
var legend = d3.legendColor()
.labelFormat(d3.format(",.0f"))
.cells(9)
.labels([abbr_labels_beta[0],abbr_labels_beta[1],abbr_labels_beta[2],abbr_labels_beta[3],abbr_labels_beta[4],abbr_labels_beta[5],abbr_labels_beta[6],abbr_labels_beta[7],abbr_labels_beta[8]])
.title("1 / sigma")
.scale(colorScale);
svg.append("g")
.attr("class", "legendLinear")
.attr("transform", "translate(10,15)");
var legend = d3.legendColor()
.labelFormat(d3.format(",.0f"))
.cells(9)
.labels([abbr_labels_beta[0],abbr_labels_beta[1],abbr_labels_beta[2],abbr_labels_beta[3],abbr_labels_beta[4],abbr_labels_beta[5],abbr_labels_beta[6],abbr_labels_beta[7],abbr_labels_beta[8]])
.title("1 / sigma")
.scale(colorScale);
svg.select(".legendLinear")
.call(legend);
} else {
var max = (d3.max(final_dataset,function(d){ return d.cost; }));
var min = (d3.min(final_dataset,function(d){ return d.cost; }));
var maxSize2 = (d3.max(final_dataset,function(d){ return d.beta; }));
var minSize2 = (d3.min(final_dataset,function(d){ return d.beta; }));
var rscale2 = d3.scaleLinear()
.domain([minSize2, maxSize2])
.range([5,10]);
var colorbrewer = ["#ffffe5","#f7fcb9","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#006837","#004529"];
var calcStep = (max-min)/9;
var colorScale = d3.scaleLinear()
.domain(d3.range(min, max, calcStep))
.range(colorbrewer);
points = points.sort(function(a, b) {
return a.cost - b.cost;
})
var labels_cost = [];
var abbr_labels_cost = [];
labels_cost = d3.range(min, max, calcStep);
for (var i=0; i<9; i++){
labels_cost[i] = labels_cost[i].toFixed(5);
abbr_labels_cost[i] = abbreviateNumber(labels_cost[i]);
}
svg.select(".legendLinear")
.call(legend);
}
var svg = d3.select("#legend1");
svg.append("g")
.attr("class", "legendLinear")
.attr("transform", "translate(10,15)");
var legend = d3.legendColor()
.labelFormat(d3.format(",.5f"))
.cells(9)
.labels([abbr_labels_cost[0],abbr_labels_cost[1],abbr_labels_cost[2],abbr_labels_cost[3],abbr_labels_cost[4],abbr_labels_cost[5],abbr_labels_cost[6],abbr_labels_cost[7],abbr_labels_cost[8]])
.title("KLD(P||Q)")
.scale(colorScale);
svg.select(".legendLinear")
.call(legend);
}
let vertices = [];
let colors = [];
let sizes = new Float32Array(points.length);
let tempSort = -1;
for (var i=0; i<points.length; i++){
if (points[i].DimON != null) {
tempSort = points[i].DimON.match(/\d+/)[0];
}
}
if (tempSort != -1){
points = points.sort(function(a, b) {
return a[tempSort] - b[tempSort];
})
}
for (var i=0; i<points.length; i++){
let singleObj = {};
@ -1553,8 +1648,18 @@ for (var i=0; i<9; i++){
singleObj = 0.0;
vertices.push(singleObj);
}
for (var i=0; i<points.length; i++){
let singleCol = {};
if (ColSizeSelector == "color"){
let singleSizeCol = rscale1(points[i].cost);
sizes[i] = singleSizeCol;
} else {
let singleSizeCol = rscale2(points[i].beta);
sizes[i] = singleSizeCol;
}
if (points[i].selected == false){
let colval = d3.rgb(211,211,211);
singleCol = colval.r/255;
@ -1563,7 +1668,28 @@ for (var i=0; i<9; i++){
colors.push(singleCol);
singleCol = colval.b/255;
colors.push(singleCol);
}else{
} else if (points[i].DimON != null) {
let temp = points[i].DimON.match(/\d+/)[0];
var maxDim = (d3.max(points,function(d){ if(d.selected == true){return d[temp]}; }));
var minDim = (d3.min(points,function(d){ if(d.selected == true){return d[temp]}; }));
let colorsBarChart = ['#fcfbfd','#efedf5','#dadaeb','#bcbddc','#9e9ac8','#807dba','#6a51a3','#54278f','#3f007d'];
var calcStepDim = (maxDim-minDim)/8;
var colorScaleDim = d3.scaleLinear()
.domain(d3.range(minDim, maxDim+calcStepDim, calcStepDim))
.range(colorsBarChart);
let colval = d3.rgb(colorScaleDim(points[i][temp]));
singleCol = colval.r/255;
colors.push(singleCol);
singleCol = colval.g/255;
colors.push(singleCol);
singleCol = colval.b/255;
colors.push(singleCol);
} else if (ColSizeSelector == "color") {
let colval = d3.rgb(colorScale(points[i].beta));
singleCol = colval.r/255;
colors.push(singleCol);
@ -1572,8 +1698,89 @@ for (var i=0; i<9; i++){
singleCol = colval.b/255;
colors.push(singleCol);
}
else{
let colval = d3.rgb(colorScale(points[i].cost));
singleCol = colval.r/255;
colors.push(singleCol);
singleCol = colval.g/255;
colors.push(singleCol);
singleCol = colval.b/255;
colors.push(singleCol);
}
}
var temporal = 0;
for (var j=0; j < points.length; j++){
if(points[j].DimON != null) {
temporal = temporal + 1;
var labels_dim = [];
var abbr_labels_dim = [];
labels_dim = d3.range(minDim, maxDim+calcStepDim, calcStepDim);
for (var i=0; i<9; i++){
labels_dim[i] = labels_dim[i].toFixed(2);
abbr_labels_dim[i] = abbreviateNumber(labels_dim[i]);
}
d3.select("#legend1").selectAll('*').remove();
var svg = d3.select("#legend1");
svg.append("g")
.attr("class", "legendLinear")
.attr("transform", "translate(10,15)");
var legend = d3.legendColor()
.labelFormat(d3.format(",.0f"))
.cells(9)
.labels([abbr_labels_dim[0],abbr_labels_dim[1],abbr_labels_dim[2],abbr_labels_dim[3],abbr_labels_dim[4],abbr_labels_dim[5],abbr_labels_dim[6],abbr_labels_dim[7],abbr_labels_dim[8]])
.title(points[j].DimON)
.scale(colorScaleDim);
svg.select(".legendLinear")
.call(legend);
break;
}
}
for (var j=0; j < points.length; j++){
if(temporal == 0 && points[j].DimON == null){
if (ColSizeSelector == "color"){
d3.select("#legend1").selectAll('*').remove();
var svg = d3.select("#legend1");
svg.append("g")
.attr("class", "legendLinear")
.attr("transform", "translate(10,15)");
var legend = d3.legendColor()
.labelFormat(d3.format(",.0f"))
.cells(9)
.labels([abbr_labels_beta[0],abbr_labels_beta[1],abbr_labels_beta[2],abbr_labels_beta[3],abbr_labels_beta[4],abbr_labels_beta[5],abbr_labels_beta[6],abbr_labels_beta[7],abbr_labels_beta[8]])
.title("1 / sigma")
.scale(colorScale);
svg.select(".legendLinear")
.call(legend);
break;
} else {
d3.select("#legend1").selectAll('*').remove();
var svg = d3.select("#legend1");
svg.append("g")
.attr("class", "legendLinear")
.attr("transform", "translate(10,15)");
var legend = d3.legendColor()
.labelFormat(d3.format(".4f"))
.cells(9)
.labels([abbr_labels_cost[0],abbr_labels_cost[1],abbr_labels_cost[2],abbr_labels_cost[3],abbr_labels_cost[4],abbr_labels_cost[5],abbr_labels_cost[6],abbr_labels_cost[7],abbr_labels_cost[8]])
.title("KLD(P||Q)")
.scale(colorScale);
svg.select(".legendLinear")
.call(legend);
break;
}
}
}
// Create an empty buffer object and store vertex data
var vertex_buffer = gl.createBuffer();
gl.bindBuffer(gl.ARRAY_BUFFER, vertex_buffer);
@ -1585,6 +1792,9 @@ for (var i=0; i<9; i++){
gl.bindBuffer(gl.ARRAY_BUFFER, color_buffer);
gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(colors), gl.STATIC_DRAW);
var size_buffer = gl.createBuffer();
gl.bindBuffer(gl.ARRAY_BUFFER, size_buffer);
gl.bufferData(gl.ARRAY_BUFFER, sizes, gl.STATIC_DRAW);
// Increase/reduce size factor selected by the user
var limitdist = document.getElementById("param-lim-value").value;
@ -1592,12 +1802,13 @@ for (var i=0; i<9; i++){
// vertex shader source code
var vertCode = 'attribute vec3 coordinates;'+
'attribute float vSizes;'+
'attribute vec3 color;'+
'varying vec3 vColor;'+
'void main(void) {' +
' gl_Position = vec4(coordinates, 1.0);' +
'gl_Position = vec4(coordinates, 1.0);' +
'vColor = color;'+
'gl_PointSize = ' + limitdist + ';'+
'gl_PointSize = '+ limitdist + '*vSizes;'+
'}';
// Create a vertex shader object
@ -1680,13 +1891,18 @@ for (var i=0; i<9; i++){
var color = gl.getAttribLocation(shaderProgram, "color");
// point attribute to the volor buffer object
gl.vertexAttribPointer(color, 3, gl.FLOAT, false,0,0) ;
gl.vertexAttribPointer(color, 3, gl.FLOAT, false, 0, 0) ;
// enable the color attribute
gl.enableVertexAttribArray(color);
gl.bindBuffer(gl.ARRAY_BUFFER, size_buffer);
var vSize = gl.getAttribLocation(shaderProgram, "vSizes");
gl.vertexAttribPointer(vSize, 1, gl.FLOAT, false, 0, 0);
gl.enableVertexAttribArray(vSize);
// Clear the canvas
gl.clearColor(1.0, 1.0, 1.0, 1.0);
@ -1701,10 +1917,11 @@ for (var i=0; i<9; i++){
resize(gl.canvas);
gl.viewport(0, 0, dimensions, dimensions);
gl.viewport(0, 0, dimensions, dimensions);
//Draw the triangle
gl.drawArrays(gl.POINTS, 0, points.length);
/*
selectedPoints = [];
selectedPoints2d = [];
var findNearestTable = [];
@ -1713,7 +1930,7 @@ for (var i=0; i<9; i++){
selectedPoints.push(points[m]);
selectedPoints2d.push(points2d[m]);
}
}
}*/
/*
for (k=2; k < 9; k++){
var findNearest = kNearestNeighbors(k, selectedPoints,points2d);

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