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pca.html
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pca.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>Patients</title>
<meta charset="utf-8">
<link rel="stylesheet" type="text/css" href="lib/jk-js/lib/bootstrap/css/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="style.css">
<script src="lib/jk-js/lib/d3/d3.min.js" charset="utf-8"></script>
<script src="lib/jk-js/jkjs/lasso.js" charset="utf-8"></script>
<script src="lib/jk-js/jkjs/path.js" charset="utf-8"></script>
<script src="lib/jk-js/jkjs/stat.js" charset="utf-8"></script>
<script src="lib/jk-js/jkjs/util.js" charset="utf-8"></script>
<script src="lib/mdsjs/mdsjs.js" charset="utf-8"></script>
</head>
<body onload="start()">
<div id="pContent"></div>
<div id="pFeatures"></div>
<script>
function start() {
var urlArgs = jkjs.util.getQueryStrings();
var UPDATE_PATIENTS = 1;
var UPDATE_FEATURES = 2;
var duration = 750;
var ease = "easeInOutCubic";
var bitvecs = "fs" in urlArgs ? urlArgs["fs"] : "feature_extraction/output_small.csv";
var COL_ID = "id";
var COL_TARGET = "outcome";
var COL_TEST = "test";
var IGNORE = /id|outcome|test/;
var PROJ_PCA = "pca";
var PROJ_MDS = "mds";
var PROJ = "proj" in urlArgs ? urlArgs["proj"] : PROJ_MDS;
var DIST_EUCLID = "euclid";
var DIST_TANIMOTO = "tanimoto";
var DIST = DIST_TANIMOTO;
var size = 500;
var radius = 3;
var pixs = [];
var fixs = [];
var svgFeatures = null;
var svg = null;
mdsjs.DEBUG = false;
function update(matArr, patients, cols, what) {
if(what & UPDATE_PATIENTS) {
project(matArr, patients, cols);
}
if(what & UPDATE_FEATURES) {
projectFeatures(matArr, patients, cols);
}
}
function Patient(id, ix, outcome) {
var that = this;
this.id = function() {
return id;
};
this.outcome = function() {
return outcome;
};
this.ix = function() {
return ix;
};
} // Patient
function projectMDS(dm, assignPos) {
var dmMat = mdsjs.convertToMatrix(dm, true);
mdsjs.landmarkMDSAsync(dmMat, 2, function(points) {
if(points.someRows(function(p) {
return Number.isNaN(p[0]) || Number.isNaN(p[1]);
})) {
console.warn("some NaN values in projection output")
}
assignPos(points);
});
}
function projectFeatures(matArr, patients, cs) {
var fVecs = [];
var rIxs = [];
var cols = jkjs.util.flatMap(cs, function(c, ix) {
var vec = [];
pixs.forEach(function(pix) {
vec.push(matArr[pix][ix]);
});
var first = null;
if(vec.some(function(v) {
if(first === null) {
first = v;
return false;
}
return v !== first;
})) {
fVecs.push(vec);
rIxs.push([ rIxs.length, ix ]);
return [ c ];
}
return [];
});
cols.length || console.warn("no columns valid");
var dm = cols.map(function(_, ix) {
var res = [];
res.length = cols.length;
return res;
});
cols.forEach(function(_, pi) {
cols.forEach(function(_, qi) {
if(pi > qi) return;
if(pi === qi) {
dm[pi][pi] = 0;
return;
}
var res = 1 - jkjs.stat.metric.pearson(fVecs[pi], fVecs[qi]);
dm[pi][qi] = res;
dm[qi][pi] = res;
});
});
function assignPos(points) {
var minX = Number.POSITIVE_INFINITY;
var minY = Number.POSITIVE_INFINITY;
var maxX = Number.NEGATIVE_INFINITY;
var maxY = Number.NEGATIVE_INFINITY;
var pos = [];
pos.length = points.rows();
points.rowsIter(function(row, ix) {
var x = row[0];
var y = row[1];
minX = Math.min(minX, x);
maxX = Math.max(maxX, x);
minY = Math.min(minY, y);
maxY = Math.max(maxY, y);
pos[ix] = [ x, y ];
});
var circles = svgFeatures.selectAll("circle").data(rIxs, function(r) {
return r[0];
});
circles.exit().transition().duration(duration).ease(ease).attr({
"r": 0
}).remove();
circles.enter().append("circle").attr({
"stroke": "black",
"r": 0,
"cx": function(r) {
return get(r[0], true);
},
"cy": function(r) {
return get(r[0], false);
},
"fill": "cornflowerblue"
}).append("title");
circles.order();
function get(ix, x) {
var min = x ? minX : minY;
var max = x ? maxX : maxY;
return (pos[ix][x ? 0 : 1] - min) / (max - min) * (size - radius * 2) + radius;
}
circles.selectAll("title").text(function(r) {
return cols[r[0]];
});
circles.transition().duration(duration).ease(ease).attr({
"cx": function(r) {
return get(r[0], true);
},
"cy": function(r) {
return get(r[0], false);
},
"fill": "cornflowerblue",
"r": radius
});
var lassoSel = svgFeatures.select("path#lasso");
if(lassoSel.empty()) {
lassoSel = svgFeatures.append("path").attr({
"id": "lasso"
}).style({
"opacity": 0.5,
"stroke": "darkgray",
"fill": "lightgray"
});
}
var lasso = new jkjs.Lasso(svgFeatures);
lasso.objProvider(function() {
return rIxs;
});
lasso.objToPos(function(r) {
return [ get(r[0], true), get(r[0], false) ];
});
lasso.updateSel(function(selection, polygon) {
var path = new jkjs.Path(); // update the lasso
path.addPoly(polygon);
lassoSel.attr({
"d": path
});
if(!polygon.length) { // end of lasso selection
if(selection.length) {
fixs = selection.map(function(r) {
return r[1];
});
} else {
fixs = cs.map(function(_, ix) {
return ix;
});
}
update(matArr, patients, cs, UPDATE_PATIENTS);
} else { // temporarily select circles
var fs = {};
selection.forEach(function(r) {
fs[r[0]] = r[1];
});
circles.attr({
"fill": function(r) {
return r[0] in fs ? "white" : "cornflowerblue";
}
});
}
});
}
projectMDS(dm, assignPos);
}
function project(ma, patients, cols) {
var matArr = ma.map(function(row) {
return fixs.map(function(fix) {
return row[fix];
});
});
if(PROJ === PROJ_PCA) {
var mat = mdsjs.convertToMatrix(matArr);
mdsjs.pcaAsync(mat, function(pcs) {
var points = mat.mul(pcs);
assignPos(pcs);
});
} else if(PROJ === PROJ_MDS) {
var dm = patients.map(function() {
var res = [];
res.length = patients.length;
return res;
});
patients.forEach(function(p) {
patients.forEach(function(q) {
var pi = p.ix();
var qi = q.ix();
if(pi > qi) return;
if(pi === qi) {
dm[pi][pi] = 0;
return;
}
var vecA = matArr[pi];
var vecB = matArr[qi];
var sum = 0;
if(DIST === DIST_EUCLID) {
for(var ix = 0;ix < vecA.length;ix += 1) {
var a = vecA[ix];
var b = vecB[ix];
sum += (a - b) * (a - b);
}
sum = Math.sqrt(sum);
} else if(DIST === DIST_TANIMOTO) {
var union = 0;
var intersect = 0;
for(var ix = 0;ix < vecA.length;ix += 1) {
var a = vecA[ix];
var b = vecB[ix];
union += (a || b) ? 1 : 0;
intersect += (a && b) ? 1 : 0;
}
if(union) {
sum = 1 - intersect / union;
} else {
sum = 0;
}
} else {
console.warn("invalid distance function: " + DIST);
throw new Error();
}
dm[pi][qi] = sum;
dm[qi][pi] = sum;
});
});
projectMDS(dm, assignPos);
} else {
console.warn("invalid projection: " + PROJ);
}
function assignPos(points) {
var minX = Number.POSITIVE_INFINITY;
var minY = Number.POSITIVE_INFINITY;
var maxX = Number.NEGATIVE_INFINITY;
var maxY = Number.NEGATIVE_INFINITY;
var pos = [];
pos.length = points.rows();
points.rowsIter(function(row, ix) {
var x = row[0];
var y = row[1];
minX = Math.min(minX, x);
maxX = Math.max(maxX, x);
minY = Math.min(minY, y);
maxY = Math.max(maxY, y);
pos[ix] = [ x, y ];
});
var circles = svg.selectAll("circle").data(patients, function(p) {
return p.id();
});
circles.exit().transition().duration(duration).ease(ease).attr({
"r": 0
}).remove();
circles.enter().append("circle").attr({
"stroke": "black",
"r": 0,
"fill": function(p) {
return p.outcome() ? "crimson" : "cornflowerblue"
},
"cx": function(p) {
return get(p, true);
},
"cy": function(p) {
return get(p, false);
}
}).append("title");
function get(p, x) {
var min = x ? minX : minY;
var max = x ? maxX : maxY;
return (pos[p.ix()][x ? 0 : 1] - min) / (max - min) * (size - radius * 2) + radius;
}
circles.selectAll("title").text(function(p) {
return p.id();
});
circles.transition().duration(duration).ease(ease).attr({
"r": radius,
"fill": function(p) {
return p.outcome() ? "crimson" : "cornflowerblue"
},
"cx": function(p) {
return get(p, true);
},
"cy": function(p) {
return get(p, false);
}
});
var lassoSel = svg.select("path#lasso");
if(lassoSel.empty()) {
lassoSel = svg.append("path").attr({
"id": "lasso"
}).style({
"opacity": 0.5,
"stroke": "darkgray",
"fill": "lightgray"
});
}
var lasso = new jkjs.Lasso(svg);
lasso.objProvider(function() {
return patients;
});
lasso.objToPos(function(p) {
return [ get(p, true), get(p, false) ];
});
lasso.updateSel(function(selection, polygon) {
var path = new jkjs.Path(); // update the lasso
path.addPoly(polygon);
lassoSel.attr({
"d": path
});
var pids = {};
selection.forEach(function(p) {
pids[p.id()] = true;
});
if(!polygon.length) { // end of lasso selection
if(selection.length) {
pixs = jkjs.util.flatMap(patients, function(p, ix) {
return p.id() in pids ? [ ix ] : [];
});
} else {
pixs = patients.map(function(_, ix) {
return ix;
});
}
update(matArr, patients, cols, UPDATE_FEATURES);
} else { // temporarily select circles
circles.attr({
"fill": function(p) {
return p.id() in pids ? "white" : p.outcome() ? "crimson" : "cornflowerblue";
}
});
}
});
}
}
function load(bitvecs) {
d3.csv(bitvecs, function(err, csv) {
if(err) {
console.warn("Failed loading bitvectors: '"+bitvecs+"'");
return console.warn(err);
}
var error = true;
try {
svg = d3.select("#pContent").style({
"display": "inline-block"
}).append("svg").attr({
"width": size,
"height": size
}).style({
"width": size + "px",
"height": size + "px",
"cursor": "crosshair"
});
svg.append("rect").attr({
"fill": "none",
"stroke": "black",
"width": size,
"height": size,
"x": 0,
"y": 0
});
svgFeatures = d3.select("#pFeatures").style({
"display": "inline-block"
}).append("svg").attr({
"width": size,
"height": size
}).style({
"width": size + "px",
"height": size + "px",
"cursor": "crosshair"
});
svgFeatures.append("rect").attr({
"fill": "none",
"stroke": "black",
"width": size,
"height": size,
"x": 0,
"y": 0
});
var matArr = [];
var patients = [];
var cols = null;
csv.forEach(function(row) {
if(!cols) {
cols = Object.keys(row).filter(function(c) {
return c != COL_ID && c != COL_TARGET && c != COL_TEST && !c.match(IGNORE);
});
}
var skip = !!(+row[COL_TEST]);
if(skip) return;
var id = row[COL_ID];
var vec = cols.map(function(c) {
return +row[c];
});
var outcome = !!(+row[COL_TARGET]);
patients.push(new Patient(id, matArr.length, outcome));
matArr.push(vec);
});
pixs = patients.map(function(_, ix) {
return ix;
});
fixs = cols.map(function(_, ix) {
return ix;
});
update(matArr, patients, cols, UPDATE_PATIENTS | UPDATE_FEATURES);
error = false;
} finally {
if(error) {
console.warn("error loading");
}
}
});
}
load(bitvecs);
}
</script>
</body>
</html>