mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-23 00:18:11 +08:00
initial commit
This commit is contained in:
Colin Megill
@@ -0,0 +1,18 @@
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import React from 'react';
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import _ from "lodash";
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import cells from "../../../data/GBM_metadata.js";
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import drawParallelCoordinates from "./drawParallelCoordinates";
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import createContinuousRanges from "./createContinuousRanges";
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const Continuous = () => {
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drawParallelCoordinates(cells)
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return (
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<div>
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<h3> Continuous Metadata </h3>
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</div>
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)
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};
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export default Continuous;
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@@ -0,0 +1,25 @@
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import * as globals from "../../globals.js"
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/*
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end result:
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ranges: {
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Total_reads: {
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min: 11111,
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max: 33333
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},
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Genes_detected: {
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min: 444,
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max: 555
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}
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}
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*/
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const createContinuousRanges = (cells) => {
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const ranges = {};
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return ranges;
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}
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export default createContinuousRanges;
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@@ -0,0 +1,314 @@
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import styles from './parallelCoordinates.css';
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import {
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margin,
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width,
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height,
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innerHeight,
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color,
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dimensions,
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types,
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xscale,
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yAxis,
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} from "./util";
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/*****************************************
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******************************************
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Canvas Parallel coordinates with svg brushing via /* via https://bl.ocks.org/syntagmatic/05a5b0897a48890133beb59c815bd953
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******************************************
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******************************************/
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/*****************************************
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******************************************
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Render Queue via http://bl.ocks.org/syntagmatic/raw/3341641/render-queue.js
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******************************************
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******************************************/
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const renderQueue = (function(callback1234) {
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var _queue = [], // data to be rendered
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_rate = 1000, // number of calls per frame
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_invalidate = function() {}, // invalidate last render queue
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_clear = function() {}; // clearing function
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var rq = function(data) {
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if (data) rq.data(data);
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_invalidate();
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_clear();
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rq.render();
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};
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rq.render = function() {
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var valid = true;
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_invalidate = rq.invalidate = function() {
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valid = false;
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};
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function doFrame() {
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if (!valid) return true;
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var chunk = _queue.splice(0,_rate);
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chunk.map(callback1234);
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timer_frame(doFrame);
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}
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doFrame();
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};
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rq.data = function(data) {
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_invalidate();
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_queue = data.slice(0); // creates a copy of the data
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return rq;
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};
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rq.add = function(data) {
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_queue = _queue.concat(data);
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};
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rq.rate = function(value) {
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if (!arguments.length) return _rate;
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_rate = value;
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return rq;
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};
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rq.remaining = function() {
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return _queue.length;
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};
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// clear the canvas
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rq.clear = function(func) {
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if (!arguments.length) {
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_clear();
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return rq;
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}
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_clear = func;
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return rq;
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};
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rq.invalidate = _invalidate;
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var timer_frame = window.requestAnimationFrame
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|| window.webkitRequestAnimationFrame
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|| window.mozRequestAnimationFrame
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|| window.oRequestAnimationFrame
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|| window.msRequestAnimationFrame
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|| function(callback) { setTimeout(callback, 17); };
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return rq;
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});
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/*****************************************
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******************************************
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MAIN: drawParallelCoordinates
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******************************************
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******************************************/
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const drawParallelCoordinates = (data) => {
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const d3_functor = (v) => {
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return typeof v === "function" ? v : function() { return v; };
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};
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/*****************************************
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******************************************
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Setup SVG & Canvas elements
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******************************************
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******************************************/
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var container = d3.select("body").append("div")
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.attr("class", styles.parcoords)
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.style("width", width + margin.left + margin.right + "px")
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.style("height", height + margin.top + margin.bottom + "px");
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var svg = container.append("svg")
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.attr("width", width + margin.left + margin.right)
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.attr("height", height + margin.top + margin.bottom)
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.append("g")
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.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
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var canvas = container.append("canvas")
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.attr("width", width * devicePixelRatio)
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.attr("height", height * devicePixelRatio)
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.style("width", width + "px")
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.style("height", height + "px")
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.style("margin-top", margin.top + "px")
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.style("margin-left", margin.left + "px");
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var ctx = canvas.node().getContext("2d");
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ctx.globalCompositeOperation = 'darken';
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ctx.globalAlpha = 0.15;
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ctx.lineWidth = 1.5;
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ctx.scale(devicePixelRatio, devicePixelRatio);
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var output = d3.select("body").append("pre");
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var axes = svg.selectAll(".axis")
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.data(dimensions)
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.enter().append("g")
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.attr("class", styles.axis)
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.attr("transform", function(d,i) { return "translate(" + xscale(i) + ")"; });
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/*****************************************
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******************************************
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Setup SVG & Canvas elements
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******************************************
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******************************************/
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d3.csv("https://gist.githubusercontent.com/syntagmatic/05a5b0897a48890133beb59c815bd953/raw/310a68d713eb4d351f809b6cfbcffe3d9d96a205/nutrient.csv", (error, data) => {
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if (error) throw error;
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// shuffle the data!
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data = d3.shuffle(data);
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data.forEach(function(d) {
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dimensions.forEach(function(p) {
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d[p.key] = !d[p.key] ? null : p.type.coerce(d[p.key]);
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});
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// truncate long text strings to fit in data table
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for (var key in d) {
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if (d[key] && d[key].length > 35) d[key] = d[key].slice(0,36);
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}
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});
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// type/dimension default setting happens here
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dimensions.forEach(function(dim) {
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if (!("domain" in dim)) {
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// detect domain using dimension type's extent function
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dim.domain = d3_functor(dim.type.extent)(data.map(function(d) { return d[dim.key]; }));
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}
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if (!("scale" in dim)) {
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// use type's default scale for dimension
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dim.scale = dim.type.defaultScale.copy();
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}
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dim.scale.domain(dim.domain);
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});
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const draw = (d) => {
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ctx.strokeStyle = "rgba(0,0,0,.4)" /* color(d.food_group); */
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ctx.beginPath();
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var coords = project(d);
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coords.forEach((p,i) => {
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// this tricky bit avoids rendering null values as 0
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if (p === null) {
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// this bit renders horizontal lines on the previous/next
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// dimensions, so that sandwiched null values are visible
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if (i > 0) {
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var prev = coords[i-1];
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if (prev !== null) {
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ctx.moveTo(prev[0],prev[1]);
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ctx.lineTo(prev[0]+6,prev[1]);
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}
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}
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if (i < coords.length-1) {
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var next = coords[i+1];
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if (next !== null) {
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ctx.moveTo(next[0]-6,next[1]);
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}
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}
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return;
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}
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if (i == 0) {
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ctx.moveTo(p[0],p[1]);
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return;
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}
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ctx.lineTo(p[0],p[1]);
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});
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ctx.stroke();
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}
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/*****************************************
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******************************************
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Handles a brush event, toggling the display of foreground lines.
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******************************************
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******************************************/
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const brush = () => {
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render.invalidate();
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var actives = [];
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svg.selectAll(".axis .brush")
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.filter((d) => {
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return d3.brushSelection(this);
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})
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.each(function(d) {
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actives.push({
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dimension: d,
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extent: d3.brushSelection(this)
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});
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});
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var selected = data.filter(function(d) {
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if (actives.every(function(active) {
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var dim = active.dimension;
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// test if point is within extents for each active brush
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return dim.type.within(d[dim.key], active.extent, dim);
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})) {
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return true;
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}
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});
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ctx.clearRect(0,0,width,height);
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ctx.globalAlpha = d3.min([0.85/Math.pow(selected.length,0.3),1]);
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render(selected);
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output.text(d3.tsvFormat(selected.slice(0,24)));
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console.log('fires brush', actives)
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}
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function brushstart() {
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d3.event.sourceEvent.stopPropagation();
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}
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var render = renderQueue(draw).rate(50);
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ctx.clearRect(0,0,width,height);
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ctx.globalAlpha = d3.min([0.85/Math.pow(data.length,0.3),1]);
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render(data);
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axes.append("g")
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.each(function(d) {
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var renderAxis = "axis" in d
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? d.axis.scale(d.scale) // custom axis
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: yAxis.scale(d.scale); // default axis
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d3.select(this).call(renderAxis);
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})
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.append("text")
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.attr("class", styles.title)
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.attr("text-anchor", "start")
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.text(function(d) { return "description" in d ? d.description : d.key; });
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// Add and store a brush for each axis.
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axes.append("g")
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.attr("class", styles.brush)
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.each(function(d) {
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d3.select(this).call(d.brush = d3.brushY()
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.extent([[-10,0], [10,height]])
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.on("start", brushstart)
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.on("brush", brush)
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.on("end", brush)
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)
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})
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.selectAll("rect")
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.attr("x", -8)
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.attr("width", 16);
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output.text(d3.tsvFormat(data.slice(0,24)));
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function project(d) {
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return dimensions.map(function(p,i) {
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// check if data element has property and contains a value
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if (
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!(p.key in d) ||
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d[p.key] === null
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) return null;
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return [xscale(i),p.scale(d[p.key])];
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});
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};
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});
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}
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export default drawParallelCoordinates;
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@@ -0,0 +1,91 @@
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/*
|
||||
|
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This code can be found: https://bl.ocks.org/syntagmatic/05a5b0897a48890133beb59c815bd953
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|
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body {
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min-width: 760px;
|
||||
}
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*/
|
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.parcoords {
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display: block;
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}
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.parcoords svg,
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.parcoords canvas {
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font: 10px sans-serif;
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position: absolute;
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}
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.parcoords canvas {
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opacity: 0.9;
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pointer-events: none;
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}
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.axis .title {
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font-size: 10px;
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transform: rotate(-21deg) translate(-5px,-6px);
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fill: #222;
|
||||
}
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.axis line,
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.axis path {
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fill: none;
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stroke: #ccc;
|
||||
stroke-width: 1px;
|
||||
}
|
||||
|
||||
.axis .tick text {
|
||||
fill: #222;
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||||
opacity: 0;
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||||
pointer-events: none;
|
||||
}
|
||||
|
||||
/*
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old, from reference bl.ocks
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||||
.axis.manufac_name .tick text,
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||||
.axis.food_group .tick text {
|
||||
opacity: 1;
|
||||
}
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||||
*/
|
||||
|
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.axis:hover line,
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.axis:hover path,
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||||
.axis.active line,
|
||||
.axis.active path {
|
||||
fill: none;
|
||||
stroke: #222;
|
||||
stroke-width: 1px;
|
||||
}
|
||||
|
||||
.axis:hover .title {
|
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font-weight: bold;
|
||||
}
|
||||
|
||||
.axis:hover .tick text {
|
||||
opacity: 1;
|
||||
}
|
||||
|
||||
.axis.active .title {
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
.axis.active .tick text {
|
||||
opacity: 1;
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
.brush .extent {
|
||||
fill-opacity: .3;
|
||||
stroke: #fff;
|
||||
stroke-width: 1px;
|
||||
}
|
||||
|
||||
pre {
|
||||
width: 100%;
|
||||
height: 300px;
|
||||
margin: 6px 12px;
|
||||
tab-size: 40;
|
||||
font-size: 10px;
|
||||
overflow: auto;
|
||||
}
|
||||
@@ -0,0 +1,162 @@
|
||||
export const margin = {top: 66, right: 110, bottom: 20, left: 188};
|
||||
export const width = document.body.clientWidth - margin.left - margin.right;
|
||||
export const height = 340 - margin.top - margin.bottom;
|
||||
export const innerHeight = height - 2;
|
||||
|
||||
export const devicePixelRatio = window.devicePixelRatio || 1;
|
||||
|
||||
export const color = d3.scaleOrdinal()
|
||||
.range(["#5DA5B3","#D58323","#DD6CA7","#54AF52","#8C92E8","#E15E5A","#725D82","#776327","#50AB84","#954D56","#AB9C27","#517C3F","#9D5130","#357468","#5E9ACF","#C47DCB","#7D9E33","#DB7F85","#BA89AD","#4C6C86","#B59248","#D8597D","#944F7E","#D67D4B","#8F86C2"]);
|
||||
|
||||
export const types = {
|
||||
"Number": {
|
||||
key: "Number",
|
||||
coerce: function(d) { return +d; },
|
||||
extent: d3.extent,
|
||||
within: function(d, extent, dim) { return extent[0] <= dim.scale(d) && dim.scale(d) <= extent[1]; },
|
||||
defaultScale: d3.scaleLinear().range([innerHeight, 0])
|
||||
},
|
||||
"String": {
|
||||
key: "String",
|
||||
coerce: String,
|
||||
extent: function (data) { return data.sort(); },
|
||||
within: function(d, extent, dim) { return extent[0] <= dim.scale(d) && dim.scale(d) <= extent[1]; },
|
||||
defaultScale: d3.scalePoint().range([0, innerHeight])
|
||||
},
|
||||
"Date": {
|
||||
key: "Date",
|
||||
coerce: function(d) { return new Date(d); },
|
||||
extent: d3.extent,
|
||||
within: function(d, extent, dim) { return extent[0] <= dim.scale(d) && dim.scale(d) <= extent[1]; },
|
||||
defaultScale: d3.scaleTime().range([0, innerHeight])
|
||||
}
|
||||
};
|
||||
|
||||
export const dimensions = [
|
||||
{
|
||||
key: "Total lipid (fat) (g)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Sugars, total (g)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Calcium, Ca (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Sodium, Na (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Phosphorus, P (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Potassium, K (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Thiamin (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Riboflavin (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Niacin (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Iron, Fe (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Magnesium, Mg (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Protein (g)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Zinc, Zn (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Vitamin B-6 (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Vitamin B-12 (mcg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Folic acid (mcg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Selenium, Se (mcg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Vitamin A, IU (IU)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Vitamin K (phylloquinone) (mcg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Vitamin C, total ascorbic acid (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Vitamin D (IU)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Cholesterol (mg)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Fiber, total dietary (g)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
},
|
||||
{
|
||||
key: "Carbohydrate, by difference (g)",
|
||||
type: types["Number"],
|
||||
scale: d3.scaleSqrt().range([innerHeight, 0])
|
||||
}
|
||||
];
|
||||
|
||||
export const xscale = d3.scalePoint()
|
||||
.domain(d3.range(dimensions.length))
|
||||
.range([0, width]);
|
||||
|
||||
export const yAxis = d3.axisLeft();
|
||||
Reference in New Issue
Block a user