Working as a scientific software engineer in Max Planck Institute of Molecular Cell Biology and Genetic
data = FileAttachment("gate-data@1.json").json({ typed: true })
dat = data.dat
scores = _.map(dat, (d) => d.score)
residues = _.map(dat, (d) => d.residue)
Table(dat, {
format: {
score: sparkbar(d3.max(dat, (d) => d.score))
}
})
Table = Inputs.table // deprecated alias
Plot.plot({
caption: "Score distribution in residue",
x: {
label: "Residue"
},
marks: [Plot.ruleY([0]), Plot.barY(dat, { x: "residue", y: "score" })]
})
chart = {
const svg = d3.select(DOM.svg(width, height));
const x = d3
.scaleBand()
.domain(dat.map((d) => d.residue))
.range([margin.left, width - margin.right])
.padding(0.1);
const y = d3
.scaleBand()
.domain(["gate"])
.range([margin.top, height - margin.bottom])
.padding(0.1);
const z = d3.scaleSequential(d3.interpolateOrRd).domain([0, d3.max(scores)]);
const xAxis = (g) =>
g
.attr("transform", `translate(0, ${height - margin.bottom})`)
.call(d3.axisBottom(x).tickSizeOuter(0))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.attr("y", 0)
.attr("x", -9)
.attr("dy", ".35em")
.attr("transform", "rotate(270)")
.style("text-anchor", "end")
.style("fill", "#777");
const yAxis = (g) =>
g
.attr("transform", `translate(${margin.left},0)`)
.call(d3.axisLeft(y).tickSize(0).tickPadding(4))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.style("fill", "#777");
svg.append("g").call(xAxis);
svg.append("g").call(yAxis);
const serie = svg
.append("g")
.selectAll("g")
.data([{ key: "gate", dat }])
.enter()
.append("g")
.attr("transform", (d) => `translate(0,${y(d.key) + 1})`);
const tip = d3tip()
.attr("class", "d3-tip")
.html((d, x) => x.residue);
svg.call(tip);
serie
.append("g")
.selectAll("rect")
.data((d) => d.dat)
.enter()
.append("rect")
.attr("fill", (d) => z(d.score))
.attr("x", (d, i) => x(residues[i]))
.attr("y", 0)
.attr("height", y.bandwidth())
.attr("width", x.bandwidth())
.on("mouseover", tip.show)
.on("mouseout", tip.hide);
return svg.node();
}
chart2 = {
const svg = d3.select(DOM.svg(width, height));
const x = d3
.scaleBand()
.domain(dat.map((d) => d.residue))
.range([margin.left, width - margin.right])
.padding(0.1);
const y = d3
.scaleBand()
.domain(["gate"])
.range([margin.top, height - margin.bottom])
.padding(0.1);
const z = d3.scaleSequential(d3.interpolateOrRd).domain([0, d3.max(scores)]);
const xAxis = (g) =>
g
.attr("transform", `translate(0, ${height - margin.bottom})`)
.call(d3.axisBottom(x).tickSizeOuter(0))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.attr("y", 0)
.attr("x", -9)
.attr("dy", ".35em")
.attr("transform", "rotate(270)")
.style("text-anchor", "end")
.style("fill", "#777");
const yAxis = (g) =>
g
.attr("transform", `translate(${margin.left},0)`)
.call(d3.axisLeft(y).tickSize(0).tickPadding(4))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.style("fill", "#777");
svg.append("g").call(xAxis);
svg.append("g").call(yAxis);
const serie = svg
.append("g")
.selectAll("g")
.data([{ key: "gate", dat }])
.enter()
.append("g")
.attr("transform", (d) => `translate(0,${y(d.key) + 1})`);
const tip = d3tip()
.attr("class", "d3-tip")
.html((d, x) => x.residue);
svg.call(tip);
serie
.append("g")
.selectAll("rect")
.data((d) => d.dat)
.enter()
.append("rect")
.attr("fill", (d) => z(d.score))
.attr("x", (d, i) => x(residues[i]))
.attr("y", 0)
.attr("height", y.bandwidth())
.attr("width", x.bandwidth())
.on("mouseover", tip.show)
.on("mouseout", tip.hide);
return svg.node();
}
{
const a = _.chunk(dat, 50);
return a;
}
height = 80
{
return seqChart(data);
}
coreData = FileAttachment("core-data.json").json()
{
return seqChart(coreData);
}
function seqChart(data) {
const dat = _.chunk(data.dat, 50);
const svg = d3.select(DOM.svg(width, height * dat.length + margin.bottom));
const scores = _.map(data.dat, (d) => d.score);
dat.forEach((chunk, index) => {
const residues = chunk.map((d) => d.residue);
const x = d3
.scaleBand()
.domain(residues)
.range([margin.left, 18 * chunk.length])
.padding(0.1);
const y = d3
.scaleBand()
.domain([data.name])
.range([margin.top, height - margin.bottom])
.padding(0.1);
const z = d3
.scaleSequential(d3.interpolateOrRd)
.domain([0, d3.max(scores)]);
const xAxis = (g) =>
g
.attr("transform", `translate(0, ${height * index + 50})`)
.call(d3.axisBottom(x).tickSizeOuter(0))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.attr("y", 0)
.attr("x", -9)
.attr("dy", ".35em")
.attr("transform", "rotate(270)")
.style("text-anchor", "end")
.style("fill", "#444");
const yAxis = (g) =>
g
.attr("transform", `translate(${margin.left},0)`)
.call(d3.axisLeft(y).tickSize(0).tickPadding(4))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.style("fill", "#444");
svg.append("g").call(xAxis);
if (index === 0) {
svg.append("g").call(yAxis);
}
const serie = svg
.append("g")
.selectAll("g")
.data([{ key: data.name, dat: chunk }])
.enter()
.append("g")
.attr(
"transform",
(d) => `translate(0,${y(d.key) + 1 + height * index})`
);
const tip = d3tip()
.attr("class", "d3-tip")
.html((d, x, i) => x.residue);
svg.call(tip);
serie
.append("g")
.selectAll("rect")
.data((d) => d.dat)
.enter()
.append("rect")
.attr("fill", (d) => z(d.score))
.attr("x", (d, i) => x(residues[i]))
.attr("y", 0)
.attr("height", y.bandwidth())
.attr("width", x.bandwidth())
.on("mouseover", tip.show)
.on("mouseout", tip.hide);
});
return svg.node();
}
{
return chainChart([data, coreData, data, coreData]);
}
function chainChart(data) {
const length = _.reduce(data, (sum, n) => sum + n.dat.length / 50, 0);
const svgHeight = height * (length + 2.2);
const svg = d3.select(DOM.svg(width, svgHeight));
const scores = _.flatMap(data, (d) => _.map(d.dat, (d) => d.score));
const z = d3.scaleSequential(d3.interpolateOrRd).domain([0, d3.max(scores)]);
let accHeight = 0;
data.forEach((data, idx) => {
const dat = _.chunk(data.dat, 50);
dat.forEach((chunk, index) => {
const residues = chunk.map((d) => d.residue);
const x = d3
.scaleBand()
.domain(residues)
.range([margin.left, 18 * chunk.length])
.padding(0.1);
const y = d3
.scaleBand()
.domain([data.name])
.range([margin.top, height - margin.bottom])
.padding(0.1);
const xAxis = (g) =>
g
.attr("transform", `translate(0, ${accHeight + height * index + 50})`)
.call(d3.axisBottom(x).tickSizeOuter(0))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.attr("y", 0)
.attr("x", -9)
.attr("dy", ".35em")
.attr("transform", "rotate(270)")
.style("text-anchor", "end")
.style("fill", "#444");
const yAxis = (g) =>
g
.attr("transform", `translate(${margin.left},${accHeight})`)
.call(d3.axisLeft(y).tickSize(0).tickPadding(4))
.call((g) => g.select(".domain").remove())
.selectAll("text")
.style("fill", "#444");
svg.append("g").call(xAxis);
if (index === 0) {
svg.append("g").call(yAxis);
}
const serie = svg
.append("g")
.selectAll("g")
.data([{ key: data.name, dat: chunk }])
.enter()
.append("g")
.attr(
"transform",
(d) => `translate(0,${y(d.key) + 1 + accHeight + height * index})`
);
const tip = d3tip()
.attr("class", "d3-tip")
.html((d, x, i) => x.residue + ": " + x.score.toFixed(2));
svg.call(tip);
function check(e, d) {
const prefix = d.residue.substring(0, 3);
// console.log(prefix);
const parent = e.target.parentElement.parentElement.parentElement;
// console.log(parent);
svg
.selectAll("rect")
.attr("stroke", (f) =>
prefix && f.residue && f.residue.startsWith(prefix)
? "black"
: undefined
);
}
serie
.append("g")
.selectAll("rect")
.data((d) => d.dat)
.enter()
.append("rect")
.attr("fill", (d) => z(d.score))
.attr("x", (d, i) => x(residues[i]))
.attr("y", 0)
.attr("height", y.bandwidth())
.attr("width", x.bandwidth())
.on("mouseover", tip.show)
.on("mouseout", tip.hide)
.on("click", (e, d) => check(e, d));
});
accHeight += height * dat.length;
});
// Legend
const legendBins = [...Array(9).keys()].map((x) =>
d3.quantile([0, d3.max(scores)], x * 0.1)
);
const legendElementWidth = 56;
const legendHeight = 20;
const legend = svg
.append("g")
.attr("transform", (d) => `translate(${margin.left}, ${svgHeight - 100})`);
legend
.selectAll("rect")
.data(legendBins)
.enter()
.append("rect")
.attr("x", (d, i) => legendElementWidth * i)
.attr("y", height - 2 * legendHeight)
.attr("width", legendElementWidth)
.attr("height", legendHeight)
.style("fill", (d) => z(d));
legend
.selectAll("text")
.data(legendBins)
.enter()
.append("text")
.text((d) => "≥ " + d.toFixed(1))
.attr("x", (d, i) => legendElementWidth * i)
.attr("y", height - legendHeight / 2)
.style("font-size", "9pt")
.style("font-family", "Consolas, courier")
.style("fill", "#aaa");
return svg.node();
}
margin = ({ top: 30, right: 30, bottom: 30, left: 80 })
d3tip = require("https://cdnjs.cloudflare.com/ajax/libs/d3-tip/0.9.1/d3-tip.js")
html`<link rel="stylesheet" href="//rawgithub.com/Caged/d3-tip/master/examples/example-styles.css">`
_ = require("lodash")
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.