30:T446b,bfab = { //////////////////////////////////////////////////////////////////////////////// // // Released under "The MIT License": // // Copyright (c) 2014 William J.R. Longabaugh // // Permission is hereby granted, free of charge, to any person obtaining a copy // of this software and associated documentation files (the "Software"), to deal // in the Software without restriction, including without limitation the rights // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell // copies of the Software, and to permit persons to whom the Software is // furnished to do so, subject to the following conditions: // // The above copyright notice and this permission notice shall be included in // all copies or substantial portions of the Software. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN // THE SOFTWARE. // //////////////////////////////////////////////////////////////////////////////// var bfab = {}; /////////////////////////////////////////////////////////////////// // // Data to build the color cycle // bfab.BioFabricD3 = function(width, height, md3) { this._tagOrder = [ "EX-blue", "EX-orange", "EX-dark-cyan", "EX-red", "EX-dark-orange", "EX-dark-gray-purple", "EX-cyan", "EX-yellow-orange", "EX-pure-blue", "EX-dark-yellow-green", "EX-dark-magenta", "EX-dark-green", "EX-blue-magenta", "EX-yellow-green", "EX-magenta", "EX-green", "EX-yellow", "EX-purple", "EX-dark-purple", "EX-dark-red", "EX-pale-green", "EX-pale-blue", "EX-dark-tan", "EX-pale-blue-magenta", "EX-pale-yellow orange", "EX-medium-magenta", "EX-pale-red", "EX-pale-cyan", "EX-pale-yellow-green", "EX-pale-purple", "EX-pale-magenta", "EX-pale-red-orange" ]; this._baseColors = { "EX-cyan": { r: 0, g: 255, b: 255 }, "EX-dark-cyan": { r: 0, g: 100, b: 128 }, "EX-yellow-orange": { r: 255, g: 153, b: 0 }, "EX-pale-green": { r: 133, g: 205, b: 102 }, "EX-dark-green": { r: 39, g: 128, b: 0 }, "EX-pale-red-orange": { r: 230, g: 156, b: 138 }, "EX-yellow-green": { r: 154, g: 255, b: 0 }, "EX-yellow": { r: 255, g: 203, b: 0 }, "EX-dark-gray-purple": { r: 0, g: 25, b: 128 }, "EX-pale-magenta": { r: 212, g: 138, b: 230 }, "EX-pale-purple": { r: 149, g: 165, b: 230 }, "EX-purple": { r: 102, g: 51, b: 255 }, "EX-dark-red": { r: 140, g: 56, b: 56 }, "EX-red": { r: 255, g: 0, b: 0 }, "EX-pale-yellow-green": { r: 222, g: 230, b: 138 }, "EX-dark-purple": { r: 77, g: 56, b: 140 }, "EX-pale-cyan": { r: 138, g: 230, b: 181 }, "EX-pure-blue": { r: 0, g: 0, b: 255 }, "EX-dark-yellow-green": { r: 114, g: 128, b: 0 }, "EX-magenta": { r: 255, g: 0, b: 255 }, "EX-dark-tan": { r: 166, g: 133, b: 83 }, "EX-pale-blue": { r: 102, g: 183, b: 205 }, "EX-orange": { r: 255, g: 103, b: 0 }, "EX-medium-magenta": { r: 166, g: 83, b: 166 }, "EX-blue-magenta": { r: 155, g: 0, b: 255 }, "EX-green": { r: 0, g: 255, b: 0 }, "EX-dark-magenta": { r: 102, g: 0, b: 128 }, "EX-pale-blue-magenta": { r: 146, g: 102, b: 205 }, "EX-pale-yellow orange": { r: 205, g: 175, b: 102 }, "EX-dark-orange": { r: 128, g: 92, b: 0 }, "EX-blue": { r: 0, g: 152, b: 255 }, "EX-pale-red": { r: 205, g: 102, b: 153 } }; this._d3 = md3; this._width = width; this._hw = this._width / 2; this._height = height; this._hh = this._height / 2; this._PAD = 40; this._GRID = 18; this._LINK_WIDTH = 3; this._NODE_WIDTH = 3; this._bsvg = this._d3 .select(".inner") .append("svg:svg") .attr("width", this._width) .attr("height", this._height) .style("background-color", "#FFFFFF"); }; /////////////////////////////////////////////////////////////////// // // Generate colors from the color cycle // bfab.BioFabricD3.prototype._cycleColor = function(mult) { var that = this; return function(d, i) { var tag = that._tagOrder[i % that._tagOrder.length]; var myR = Math.min(255, that._baseColors[tag].r * mult); var myG = Math.min(255, that._baseColors[tag].g * mult); var myB = Math.min(255, that._baseColors[tag].b * mult); return that._d3.rgb(myR, myG, myB); }; }; /////////////////////////////////////////////////////////////////// // // Draw the endpoint glyphs while bringing the links forward: // bfab.BioFabricD3.prototype._drawGlyphs = function(mySvg, myGraph) { var that = this; var myg = mySvg .selectAll(".glyph") .data(myGraph.links) .enter() .append("svg:rect") .attr("class", "glyph") .attr("x", function(d) { return that._PAD + d.col * that._GRID - 5; }) .attr("y", function(d) { return that._PAD + myGraph.nodes[d.source].row * that._GRID - 5; }) .attr("width", 10) .attr("height", 10) .style("stroke-width", function(d) { return 4; }) .style("stroke", "black") .style("fill", this._cycleColor(1 / 1.43)) .style("opacity", "1.0") .append("svg:title") .text(function(d) { return ( myGraph.nodes[d.source].name + "-" + myGraph.nodes[d.target].name ); }); var myg2 = mySvg .selectAll(".glyph2") .data(myGraph.links) .enter() .append("svg:rect") .attr("class", "glyph2") .attr("x", function(d) { return that._PAD + d.col * that._GRID - 5; }) .attr("y", function(d) { return that._PAD + myGraph.nodes[d.target].row * that._GRID - 5; }) .attr("width", 10) .attr("height", 10) .style("stroke-width", function(d) { return 4; }) .style("stroke", "black") .style("fill", this._cycleColor(1 / 1.43)) .style("opacity", "1.0") .append("svg:title") .text(function(d) { return ( myGraph.nodes[d.source].name + "-" + myGraph.nodes[d.target].name ); }); }; /////////////////////////////////////////////////////////////////// // // Draw node labels: // bfab.BioFabricD3.prototype._drawLabels = function(mySvg, myGraph) { var that = this; mySvg .selectAll(".nodeLabel") .data(myGraph.nodes) .enter() .append("svg:text") .attr("class", "nodeLabel") .text(function(d) { return d.name; }) .style("opacity", "0.98") .attr("x", function(d) { return that._PAD + that._GRID * d.minCol; }) .attr("y", function(d) { return that._PAD + that._GRID * d.row; }) .append("svg:title") .text(function(d) { return d.name; }); var zlSel = mySvg .selectAll(".zoneLabel") .data(myGraph.nodes) .enter() .append("svg:text") .attr("transform", function(d) { return "translate(0, 0)"; }) .attr("class", "zoneLabel") .text(function(d) { return d.name; }) .style("opacity", "0.98"); zlSel.append("svg:title").text(function(d) { return d.name; }); function _sizeIt(d, i) { // fixed for d3v5 var bbw = zlSel.nodes()[i].getBBox().width; var bbh = zlSel.nodes()[i].getBBox().height; var sfac = (that._GRID * (d.zoneMax - d.zoneMin) * 0.667) / bbw; if (sfac > 0.33) { return ( "translate(" + (that._PAD + (that._GRID * (d.zoneMin + d.zoneMax)) / 2) + "," + (that._PAD + that._GRID * (d.row - 1)) + ") scale(" + sfac + ")" ); } else { return ( "translate(" + (that._PAD + (that._GRID * (d.zoneMin + d.zoneMax)) / 2 + (0.4 * bbh) / 2) + "," + (that._PAD + that._GRID * (d.row - 1) - (0.4 * bbw) / 2) + ") rotate(" + -90 + ") scale(" + 0.4 + ")" ); } } zlSel.attr("transform", _sizeIt); }; /////////////////////////////////////////////////////////////////// // // Initialize some data: // bfab.BioFabricD3.prototype._initData = function(myGraph) { // // Add and initialize some stuff to the graph we read in: // for (var i = 0; i < myGraph.nodes.length; i++) { myGraph.nodes[i].row = -1; myGraph.nodes[i].degree = 0; myGraph.nodes[i].zoneMin = -1000; myGraph.nodes[i].zoneMax = -1000; myGraph.nodes[i].neighbors = []; myGraph.nodes[i].x = 0; myGraph.nodes[i].y = 0; } // // We calculate degree and record neighbors for later sorting: // for (var i = 0; i < myGraph.links.length; i++) { var link = myGraph.links[i]; myGraph.nodes[link.source].degree++; myGraph.nodes[link.target].degree++; myGraph.nodes[link.source].neighbors.push(myGraph.nodes[link.target]); myGraph.nodes[link.target].neighbors.push(myGraph.nodes[link.source]); } }; /////////////////////////////////////////////////////////////////// // // Build the graph // bfab.BioFabricD3.prototype._buildGraph = function(mySvg, myGraph) { var that = this; mySvg .selectAll(".node") .data(myGraph.nodes) .enter() .append("svg:line") .attr("class", "node") .attr("y1", function(d) { return that._PAD + d.row * that._GRID; }) .attr("y2", function(d) { return that._PAD + d.row * that._GRID; }) .attr("x1", function(d) { return that._PAD + that._GRID * d.minCol; }) .attr("x2", function(d) { return that._PAD + that._GRID * d.maxCol; }) .style("stroke-width", this._NODE_WIDTH) .style("stroke", this._cycleColor(1.43)) .style("opacity", "1.0"); mySvg .selectAll(".linkF") .data(myGraph.links) .enter() .append("svg:line") .attr("class", "linkF") .attr("x1", function(d) { return that._PAD + d.col * that._GRID; }) .attr("y1", function(d) { return that._PAD + myGraph.nodes[d.source].row * that._GRID; }) .attr("x2", function(d) { return that._PAD + d.col * that._GRID; }) .attr("y2", function(d) { return that._PAD + myGraph.nodes[d.target].row * that._GRID; }) .style("stroke", this._cycleColor(1 / 1.43)) .style("stroke-width", this._LINK_WIDTH) .style("opacity", "1.0"); this._drawGlyphs(mySvg, myGraph); this._drawLabels(mySvg, myGraph); }; /////////////////////////////////////////////////////////////////// // // Build the row sort. (Breadth first, from the highest degree node, // traversing neighbors in the order of degree). CRAPPY! It will only // correctly handle a single connected component // bfab.BioFabricD3.prototype._sortGraph = function(myGraph) { var sorter = myGraph.nodes.slice(0); sorter.sort(this._compareNodes); var currNode = sorter[0]; currNode.row = 0; this._orderKids(currNode, 1); }; /////////////////////////////////////////////////////////////////// // // Node sorting function based on degree and name: // bfab.BioFabricD3.prototype._compareNodes = function(a, b) { if (a.degree < b.degree) { return 1; } else if (a.degree > b.degree) { return -1; } else { return -a.name.localeCompare(b.name); } }; /////////////////////////////////////////////////////////////////// // // Order the neighbors: // bfab.BioFabricD3.prototype._orderKids = function(myNode, currVal) { myNode.neighbors.sort(this._compareNodes); var toCheck = 0; for (var i = 0; i < myNode.neighbors.length; i++) { var checkNode = myNode.neighbors[i]; if (checkNode.row === -1) { checkNode.row = currVal++; toCheck++; } } if (toCheck > 0) { for (var i = 0; i < myNode.neighbors.length; i++) { var checkNode = myNode.neighbors[i]; if (checkNode.row !== -1) { currVal = this._orderKids(checkNode, currVal); } } } return currVal; }; /////////////////////////////////////////////////////////////////// // // Link sorting comparator // bfab.BioFabricD3.prototype._compareGuys = function(a, b) { if (a.min < b.min) { return -1; } if (a.min > b.min) { return 1; // mins are the same: } if (a.max < b.max) { return -1; } if (a.max > b.max) { return 1; } return 0; }; /////////////////////////////////////////////////////////////////// // // Link sorting // // Horribly inefficient, but this is a small demo... bfab.BioFabricD3.prototype._sortLinks = function(myGraph) { var sorter = []; for (var i = 0; i < myGraph.links.length; i++) { var link = myGraph.links[i]; var aGuy = {}; aGuy.min = Math.min( myGraph.nodes[link.source].row, myGraph.nodes[link.target].row ); aGuy.max = Math.max( myGraph.nodes[link.source].row, myGraph.nodes[link.target].row ); aGuy.index = i; sorter.push(aGuy); } sorter.sort(this._compareGuys); var lastGuy = null; for (var i = 0; i < sorter.length; i++) { var aGuy = sorter[i]; var useLink = myGraph.links[aGuy.index]; useLink.col = i; if (lastGuy != null && aGuy.min > lastGuy.min) { var gotIt = false; for (var j = i - 1; j >= 0; j--) { if (sorter[j].min < lastGuy.min || j === 0) { for (var k = 0; k < myGraph.nodes.length; k++) { var chkNode = myGraph.nodes[k]; if (chkNode.row === lastGuy.min) { gotIt = true; myGraph.nodes[k].zoneMin = j; myGraph.nodes[k].zoneMax = i; break; } } if (gotIt) { break; } } } } lastGuy = aGuy; } }; /////////////////////////////////////////////////////////////////// // // Figure out the final node lengths: // bfab.BioFabricD3.prototype._boundNodes = function(myGraph) { for (var i = 0; i < myGraph.nodes.length; i++) { myGraph.nodes[i].minCol = Number.MAX_VALUE / 2; myGraph.nodes[i].maxCol = -Number.MAX_VALUE / 2; } for (var i = 0; i < myGraph.links.length; i++) { var link = myGraph.links[i]; if (link.col < myGraph.nodes[link.source].minCol) { myGraph.nodes[link.source].minCol = link.col; } if (link.col > myGraph.nodes[link.source].maxCol) { myGraph.nodes[link.source].maxCol = link.col; } if (link.col < myGraph.nodes[link.target].minCol) { myGraph.nodes[link.target].minCol = link.col; } if (link.col > myGraph.nodes[link.target].maxCol) { myGraph.nodes[link.target].maxCol = link.col; } } }; /////////////////////////////////////////////////////////////////// // // Closure of function // bfab.BioFabricD3.prototype._d3FuncClosure = function() { var that = this; return function(error, graph) { that._d3Func(error, graph); }; }; /////////////////////////////////////////////////////////////////// // // Function to hand d3 with argument to instantiate: // bfab.BioFabricD3.prototype._d3Func = function(error, graph) { // // Add and initialize some stuff to the graph we read in: // this._initData(graph); // // Figure out the width and height we need to zoom to fit it all in. // Note we are assuming more links than nodes: // var gwidth = 2 * this._PAD + this._GRID * graph.links.length; var gheight = 2 * this._PAD + this._GRID * graph.nodes.length; var sfac = this._width / gwidth; // // Add the zooming transform at the top of the SVG tree. // var svg = this._bsvg .append("svg:g") .attr( "transform", "translate(" + this._hw + "," + this._hh + ") scale(" + sfac + ") translate(-" + gwidth / 2 + ",-" + gheight / 2 + ")" ); // // Lay it out: // this._sortGraph(graph); this._sortLinks(graph); this._boundNodes(graph); // // Draw it: // this._buildGraph(svg, graph); }; /////////////////////////////////////////////////////////////////// // // WARNING! The code has NOT been tested on different networks! Probably handles singleton nodes and duplicate links incorrectly! // bfab.BioFabricD3.prototype.drawFabric = async function(fileName) { // fixes for d3v5 const callback = this._d3FuncClosure(); this._d3.json(fileName).then(d => callback(null, d)); }; return bfab; }31:[] 2e:{"title":"Hello Biofabric","cells":[{"id":0,"value":"md`# Hello Biofabric\n\n> Longabaugh, W.J.R. [Combing the hairball with BioFabric: a new approach for visualization of large networks](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-275). BMC Bioinformatics, 13:275, 2012. \n\n\n\nRef: https://raw.githubusercontent.com/wjrl/D3BioFabric/\n\nw/ two small fixes for compatibility with d3v5.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"{\n yield html`${style}\n\t\t

\n\t\t\t

\n\t \t

\n\t \t\t

\n`;\n\n const mbfd3 = new bfab.BioFabricD3(1200, 500, d3);\n mbfd3.drawFabric(netDef);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":15,"value":"netDef =\n \"https://raw.githubusercontent.com/wjrl/D3BioFabric/master/src/data/miserablesSimple.json\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":24,"value":"style = ``","pinned":false,"hidden":false,"mode":"ojs"},{"id":3,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":18,"value":"d3 = require(\"d3@5\")","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W31","stdlib":"1","titling":"auto"}