Published
Edited
Nov 26, 2020
2 forks
Importers
20 stars
Word Tour: 40k words and their friendsHello, orbHello, cosmograph3D graph on a sphereFour-color world map with ClingoUnconnected Delaunay NeighborsColorized Manhattan Spanning TreeShortest pathDijkstra’s algorithm in gpu.jsLloyd’s relaxation on a graphManhattan Voronoi IIManhattan DiameterManhattan VoronoiGraph VoronoiMobility landscapes — an introductionDijkstra’s shortest-path treeWorld Cities UrquhartConvex Spectral WeightsDelaunay.findTriangleForce Simulation Web WorkerSave a Force-Directed Graph to localStorageHello BiofabricTravelling with a self-organizing mapLevenshtein transitionngraph: pagerank, louvain…
Protein Matrix
function nodes_sorted() {
const nodes = order_by_distance(data.nodes);
// largest group must come first: reverse if it's not the case
const order = nodes.map(d => data.nodes.indexOf(d)),
n = nodes.length;
var sum = 0;
for (let i = 0; i < n; i++) {
for (let j = 0; j < n; j++) {
sum += (A[order[i]][order[j]] < 0.2 ? 1 : 0) * Math.sign(n - (i + j));
}
}
if (sum < 0) nodes.reverse();
return nodes;
}
function makevis() {
return chart(sorted ? nodes_sorted() : nodes, value);
}
value = {
const index = d3.group(links, d => d.source, d => d.target);
return ({ source, target }) => {
const li = index.get(source);
if (li) {
const lj = li.get(target);
if (lj) return lj[0].value;
}
return -1;
};
}
A = {
const A = Array.from(data.nodes).map((_, i) =>
Array.from(data.nodes, (_, j) => (i === j ? 0 : 2))
),
m = [...new Set(data.nodes.map(d => d.id)).values()];
data.links
.filter(l => l.value > 0.001)
.forEach(l => {
const i = m.indexOf(l.source),
j = m.indexOf(l.target),
v = Math.pow(
1.0 - l.value,
1
) /* * (nodes[i].group == nodes[j].group ? 1 : 1) */;
if (i > -1 && j > -1) {
A[i][j] = v;
A[j][i] = v;
}
});
return A;
}
B = {
const B = A.map(d => d.slice());
for (let i = 0; i < B.length; i++) {
for (let j = 0; j < B.length; j++) {
B[i][j] = A[i][j];
for (let k = 0; k < B.length; k++) {
B[i][j] +=
Math.max(Math.abs(A[i][k] - A[j][k]) - alpha, 0) / 3 / nodes.length;
}
}
}
return B;
}
mutable debug = undefined
function chart(nodes, accessor) {
const height = width;
var w = width - margin.left - margin.right;
var h = width - margin.top - margin.bottom;
const ids = nodes.map(d => d.id),
matrix = ids.map(source =>
ids.map(target => ({ source, target, val: accessor({ source, target }) }))
);
function colored(d) {
const val = d.val;
if (val === "UNAVAILABLE") return "lime";
if (val === "NA") return "#ccc";
if (d.source == d.target) return "#333";
if (+val > 0) return color(+val);
return "white";
}
var x = d3
.scaleBand()
.rangeRound([0, w])
.paddingInner(0.1)
.align(0)
.domain(ids);
var svgDOM = d3
.select(DOM.svg(width, height))
.attr("class", "matrixdiagram")
.attr("width", w + margin.left + margin.right)
.attr("height", h + margin.top + margin.bottom);
svgDOM.append("defs").html(css);
var svg = svgDOM.append("g");
var row = svg
.selectAll("g.row")
.data(matrix)
.enter()
.append("g")
.attr("class", "row")
.attr("transform", d => `translate(0,${x(d[0].source)})`)
.each(makeRow);
row
.append("text")
.attr("class", "label")
.attr("x", -4)
.attr("y", x.bandwidth() / 2)
.attr("dy", "0.32em")
.text(d => d[0].source);
var column = svg
.selectAll("g.column")
.data(matrix)
.enter()
.append("text")
.attr("class", "column label")
.attr("transform", d => `translate(${x(d[0].source)},0)rotate(-90)`)
.attr("x", 4)
.attr("y", x.bandwidth() / 2)
.attr("dy", "0.32em")
.text(d => d[0].source);
function makeRow(rowData) {
var cell = d3
.select(this)
.selectAll("rect")
.data(rowData)
.enter()
.append("rect")
.attr("x", d => x(d.target))
.attr("width", x.bandwidth())
.attr("height", x.bandwidth())
.style("fill-opacity", 1)
.style("fill", colored)
.on("mouseover", d => {
row
.filter(e => e[0].source === d.source)
.style("fill", "#d62333")
.style("font-weight", "bold");
column
.filter(e => e[0].source === d.target)
.style("fill", "#d62333")
.style("font-weight", "bold");
})
.on("mouseout", () => {
row.style("fill", null).style("font-weight", null);
column.style("fill", null).style("font-weight", null);
});
cell
.append("title")
.text(d =>
d.source === d.target
? d.source
: `${d.source} ↔︎ ${d.target} (${d.val})`
);
}
const zoom = d3
.zoom()
.on("zoom", ({ transform }) => svg.attr("transform", transform));
return svgDOM
.call(zoom)
.call(zoom.transform, d3.zoomIdentity.translate(margin.left, margin.top))
.node();
}
css = {
const w = width - margin.left - margin.right,
n = data.nodes.length,
r = (0.75 * w) / n;
return `<style>
svg.matrixdiagram {
font: ${r}px sans-serif;
}
svg.matrixdiagram .label {
fill: #999;
font-size: ${r}px;
text-anchor: end;
}
svg.matrixdiagram .column.label {
text-anchor: start;
}
svg.matrixdiagram rect {
fill: #eee;
stroke: #d62333;
stroke-width: 0;
}
svg.matrixdiagram rect:hover {
stroke-width: 1px;
}
</style>`;
}
color = {
function domain(color) {
return color.domain(truedomain ? [0, 1] : [0, d3.max(links, d => d.value)]);
}
switch (colorI) {
case "diverging":
return domain(d3.scaleSequential(t => d3.interpolateRdYlBu(1 - t)));
break;
case "plasma":
return domain(d3.scaleSequential(t => d3.interpolatePlasma(1 - t)));
break;
case "reds":
return domain(d3.scaleSequential(d3.interpolateReds));
break;
}
}
import {legend as colorLegend} from "@d3/color-legend"
margin = {
const r =
d3.max(data.nodes, d => d.id.length) *
(width / (20 + data.nodes.length) / 2.5);
return {
top: 10 + r,
left: 10 + r,
right: 10,
bottom: 10
};
}
d3 = require("d3@6")
One platform to build and deploy the best data apps
Experiment and prototype by building visualizations in live JavaScript notebooks. Collaborate with your team and decide which concepts to build out.
Use Observable Framework to build data apps locally. Use data loaders to build in any language or library, including Python, SQL, and R.
Seamlessly deploy to Observable. Test before you ship, use automatic deploy-on-commit, and ensure your projects are always up-to-date.