44:["$","title",null,{"children":"seasonal CoV Spike | CVR Bioinformatics | Observable"}] 4c:T9b6,{ //var svg = d3.select(DOM.svg(width,height)) const svg = d3.create('svg') .attr('height', height) .attr('width', width) .style('font-family', 'georgia') .style('font-size', '40px'); svg.append("g") .call(d3.axisBottom(x)) .attr("transform",`translate(0,${height-margin.bottom})`); svg.append("g") .call(d3.axisLeft(y)) .attr("transform",`translate(${margin.left},0)`); const yscale = 30; const txtyscale = 500; const txtxscale = 100; //rbd shading if(regions.length > 0){ var rbdx1 = 534; var rbdx2 = 883; svg.append("rect") .attr('stroke-width', 0) .attr("fill", 'lightgrey') .attr('opacity', 0.2) .attr("x", margin.left + recxtran(rbdx1)) .attr("y", 3*margin.top) .attr("width", recxtran(rbdx2) - recxtran(rbdx1)) .attr("height", height - 3*margin.bottom); svg.append('text') .attr('x', recxtran(rbdx1 + (rbdx2 - rbdx1)/2)) .attr('y', 2* margin.top) .text("RBD") .attr('fill', 'black') .attr("font-family", "Georgia") .attr("font-size", "28px") } //similarity line plots var i; for (i = 0; i < vir.length; i++) { svg.append("path") .datum(thecalc(vir[i]).slice(triml,trimr)) .attr("fill", "none") .attr("stroke", colorRange[i+1]) .attr("opacity", 1) .attr("stroke-width", 4) .attr("d", line) .style("stroke-dasharray", (dashit)); } //gap plots and virus labels var g; const gscale = 0.025; for (g = 0; g < gapvir.length; g++) { svg.append("path") .datum(cgaps(gapvir[g], (gscale * gapvir.length) - gscale*(g+1)/2).slice(triml,trimr)) .attr("fill", "none") .attr("stroke", colorRange[g]) .attr("opacity", 1) .attr("stroke-width", 8) .attr("d", gline); svg.append('text') .attr('x',margin.left + txtxscale) .attr('y', height - margin.bottom - txtyscale + g*yscale) .text(virkey[gapvir[g].split('|')[0]]) .attr('fill', 'black') .attr("font-family", "Georgia") .attr("font-size", "20px") svg.append('circle') .attr('r', 10) .attr('cx', margin.left + txtxscale-15) .attr('cy', height - margin.bottom - txtyscale-9 + g*yscale) .attr('stroke', 'transparent') .attr('fill', colorRange[g]); } return svg.node(); }4d:T508,function thecalc(thev){ function winslide(position, windowSize) { let sites; if (position <= windowSize/2) { sites = dataj[thev].slice(0, (windowSize)) } else if (position + windowSize/2 >= dataj[thev].length) { sites = dataj[thev].slice(dataj[thev].length-(windowSize), dataj[thev].length) } else { sites = dataj[thev].slice(position - (windowSize/2), position + (windowSize/2)) } //if (position + windowSize <= dataj[vir].length) { //s = dataj[vir].slice(position, position + windowSize)} //else { //let missinglen = (position + windowSize) - dataj[vir].length //s = dataj[vir].slice(0, missinglen)} //skip na values from calculation var s = sites.filter(site => (site.cases != 'nan')); let winavgraw = s.map(({ cases }) => cases) //let winsum = winavgraw.map((i) => Number(i)).reduce((a, b) => a + b) let winsum = winavgraw.reduce((partial_sum, a) => partial_sum + Number(a),0) return (winsum / winavgraw.length) //return (winsum / windowSize) } let resultsArr = [] for (let i = 0 ; i < dataj[thev].length ; i = i + stepSize) { resultsArr[i] = {position:i+1, similarity:winslide(i, winsize)} } return resultsArr }4e:[{"id":"02eb5a29410d1c896ea0d00de707517b144628ffb1be3eba8f16360aef2c293ff7c8f93f524067ac5604e608b64e49cc455d8af873c0844151f5f3b4de40ec66","href":"https://static.observableusercontent.com/files/02eb5a29410d1c896ea0d00de707517b144628ffb1be3eba8f16360aef2c293ff7c8f93f524067ac5604e608b64e49cc455d8af873c0844151f5f3b4de40ec66","name":"humanCoV_tree1.png","type":"image/png","lastModified":1636124070023.427,"size":76112},{"id":"1051e8ff25af0e3d09f7db3ef03b35dea3dd44f1d102573c318c22f5e6afda1bd56edc593492cf587f5abdafd05967e5988dedfb4e7e11e848a493b2776f70c8","href":"https://static.observableusercontent.com/files/1051e8ff25af0e3d09f7db3ef03b35dea3dd44f1d102573c318c22f5e6afda1bd56edc593492cf587f5abdafd05967e5988dedfb4e7e11e848a493b2776f70c8","name":"al_seas_CoV_S_aa_tonly_SC2_sim@4.json","type":"application/json","lastModified":1635873686434.983,"size":418877}] 48:{"id":"8598c7028c9e3590","slug":"seasonal-cov-spike","title":"seasonal CoV Spike","thumbnail":"d6240bbc8790980236d29cc1d7957382038e720ced39e6ea75c45212b5f855bb","access_level":"public","create_time":"$D2021-10-28T10:09:20.290Z","update_time":"$D2023-01-18T16:16:12.362Z","view_time":null,"first_public_time":"$D2021-11-03T16:05:02.484Z","has_unpublished_edits":null,"fork":true,"stars":1,"starred":false,"owner":{"type":"team","id":"1157d8a0e7ace7c6","login":"cvr-bioinfo","name":"CVR Bioinformatics","avatar_url":"https://avatars-next.observableusercontent.com/022d43de01273d3d19941f51b9b2c412d919f4a74262d41e14c5379b08c7d5f2","tier":"education_2026","bio":"","followed_by_you":false,"follows_you":false},"version":1008,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"d0adadfb03845a21","login":"spyros-lytras","name":"","avatar_url":"https://avatars-next.observableusercontent.com/c95ad1f3c75de4549c43230fafb46f1f84546986881e9401d9114c2ee2354520","tier":null,"bio":"","followed_by_you":false,"follows_you":false}],"members":[{"type":"team","id":"1157d8a0e7ace7c6","login":"cvr-bioinfo","name":"CVR Bioinformatics","avatar_url":"https://avatars-next.observableusercontent.com/022d43de01273d3d19941f51b9b2c412d919f4a74262d41e14c5379b08c7d5f2","tier":"education_2026","role":"editor"},{"type":"individual","id":"d0adadfb03845a21","login":"spyros-lytras","name":"","avatar_url":"https://avatars-next.observableusercontent.com/c95ad1f3c75de4549c43230fafb46f1f84546986881e9401d9114c2ee2354520","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":3,"collection":null,"type":"notebook","body":{"titling":"auto","title":"seasonal CoV Spike","cells":[{"id":0,"value":"md`# seasonal CoV Spike`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"viewof winsize = number({\n title: \"Window Size\",\n min: 0, \n max: 10000, \n value: 400\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":906,"value":"viewof regions = checkbox({\n options: ['rbd'],\n value:['rbd']\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":385,"value":"md` ### Zoom into graph\n\nRBD is at 534 to 883`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":388,"value":"viewof triml = number({\n title: \"Left coordinate\",\n min: 0, \n max: avg1.length, \n value: 0});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":411,"value":"viewof trimr = number({\n title: \"Right coordinate\",\n min: 0, \n max: avg1.length, \n value: avg1.length});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":446,"value":"md`### Pairwise similarity to SARS-CoV-2`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":140,"value":"$4c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":932,"value":"md`\nSimilarity plot. Dashed lines on the top show amino acid pairwise similarity between SARS-CoV-2 and 3 human seasonal coronaviruses for the Spike protein, plotted using a ${winsize} amino acid window size and a step of 1. Positions with gaps were excluded from the windows. Horizontal lines on the bottom indicate residue presence for each of the 4 aligned coronaviruses across the alignment length (colour presence = amino acid presence; colour absense = gap).\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":364,"value":"viewof dashit= slider({\n min: 0, \n max: 20, \n step: 1, \n value: 10, \n title: \"Dash line\", \n description: \"Makes the plot lines more/less dashed\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":955,"value":"md`\n
\n
`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":925,"value":"md`\n${await FileAttachment(\"humanCoV_tree1.png\").image()}\nHuman coronaviruses Spike phylogeny. Maximum likelihood phylogenetic reconstruction based on the Spike gene codon alignment, constructed using [iqtree](https://doi.org/10.1093/molbev/msu300) with 10000 [ultra-fast bootstrap](https://doi.org/10.1093/molbev/msx281) replicates and a TVM+F+I+G4 substitution model, selected using [ModelFinder](https://doi.org/10.1038/nmeth.4285). Green boxes indicate viruses capable of human ACE2 binding. The genus of the virus (alpha- and beta-coronavirus) and the lineage of betacoronaviruses is annotated on the right of the phylogeny.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":260,"value":"md`
\n
\n
\n
\n
\n
\n### Code & Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":577,"value":"virkey = ({\"MN908947.3_cds_QHD43416.1_gaps\":\"SARS-CoV-2\", \"NC_006577.2_cds_YP_173238.1_gaps\": 'HKU1', \"NC_002645.1_cds_NP_073551.1_gaps\": '229E', \"NC_005831.2_cds_YP_003767.1_gaps\":'NL63'})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":682,"value":"thecalc(vir[0]).slice(triml,trimr)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":687,"value":"cgaps(gapvir[1], 0.1*1).slice(triml,trimr)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":128,"value":"viewof vir = checkbox({\n options: Object.keys(dataj),\n value: Object.keys(dataj)\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":659,"value":"viewof gapvir = checkbox({\n options: Object.keys(datagaps),\n value: Object.keys(datagaps)\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":852,"value":"recxtran(534)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":829,"value":"recxtran = function(x){\n return ( (x - triml) * (width - margin.left - margin.right) / ( trimr - triml) ) \n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"dataj = Object.fromEntries(Object.entries(alldata).filter(([key]) => !key.includes('_gaps')));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":574,"value":"alldata = FileAttachment(\"al_seas_CoV_S_aa_tonly_SC2_sim@4.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":601,"value":"datagaps = Object.fromEntries(Object.entries(alldata).filter(([key]) => key.includes('_gaps')));\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":439,"value":"avg1 = thecalc(vir[0])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":725,"value":"gline = d3.line()\n .defined(d => !isNaN(d.gap))\n .x(d => x(d.position))\n .y(d => y(d.gap))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":233,"value":"line = d3.line()\n .defined(d => !isNaN(d.similarity))\n .x(d => x(d.position))\n .y(d => y(d.similarity))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":226,"value":"y = d3.scaleLinear()\n .domain((d3.extent(d3.extent(avg1, d => d.similarity).concat(0))))\n\t .range([height-margin.bottom,margin.top]); ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":222,"value":"x = d3.scaleLinear()\n .domain(d3.extent(avg1.slice(triml,trimr), d=>d.position))\n\t .range([margin.left, width-margin.right]);\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":192,"value":"height = 600 ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":194,"value":"width = 1000 ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":141,"value":"margin = ({top: 20, right: 50, bottom: 50, left: 50})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":649,"value":"cgaps(gapvir[0], 0.1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":646,"value":"function cgaps(thev, ypos){\n let resultsArr = []\n for (let i = 0 ; i < datagaps[thev].length ; i = i + 1) {\n if (datagaps[thev][i].cases == 1){\n resultsArr[i] = {position:i+1, gap:ypos}\n }\n else{\n resultsArr[i] = {position:i+1, gap:'nan'}\n } \n }\n return resultsArr\n} ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":495,"value":"dataj['NC_006577.2_cds_YP_173238.1'].filter(site => (site.cases != 'nan'))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":127,"value":"$4d","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":522,"value":"thecalc('NC_006577.2_cds_YP_173238.1')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":106,"value":"stepSize = 1","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":290,"value":"colorRange = ['#FCA8D0', '#AC9DEE', '#7EC6FD', '#BCDD96', '#FFE89C', '#FFBEB4', 'grey']","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"d3 = require(\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"import {checkbox} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":264,"value":"import {number} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"import {slider} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":422,"value":"md`### Redundant`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":315,"value":"thecalc(vir[0])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":369,"value":"import {coordinates} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":10,"value":"import {select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"import {radio} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W4e","stdlib":"1"}} 24:E{"digest":"NEXT_REDIRECT;replace;/@cvr-bioinfo/seasonal-cov-spike;307;"}