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/*
* clanviewer
* https://github.com/4ndr01d3/clanviewer
*
* Copyright (c) 2015 gsalazar
* Licensed under the Apache-2.0 license.
*/
/**
@class clanviewer
A component to visualise the relationships between the Pfam families in a clan
*/
import {select, event as d3Event} from 'd3-selection';
import {scaleLinear} from 'd3-scale';
import {zoom as d3Zoom} from 'd3-zoom';
import {drag as d3Drag} from 'd3-drag';
import {forceSimulation, forceCenter, forceManyBody, forceLink} from 'd3-force';
import ResizeObserver from 'resize-observer-polyfill';
export default class ClanViewer {
constructor({
element="body",
directional=false,
width=undefined,
height=undefined,
r=5,
multiple_relationships=false,
useCtrlToZoom = false,
}){
this.r = r;
this._autoWidth=!width;
this._autoHeight=!height;
this.width = width;
this.height = height;
this.element = element;
this.multiple_relationships = multiple_relationships;
this.directional = directional;
this.useCtrlToZoom = useCtrlToZoom;
this.size = scaleLinear()
.range([1, 5 * this.r]);
this.tickness = scaleLinear()
.range([0.5, 1, 5])
.domain([1, 1e-4, 0]);
this.force = forceSimulation()
.force("charge", forceManyBody()
.strength(-100)
)
.force("link", forceLink()
.id(d => d.accession)
.distance(200)
)
.force("center", forceCenter(width / 2, height / 2));
this.zoom = d3Zoom()
.filter(() => {
if (!(d3Event instanceof WheelEvent)) return true;
return !this.useCtrlToZoom || d3Event.ctrlKey;
})
.scaleExtent([0.5, 10])
.on("zoom", () => {
this.maingroup.attr("transform",d3Event.transform);
});
this.drag = d3Drag()
.on("start", d => {
d3Event.sourceEvent.stopPropagation();
this.force.alphaTarget(0.1).restart();
d.fx = d.x;
d.fy = d.y;
})
.on("drag", d => {
d.fx = d3Event.x;
d.fy = d3Event.y;
})
.on("end", () => {
d3Event.sourceEvent.stopPropagation();
if (!d3Event.active) this.force.alphaTarget(0);
});
this.svg = select(this.element).append("svg")
.attr("width", this.width)
.attr("height", this.height)
.attr("class", "clanviewer")
.attr("pointer-events", "all")
.call(this.zoom).on("dblclick.zoom", null);
this.maingroup = this.svg
.append("g");
this.linksgroup = this.maingroup
.append("g")
.attr("class", "links");
this.nodeGroup = this.maingroup
.append("g")
.attr("class", "nodes");
if (this.directional)
this.maingroup.append("defs").append("marker")
.attr("id", "arrowhead")
.attr("viewBox", "0 -5 10 10")
.attr("refX", 11)
.attr("refY", 0)
.attr("markerWidth", 2)
.attr("markerHeight", 2)
.attr("orient", "auto")
.append("path")
.attr("d", "M0,-5L10,0L0,5");
if(this._autoWidth) {
this.svg.style('display', 'block');
this.svg.attr('width', '100%');
}
if(this._autoHeight) {
this.svg.style('display', 'block');
this.svg.attr('height', '100%');
}
if (this._autoHeight || this._autoWidth) {
this._autoUpdateSize();
this._ro = new ResizeObserver(this._autoUpdateSize.bind(this));
this._ro.observe(this.svg.node());
}
this.paint.bind(this)
}
_autoUpdateSize() {
const parent = select(this.element);
this.width = parseInt(parent.style('width'), 10) || 0;
this.height = parseInt(parent.style('height'), 10) || 0;
this.force.force("center", forceCenter(this.width / 2, this.height / 2));
this.svg.attr('viewBox', `0 0 ${this.width} ${this.height}`);
Iif (this.tick) {
this.force.restart();
}
}
/**
* The 'paint' method receives a json object and generates a force-directed layout that maps the memebers with ith relationships
* @param data an object structure based on a json file similar to:
* {
* "clan_acc":"CL0050",
* "clan_id":"HotDog",
* "members":[
* { "pfama_acc":"PF03061", "link":"http://pfam.xfam.org/family/PF03061", "pfama_id":"4HBT", "num_full":88944 },
* { "pfama_acc":"PF01643", "link":"http://pfam.xfam.org/family/PF01643", "pfama_id":"Acyl-ACP_TE", "num_full":7178 },
* ],
* "relationships":[
* { "pfama_acc_1":"4HBT", "pfama_acc_2":"Acyl-ACP_TE", "evalue":8.2e-6 }
* ]
* }
* * @param is_data_processed Boolean indicating if the data is already in the format:
* {
* "nodes": [
* {accession: "PF03761", id: "DUF316", score: 189},
* {accession: "PF03761", id: "DUF316", score: 189},
* ],
* "links": [
* {source: 0, target: 1, evalue: 0.000016}
* ],
* }
*
*/
paint(data, is_data_processed=false) {
Eif (!is_data_processed) this.processData(data);
this.force
.nodes(data.nodes)
.force("link").links(data.links);
const linkGData = this.linksgroup.selectAll(".link")
.data(data.links);
const linkG = linkGData.enter().append("g")
.attr("class", d => `link ${d.source.accession} ${d.target.accession}` );
linkGData.exit().remove();
const link = linkG.append("path")
.style("stroke-width", d => this.tickness(d.score))
.attr("marker-end",this.directional?"url(#arrowhead)":null);
const label_link_link = linkG.filter(d => d.link)
.append("a")
.attr("xlink:href", d => d["link"]?d["link"]:null)
.attr("target", "_blank")
.attr("class", d => d["link"]?"href":null)
.append("text")
.text(d => d.score.toExponential());
const label_link_text = linkG.filter(d => !d.link)
.append("text")
.text(d => d.score.toExponential());
const nodeGdata = this.nodeGroup
.selectAll(".node")
.data(data.nodes);
const nodeG = nodeGdata
.enter().append("g")
.attr("id", d => `node_${d.accession}`)
.attr("data-accession", d => d.accession)
.attr("class", "node");
nodeGdata.exit().remove();
const node = nodeG.append("circle")
.attr("r", d => this.size(d.score))
.call(this.drag)
.on("dblclick", function (d){
d.fx = null;
d.fy = null;
});
const label_node_link = nodeG.filter(d => d.link)
.append("a")
.attr("xlink:href", d => d["link"]?d["link"]:null)
.attr("target", "_blank")
.attr("class", d => d["link"]?"href":null)
.append("text")
.text(d => d.accession);
const label_node_text = nodeG.filter(d => !d.link)
.append("text")
.text(d => d.accession);
this.tick = () => {
link.attr("d", ClanViewer.linkArc);
label_link_link
.attr("transform", ClanViewer.labelArc);
label_link_text
.attr("transform", ClanViewer.labelArc);
node.attr("cx", d => d.x)
.attr("cy", d => d.y);
label_node_link
.attr("x", d => d.x+this.size(d.score)+2)
.attr("y", d => d.y+this.r);
label_node_text
.attr("x", d => d.x+this.size(d.score)+2)
.attr("y", d => d.y+this.r);
};
this.force.on("tick", this.tick);
this.force.alpha(1);
}
clear(){
this.paint({
nodes:[],
relationships: [],
})
}
static linkArc(d) {
const dx = d.target.x - d.source.x,
dy = d.target.y - d.source.y,
dr = Math.sqrt(dx * dx + dy * dy);
d.dr = dr;
return "M" + d.source.x + "," + d.source.y + "A" + dr + "," + dr + " 0 0,1 " + d.target.x + "," + d.target.y;
}
static labelArc(d){
const x = (d.target.x + d.source.x)/2;
const y = (d.target.y + d.source.y)/ 2; // (x,y) is the point in the middle of target and source
const h = d.dr;
const A = h/ 2;
const B = h - Math.sqrt(h * h - A * A);
const mB = (d.source.x - x)/(y - d.source.y); //TODO: check division by 0
const div = Math.sqrt(1+mB*mB);
const px = (d.target.y>d.source.y)?x + B*(1/div):x - B*(1/div);
const py = (d.target.y>d.source.y)?y + B*(mB/div):y - B*(mB/div);
return "translate(" + px + "," + py + ")";
}
processData(data) {
let max = this.r;
data.members = data.members || data.nodes;
data.relationships = data.relationships || data.links;
data.nodes = data.members.map(e => ({
accession: e.accession || e.pfama_acc,
name: e.name || e.pfama_id,
score: Number.parseFloat(('score' in e && e.score !== null)? e.score : e.num_full),
}));
data.nodes.forEach( e => {
max = Math.max(max, e.score);
});
if (this.multiple_relationships) {
data.relationships.forEach(e => {
e.source = e.source || e.pfama_acc_1;
e.target = e.target || e.pfama_acc_2;
e.score = Number.parseFloat(('score' in e && e.score !== null) ? e.score : e.evalue);
});
data.links = data.relationships;
} else {
const tmp_relationships = {};
data.relationships.forEach(e => {
const acc1 = e.source || e.pfama_acc_1;
const acc2 = e.target || e.pfama_acc_2;
const score = Number.parseFloat(e.score || e.evalue);
let key = `${acc1}_${acc2}`;
Iif (key in tmp_relationships) {
tmp_relationships[key].score = Math.max(tmp_relationships[key].score, score);
} else Iif (`${acc2}_${acc1}` in tmp_relationships) {
key = `${acc2}_${acc1}`;
// tmp_relationships[key].evalue =tmp_relationships[key].evalue> e.evalue? e.evalue:tmp_relationships[key].evalue;
tmp_relationships[key].score = Math.max(tmp_relationships[key].score, score);
} else {
tmp_relationships [key] = {
source: acc1,
target: acc2,
score: score
};
}
});
data.links = Object.keys(tmp_relationships).map(key => tmp_relationships[key]);
}
this.size.domain([0, max]);
}
}
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