29:null 2a:["$","title",null,{"children":"The Poster Example (PReC - PROPERTY VIZ 1.0b) | ACME Computational Molecular Evolution Group | Observable"}] 2f:T8d9,myChart = { const svg = d3.select(DOM.svg(width, height+(margin*2))); const containerWidth = width-(margin*2); const containerHeight = height-(margin*2); const container = svg.append('g') .attr("width", containerWidth) .attr("height", containerHeight) .attr('transform', `translate(${(width/2)+margin}, ${(height/2)+margin})`) var axisGrid = container.append("g") .attr("class", "axisWrapper"); axisGrid.selectAll(".levels") .data(d3.range(1,(axisCircles+1)).reverse()) .enter() .append("circle") .attr("class", "gridCircle") .attr("r", (d, i) => radius/axisCircles*d) .style("fill", "#CDCDCD") .style("stroke", "#CDCDCD") .style("fill-opacity", 0.7); const axis = axisGrid.selectAll(".axis") .data(axesDomain) .enter() .append("g") .attr("class", "axis"); axis.append("line") .attr("x1", 0) .attr("y1", 0) .attr("x2", (d, i) => rScale(maxValue) * Math.cos(angleSlice*i - Math.PI/2)) .attr("y2", (d, i) => rScale(maxValue) * Math.sin(angleSlice*i - Math.PI/2)) .attr("class", "line") .style("stroke", "gray") .style("stroke-width", "5px") // .style("stroke-opacity", 0.5); axis.append("circle") .attr("r", dotRadius*3) .attr("cx", (d, i) => rScale(maxValue) * Math.cos(angleSlice*i - Math.PI/2)) .attr("cy", (d, i) => rScale(maxValue) * Math.sin(angleSlice*i - Math.PI/2)) .style("stroke", "gray") .style("stroke-width", "3px") // .style("stroke-opacity", 0.5) .style("fill", "#CDCDCD") // .style("fill-opacity", 0.7); const plots = container.append('g') .selectAll('g') .data(data) .join('g') plots.append('path') .attr("d", d => radarLine(d.map(v => v.value))) .attr("fill", (d, i) => color(i)) .attr("fill-opacity", 0.5) .attr("stroke", (d, i) => color(i)) .attr("stroke-width", 2); plots.selectAll("circle") .data(d => d) .join("circle") .attr("r", dotRadius*2) .attr("cx", (d,i) => rScale(d.value) * Math.cos(angleSlice*i - Math.PI/2)) .attr("cy", (d,i) => rScale(d.value) * Math.sin(angleSlice*i - Math.PI/2)) .attr("fill",(d, i) => color(i)) .attr("stroke", (d, i) => color(i)) // .style("fill-opacity", 0.8); return svg.node(); }30:[] 2d:{"id":"cf2930a166dc4607","slug":"the-poster-example-prec-property-viz-1-0b","title":"The Poster Example (PReC - PROPERTY VIZ 1.0b)","thumbnail":"d3adfa8da2a653826a92fb7505fa5ac015fc9d3803a4b9db542ac0707bdc8fcf","access_level":"public","create_time":"$D2023-07-25T15:10:35.509Z","update_time":"$D2023-07-25T15:16:06.446Z","view_time":null,"first_public_time":"$D2023-07-25T15:18:48.545Z","has_unpublished_edits":null,"fork":true,"stars":0,"starred":false,"owner":{"type":"team","id":"7ada8a89538f700a","login":"hyphy","name":"ACME Computational Molecular Evolution 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Group"}},"type":"notebook","body":{"title":"The Poster Example (PReC - PROPERTY VIZ 1.0b)","cells":[{"id":802,"value":"md`# The Poster Example (PReC - PROPERTY VIZ 1.0b)\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":424,"value":"md`## ${propertySelect} Property Set Summary`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":782,"value":"viewof propertySelect = select({\n title: \"Physicochemical Property Set of Interest\",\n options: Object.keys(residue_properties),\n value: \"Atchley\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":529,"value":"viewof aaSelect = select({\n title: \"Amino Acid of Interest\",\n options: Object.keys(residue_properties[propertySelect][Object.keys(residue_properties[propertySelect])[0]]),\n value: \"A\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":756,"value":"md`---\n### Implementation`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":432,"value":"currentAA = aaSelect","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":270,"value":"function minmax(propertySet) { // min-max normalization to absolute values.\n let newPropertySet = {};\n let curPropertySet = Object.values(propertySet).map(Math.abs);\n let pMin = Math.min.apply(Math, curPropertySet);\n let pMax = Math.max.apply(Math, curPropertySet);\n Object.keys(propertySet).forEach (aa => {\n newPropertySet[aa] = (Math.abs(propertySet[aa])-pMin)/(pMax-pMin);\n })\n return newPropertySet;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":301,"value":"aaData = {\n let aaMINMAX = {};\n Object.keys(residue_properties[propertySelect]).forEach( prop => {\n let minmaxPropSet = minmax(residue_properties[propertySelect][prop])\n Object.keys(minmaxPropSet).forEach( aa => {\n if (!(aa in aaMINMAX)) {\n aaMINMAX[aa] = [];\n }\n aaMINMAX[aa].push({\"axis\":prop, \"value\":minmaxPropSet[aa]});\n })\n })\n return Object.values(aaMINMAX);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":347,"value":"data = [aaData[Object.keys(residue_properties[propertySelect][Object.keys(residue_properties[propertySelect])[0]]).indexOf(currentAA)]]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":930,"value":"translation_table0 = fetch(\"https://raw.githubusercontent.com/hannahkimincompbio/PRIME_reboot_git/main/references/universal-translation-table.json\")\n .then(function(response){\n return response.json();\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":419,"value":"ttable = translation_table0['translation-table']","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":496,"value":"ntable = {\n let myObj = {A: \"Ala\",\n C: \"Cys\",\n D: \"Asp\",\n E: \"Glu\",\n F: \"Phe\",\n G: \"Gly\",\n H: \"His\",\n I: \"Ile\",\n K: \"Lys\",\n L: \"Leu\",\n M: \"Met\",\n N: \"Asn\",\n P: \"Pro\",\n Q: \"Gln\",\n R: \"Arg\",\n S: \"Ser\",\n T: \"Thr\",\n V: \"Val\",\n W: \"Trp\",\n Y: \"Tyr\"}\n return myObj\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":619,"value":"currentCodon = {\n let codons = [];\n for (let k=0; k !currentCodon.includes(item)).filter(item => ttable[item]!=\"X\"));\n }\n return subCodon;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":667,"value":"singleSubVal = {\n let dist = [];\n for (let cInd=0;cInd eachSub[b] ? 1 : 0; });\n let closestThree = [singleSubCodon[cInd][indices.indexOf(0)], singleSubCodon[cInd][indices.indexOf(1)], singleSubCodon[cInd][indices.indexOf(2)]];\n // each.push(eachSub)\n each.push(closestThree.map(d=>`${ntable[ttable[d]]}|${ttable[d]}|${d}`)); \n }\n dist.push(each);\n }\n return dist;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":639,"value":"codonColors = [\"#0088ca\", \"#18b3ff\", \"#f1cf52\", \"#b2600e\", \"#861b0b\", \"#4a5f48\"] // https://www.color-hex.com/color-palettes/","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":180,"value":"md`---\n### Configuration`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":54,"value":"curveSelect = \"curveLinearClosed\";","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":108,"value":"axesDomain = data[0].map(d => d.axis)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":81,"value":"axesLength = data[0].length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":104,"value":"formatPercent = d3.format(',.0%')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":141,"value":"wrapWidth = 60","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":128,"value":"axisLabelFactor = 1.12","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":99,"value":"axisCircles = 2","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":223,"value":"dotRadius = 4","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":20,"value":"radius = (height-(margin*2)) / 2","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"margin = 30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"height = 900","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":206,"value":"md`### Plotting`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"radarLine = d3.lineRadial()\n .curve(d3[curveSelect])\n .radius(d => rScale(d))\n .angle((d, i) => i * angleSlice)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":121,"value":"angleSlice = Math.PI * 2 / axesLength","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"rScale = d3.scaleLinear()\n .domain([0, maxValue]) //\n .range([0, radius])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":"color = d3.scaleOrdinal()\n .range([\"#CC333F\",]) //,\"#00A0B0\",\"#EDC951\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":208,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":446,"value":" maxValue = 1 // for MINMAX // d3.max(_.flatten(data).map(d => d.value))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":403,"value":"residue_properties0 = fetch(\"https://raw.githubusercontent.com/hannahkimincompbio/PRIME_reboot_git/main/references/default_residue_properties.json\")\n .then(function(response){\n return response.json();\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":922,"value":"residue_properties = residue_properties0['residue_properties']","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":455,"value":"md`---\n### Sources of Physicochemical Property Set`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":458,"value":"md`_**Atchley Property Set**_: William R. Atchley, Jieping Zhao, Andrew D. Fernandes, and Tanja Drüke \"Solving the protein sequence metric problem\" PNAS 2005 102 (18) 6395-6400; published ahead of print April 25, 2005, http://dx.doi.org/doi:10.1073/pnas.0408677102`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":614,"value":"md`_**LCAP Property Set**_: Gavin C. Conant, Günter P. Wagner, Peter F. Stadler \"Modeling amino acid substitution patterns in orthologous and paralogous genes\" Molecular Phylogenetics and Evolution, Volume 42, Issue 2, February 2007, Pages 298–307 http://dx.doi.org/10.1016/j.ympev.2006.07.006`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":138,"value":"md`---\n### Dependencies`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":56,"value":"import {select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"import {curveTypes} from \"@palewire/d3-curves-inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":41,"value":"_ = require(\"underscore\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"d3 = require(\"d3@5\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":985,"value":"md`\n---\n## Table of PReC Collection\n\n1. [PReC Introduction](https://observablehq.com/@hyphy/prec?collection=@hyphy/prec)\n1. The Poster Example\n1. PREI\n1. PROPERTY - you are here!\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2e:"$2d:body"