2d:null 2e:["$","title",null,{"children":"CoV rec viz | CVR Bioinformatics | Observable"}] 33:T1289,full_plot = { const svg = d3.create('svg') .attr('height', height) .attr('width', width) .style('font-family', 'Georgia') .style('font-size', '16px') // add the x Axis var x = d3.scaleLinear() .domain([0, d3.extent(data_bdt, d => parseFloat(d.alpos))[1]]) .range([margin.left, width - margin.right]); const xAxis = g => g .style("font", "14px times") .attr('transform', `translate(0, ${height - margin.bottom})`) .call(d3.axisBottom(x).tickSizeOuter(0)) svg.append('g') .call(xAxis) // add the y Axis var y = d3.scaleLinear() .range([height-margin.bottom,margin.top]) .domain([0,1]) //.domain([d3.extent(data_bdt, d => parseFloat(d.avgGC))[0], d3.extent(data_bdt, d => parseFloat(d.avgsim))[1]]) const yAxis = g => g .style("font", "14px times") .attr("transform",`translate(${margin.left},0)`) .call(d3.axisLeft(y)); svg.append('g') .call(yAxis) // Add X axis label: svg.append("text") .attr("text-anchor", "end") .attr("x", width/2 + margin.left) .attr("y", height - margin.bottom + 60) .text("alignment position"); // Y axis label: // svg.append("text") // .attr("text-anchor", "end") // .attr("transform", "rotate(-90)") // .attr("y", margin.left -40) // .attr("x", -height/2 + 130) // .text("Breakpoints per 200nt window"); //average pairwise similarity svg.append("path") .attr("d",d3.line() .x(d => x(d.alpos)) .y(d => y(d.avgsim))(data_bdt)) .attr('opacity', alpha) .attr("stroke",colourScheme[0]) .attr("stroke-width","1") //.style("stroke-dasharray", (5)) .attr("fill","none"); //average GC svg.append("path") .attr("d",d3.line() .x(d => x(d.alpos)) .y(d => y(d.avgGC))(data_bdt)) .attr('opacity', alpha) .attr("stroke",colourScheme[1]) .attr("stroke-width","1") //.style("stroke-dasharray", (5)) .attr("fill","none"); //category labels var txtxscale = 30; var txtyscale = 225; var yscale = 20; var lab; for(lab of linecats){ svg.append('text') .attr('x',margin.left + txtxscale) .attr('y', height - margin.bottom - txtyscale + linecats.indexOf(lab)*yscale) .text(lab) .attr('fill', 'black') .attr("font-family", "Georgia") .attr("font-size", "12px") svg.append('rect') .attr('x', margin.left + txtxscale-20) .attr('y', height - margin.bottom - txtyscale - 5 + linecats.indexOf(lab)*yscale) .attr('height', 3) .attr('width', 15) .attr('stroke', 'transparent') .attr('fill', colourScheme[linecats.indexOf(lab)]); } //genome ORF annotation var o; for (o of genome_ann) { svg.append("rect") .attr("stroke", "black") .attr('stroke-width', 1) .attr("fill", 'none') .attr('x', x(o[1][0])) //.attr("y", schemtop - orfscale) .attr('y', function(d){ if (genome_ann.indexOf(o) % 2 == 0){return schemtop - orfscale} return schemtop - orfscale + 20}) .attr('width', x(o[1][1]-o[1][0]) - margin.left) .attr("height", schembot -2*orfscale + 10); //svg.append('text') // .attr('x', x(o[1][0])) //.attr('y', function(d){ // if (genome_ann.indexOf(o) % 2 == 0){return 10} // return 30}) //.text(o[0]) //.attr('fill', 'black') //.attr("font-size", "14px") } //breakpoint positions var bp; for (bp of thebps){ svg.append("line") .datum(thebps) .attr("x1", x(bp)) .attr("x2", x(bp)) .attr("y1", schembot + 10) .attr("y2", schembot + 10 + lineheight) .attr("stroke", colourScheme[2]) .attr('stroke-width', 1) .style("opacity", alpha); } //trsb positions var trsb; for (trsb of thetrsbs){ svg.append("line") .datum(thetrsbs) .attr("x1", x(trsb)) .attr("x2", x(trsb)) .attr("y1", schembot - 20) .attr("y2", schembot - 20 + lineheight) .attr("stroke", colourScheme[3]) .attr('stroke-width', 2) .style("opacity", 1); } //vertical line labels var vlab; var vlabxscal = 5; for(vlab of rowcats){ svg.append('text') .attr('x', vlabxscal) .attr('y', schembot - 5 + rowcats.indexOf(vlab)*30) .text(vlab) .attr('fill', 'black') .attr("font-family", "Georgia") .attr("font-size", "12px") } return svg.node() 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\n**scale variables**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":511,"value":"viewof alpha= slider({\n min: 0, \n max: 1, \n step: 0.05, \n value: 0.8, \n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":394,"value":"linecats = ['average pairwise similarity', 'average GC content']","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":496,"value":"rowcats = ['TRSB', 'breakpoints']","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":455,"value":"lineheight = 20","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":261,"value":"orfscale = 50","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":246,"value":"schemtop = 70\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":249,"value":"schembot = schemtop + 40","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":527,"value":"md`\n
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\n**universal data variables**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":706,"value":"datakey = ({'Embecovirus':embeco_gcsim, 'Igacovirus':igaco_gcsim, 'Merbecovirus':merbeco_gcsim, 'Nobecovirus':nobeco_gcsim, 'Pedacovirus':pedaco_gcsim, 'Sarbecovirus':sarbeco_gcsim })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"data_bdt = datakey[virtax].filter(function( obj ) {return obj.avgGC !== 'NA';});\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":713,"value":"trsbskey = ({'Embecovirus':embeco_trsbs, 'Igacovirus':igaco_trsbs, 'Merbecovirus':merbeco_trsbs, 'Nobecovirus':nobeco_trsbs, 'Pedacovirus':pedaco_trsbs, 'Sarbecovirus':sarbeco_trsbs })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":472,"value":"thetrsbs = Array.from(trsbskey[virtax], function(d){ return d.TRSBBP });","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":716,"value":"bpskey = ({'Embecovirus':embeco_bps, 'Igacovirus':igaco_bps, 'Merbecovirus':merbeco_bps, 'Nobecovirus':nobeco_bps, 'Pedacovirus':pedaco_bps, 'Sarbecovirus':sarbeco_bps })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":188,"value":"thebps = Array.from(bpskey[virtax], function(d){ return d.bppos });","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":722,"value":"gakey = ({'Embecovirus':embeco_ga, 'Igacovirus':igaco_ga, 'Merbecovirus':merbeco_ga, 'Nobecovirus':nobeco_ga, 'Pedacovirus':pedaco_ga, 'Sarbecovirus':sarbeco_ga })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":49,"value":"genome_ann = gakey[virtax]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":572,"value":"md`\n
\n
\n**Embeco data**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":577,"value":"embeco_bps = d3.csvParse( await FileAttachment(\"Embecovirus.csvBreakpointPositions@1.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":582,"value":"embeco_gcsim = d3.csvParse( await FileAttachment(\"AAA_EmbecovirusAligned_simgc.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":587,"value":"embeco_ga = d3.csvParse(await FileAttachment(\"Embecovirus.csvORFCoords.csv\").text(), ({gene, start, stop}) => [gene, [start, stop]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":592,"value":"embeco_trsbs = d3.csvParse(await FileAttachment(\"Embeco_trsbs.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":593,"value":"md`\n
\n
\n**Igaco data**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":596,"value":"igaco_bps = d3.csvParse( await FileAttachment(\"Igaco.csvBreakpointPositions.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":598,"value":"igaco_gcsim = d3.csvParse( await FileAttachment(\"AAA_IgacovirusAligned_simgc.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":600,"value":"igaco_ga = d3.csvParse(await FileAttachment(\"Igaco.csvORFCoords.csv\").text(), ({gene, start, stop}) => [gene, [start, stop]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":602,"value":"igaco_trsbs = d3.csvParse(await FileAttachment(\"Igaco_trsbs.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":610,"value":"md`\n
\n
\n**Merbeco data**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":613,"value":"merbeco_bps = d3.csvParse( await FileAttachment(\"Merbecovirus.csvBreakpointPositions.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":616,"value":"merbeco_gcsim = d3.csvParse( await FileAttachment(\"AAA_MerbecoAligned_simgc.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":619,"value":"merbeco_ga = d3.csvParse(await FileAttachment(\"Merbecovirus.csvORFCoords.csv\").text(), ({gene, start, stop}) => [gene, [start, stop]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":622,"value":"merbeco_trsbs = d3.csvParse(await FileAttachment(\"Merbeco_trsbs.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":535,"value":"md`\n
\n
\n**Nobeco data**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":441,"value":"nobeco_bps = d3.csvParse( await FileAttachment(\"Nobecovirus.csvBreakpointPositions.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":86,"value":"nobeco_gcsim = d3.csvParse( await FileAttachment(\"AAA_NobecovirusAligned_simgc.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":436,"value":"nobeco_ga = d3.csvParse(await FileAttachment(\"Nobecovirus.csvORFCoords.csv\").text(), ({gene, start, stop}) => [gene, [start, stop]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":470,"value":"nobeco_trsbs = d3.csvParse(await FileAttachment(\"Nobeco_trsbs.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":624,"value":"md`\n
\n
\n**Pedaco data**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":634,"value":"pedaco_bps = d3.csvParse( await FileAttachment(\"Pedacovirus.csvBreakpointPositions.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":636,"value":"pedaco_gcsim = d3.csvParse( await FileAttachment(\"AAA_PedacovirusAligned_simgc.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":639,"value":"pedaco_ga = d3.csvParse(await FileAttachment(\"Pedacovirus.csvORFCoords.csv\").text(), ({gene, start, stop}) => [gene, [start, stop]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":642,"value":"pedaco_trsbs = d3.csvParse(await FileAttachment(\"Pedaco_trsbs.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":645,"value":"md`\n
\n
\n**Sarbeco data**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":651,"value":"sarbeco_bps = d3.csvParse( await FileAttachment(\"Sarbecovirus.csvBreakpointPositions.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":653,"value":"sarbeco_gcsim = d3.csvParse( await FileAttachment(\"AAA_SarbecovirusAligned_nodup_simgc.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":656,"value":"sarbeco_ga = d3.csvParse(await FileAttachment(\"Sarbecovirus.csvORFCoords.csv\").text(), ({gene, start, stop}) => [gene, [start, stop]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":659,"value":"sarbeco_trsbs = d3.csvParse(await FileAttachment(\"Sarbeco_trsbs.csv\").text());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":543,"value":"md`\n
\n
\n**extra**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"d3 = require('d3@6')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"width = 1000","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"height = 500","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"margin = ({top: 200, right: 50, bottom: 100, left: 70})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":374,"value":"colourScheme = ['#44AA99', '#88CCEE', '#DDCC77', '#AA4499']\n//['#99B898', '#FECEAB', '#FF847C', '#E84A5F']","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":551,"value":"import {slider, select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W34","stdlib":"1","titling":"auto"}} 32:"$31:body"