2d:null 2e:["$","title",null,{"children":"Phamerator Map | Cresawn Labs | Observable"}] 33:T248b,chart = { const type = Form.checkbox; const container = d3.select( // html`

${tooltipTemplate}

` html`

${legend}

` ); const tooltipDiv = container.select(".tooltip"); const renderPhameratorMap = (svg, phage, i) => { let g = svg.append("g"); g.attr("transform", "translate(0," + -i * verticalSpacing + ")"); g.append("rect") .attr("x", margin.left) .attr("y", yScale("forwardOdd")) .attr("width", xScale(phage.genomelength) - margin.left) .attr("height", geneHeight * 4) .attr("stroke", "lightgray") .attr("fill", "white") .attr("stroke-width", 1) .attr("rx", 5) // .attr("stroke-dasharray", 3) // .attr("stroke-dashoffset", "0px") .attr("fill-opacity", 0.5) .attr("stroke-opacity", 1); g.selectAll(".generect") .data(phage.genes) .join("rect") .classed("generect", true) .attr("x", (d) => xScale(d3.min([d.start, d.stop]))) .attr("y", (d) => { // is the gene "Name" even or odd? let geneNumber = +d.name; if (geneNumber % 2 == 0) { // geneNumber is even if (d.direction == "forward") { return yScale("forwardEven"); } else { return yScale("reverseEven"); } } else { // geneNumber is odd // what's the gene "Orientation"? if (d.direction == "forward") { return yScale("forwardOdd"); } else { return yScale("reverseOdd"); } } }) .attr("width", (d) => Math.abs(xScale(d.stop) - xScale(d.start))) .attr("height", geneHeight) // .attr("fill", (d) => (d.direction === "forward" ? "blue" : "orange")) .attr("fill", (d) => d.phamColor) .attr("stroke", "#333") .attr("stroke-width", 0.5) .attr("opacity", 0.7); // .call(tooltip, tooltipDiv); g.selectAll(".genename") .data(phage.genes) .join("text") .classed("genename", true) .attr("x", (d) => xScale(d3.min([d.start, d.stop]))) .attr("x", (d) => xScale((d.start + d.stop) / 2)) .attr("y", (d) => { let geneNumber = +d.name; let yOffset = 0; if (geneNumber % 2 == 0) { yOffset = d.direction == "forward" ? yScale("forwardEven") : yScale("reverseEven"); } else { yOffset = d.direction == "forward" ? yScale("forwardOdd") : yScale("reverseOdd"); } return yOffset + geneHeight / 2; }) .style("font-size", "8px") .style("font-family", "Arial") .attr("text-anchor", "middle") .attr("alignment-baseline", "middle") .text((d) => { if (Form.checkbox.includes("reformat silly gene names")) { return typeof +d.name === "number" && !Number.isNaN(+d.name) ? +d.name : d.name; } return d.name; }); if (Form.checkbox.includes("phamilies")) { g.selectAll(".phamilies") .data(phage.genes) .join("text") .classed("phamilies", true) .attr("x", (d) => xScale(d3.min([d.start, d.stop]))) .attr("y", (d) => { // is the gene "Name" even or odd? let geneNumber = +d.name; if (geneNumber % 2 == 0) { // geneNumber is even if (d.direction == "forward") { return yScale("forwardEven"); } else { return yScale("reverseEven"); } } else { // geneNumber is odd // what's the gene "Orientation"? if (d.direction == "forward") { return yScale("forwardOdd"); } else { return yScale("reverseOdd"); } } }) .attr("x", (d) => xScale((d.start + d.stop) / 2)) .attr("y", (d) => { let geneNumber = +d.name; let yOffset = 0; if (geneNumber % 2 == 0) { yOffset = d.direction == "forward" ? yScale("forwardEven") : yScale("reverseEven"); } else { yOffset = d.direction == "forward" ? yScale("forwardOdd") : yScale("reverseOdd"); } return yOffset - 5; }) .style("font-family", "Arial") .style("font-size", "6px") .attr("text-anchor", "middle") .attr("alignment-baseline", "middle") .text((d) => { console.log(d); return `${d.phamName} (${d.phamSize})`; }); } if (Form.checkbox.includes("gene functions")) { g.selectAll(".functions") .data(phage.genes) .join("text") .classed("functions", true) .attr("x", (d) => xScale(d3.min([d.start, d.stop]))) .attr("y", (d) => { // is the gene "Name" even or odd? let geneNumber = +d.name; if (geneNumber % 2 == 0) { // geneNumber is even if (d.direction == "forward") { return yScale("forwardEven"); } else { return yScale("reverseEven"); } } else { // geneNumber is odd // what's the gene "Orientation"? if (d.direction == "forward") { return yScale("forwardOdd"); } else { return yScale("reverseOdd"); } } }) .attr("x", (d) => xScale((d.start + d.stop) / 2)) .attr("y", (d) => { let geneNumber = +d.name; let yOffset = 0; if (geneNumber % 2 == 0) { yOffset = d.direction == "forward" ? yScale("forwardEven") : yScale("reverseEven"); } else { yOffset = d.direction == "forward" ? yScale("forwardOdd") : yScale("reverseOdd"); } return yOffset - 16; }) .style("font-size", "6px") .style("font-family", "Arial") .attr("text-anchor", "middle") .attr("alignment-baseline", "middle") .text((d) => d.genefunction); } g.append("text") .attr("x", xScale(genomeLength - genomeLength)) .attr("y", yScale("forwardOdd") - 10) .style("font-size", "11px") .style("font-weight", "bold") .style("font-family", "Arial") //.attr("alignment-baseline", "left") //.attr("text-anchor", "left") .text(phage.phagename); //code below is for adding the phage name if (Form.checkbox.includes("show cluster")) { g.append("text") .attr("x", xScale(genomeLength - genomeLength)) .attr("y", yScale("forwardOdd") - 10) .style("font-size", "11px") .style("font-weight", "bold") // Arial is a font. Ariel is a mermaid. :) .style("font-family", "Arial") //.attr("alignment-baseline", "left") //.attr("text-anchor", "left") .text(phage.phagename + ` (${phage.clusterSubcluster})`); } let blastDataByQuery = parsedData.filter( (d) => d.query === phage.phagename ); let hsps = blastDataByQuery[0]?.hsps || []; hsps = hsps.filter((d) => d.evalue <= 1e-4); g.selectAll("polygon") .data(hsps) .join("polygon") .attr("points", (d) => { const query_y = yScale("reverseEven") + geneHeight; const subject_y = query_y + verticalSpacing - geneHeight * 4; console.log(`drawing polygons for phage ${phage.phagename}`); return `${xScale(d.query_from)},${query_y} ${xScale( d.query_to )},${query_y} ${xScale(d.subject_to)},${subject_y} ${xScale( d.subject_from )},${subject_y}`; }) // .attr("points", "200,10 250,190 160,210") // .style("fill", d => saturate(d3.interpolateRainbow(colorScale(d.evalue)))) .style("fill", (d) => d3.interpolateWarm(colorScale(d.evalue))) .style("fill-opacity", 0.3); // .style("stroke", "gray") // .style("strokeWidth", "1.5px"); // return container.node(); }; // get the length of the longest genome const genomeLength = d3.max(genomes.map((d) => d.genomeLength)); const body = container .append("div") .style("overflow", "auto") .style("-webkit-overflow-scrolling", "touch"); const svg = body .append("svg") .attr("id", "chart") .attr("viewBox", [0, 0, width, height]); // .attr('overflow', 'visible') svg.attr("width", width).attr("height", height); const g = svg.append("g"); // .style("display", "block") // .attr("transform", `scale(${zoom})`); svg.call( d3 .zoom() .extent([ [0, 0], [width, height] ]) .scaleExtent([1, 8]) .on("zoom", zoomed) ); function zoomed({ transform }) { g.attr("transform", transform); } // for each genome, call renderPhameratorMap, which accepts 3 args: the svg, the genome object, and the index (used for transform) for (let i = 1; i <= genomes.length; i++) { renderPhameratorMap(g, genomes[genomes.length - i], i - 1); } g.append("g").call(xAxis); return container.node(); }34:Te23,tooltipStuff = { const tooltipId = DOM.uid(); const tooltipTemplate = html``; const tooltip = (selectionGroup, tooltipDiv) => { // padding between the tooltip and mouse cursor const MOUSE_POS_OFFSET = 8; selectionGroup.each(function () { d3.select(this) .on("mouseover.tooltip", handleMouseover) .on("mousemove.tooltip", handleMousemove) .on("mouseleave.tooltip", handleMouseleave); }); function handleMouseover() { // show/reveal the tooltip, set its contents, // style the element being hovered on showTooltip(); setContents(d3.select(this).datum()); // setStyle(d3.select(this)); } function handleMousemove(event) { // update the tooltip's position const [mouseX, mouseY] = d3.pointer(event, this); // add the left & top margin values to account for the SVG g element transform // console.log(mouseY); setPosition(mouseX, mouseY); } function handleMouseleave() { // do things like hide the tooltip // reset the style of the element being hovered on hideTooltip(); resetStyle(d3.select(this)); } function showTooltip() { tooltipDiv.style("display", "block"); } function hideTooltip() { tooltipDiv.style("display", "none"); } function setPosition(mouseX, mouseY) { tooltipDiv .style( "top", mouseY < (margin.top + (height - margin.bottom)) / 2 ? `${mouseY + MOUSE_POS_OFFSET}px` : "initial" ) .style( "right", mouseX > (margin.left + (width - margin.right)) / 2 ? `${width - mouseX + MOUSE_POS_OFFSET}px` : "initial" ) .style( "bottom", mouseY > (margin.top + (height - margin.bottom)) / 2 ? `${height - mouseY + 2 * MOUSE_POS_OFFSET}px` : "initial" ) .style( "left", mouseX < (margin.left + (width - margin.right)) / 2 ? `${mouseX + MOUSE_POS_OFFSET}px` : "initial" ); } function setStyle(selection) { selection.attr("fill", "#A56EA7"); // selection.attr("stroke", "black"); selection.style("stroke-width", 3); } function resetStyle(selection) { //selection.attr("fill", "#333"); // reset the fill color to the default value after the mouse leaves a circle // selection.attr("fill", (d) => fillScale(d["Length ratio"])); //reset the outline to the default value after the mouse leaves a circle selection.style("stroke-width", 1); } function setContents(datum) { // customize this function to set the tooltip's contents however you see fit tooltipDiv .selectAll("p") .data(Object.entries(datum)) .join("p") .html(([key, value]) => { // console.log("key:", key, "value:", value); if (key == "name") return value; }); } }; }35:[] 31:{"id":"d09630dfdd28947b","slug":"phamerator-map","title":"Phamerator Map","thumbnail":"939fe867cf8fcd1c3d8b4c7e4b5c9f45de4cc6d75ad541250d3219844b39871b","access_level":"unlisted","create_time":"$D2024-01-07T22:41:27.368Z","update_time":"$D2026-04-22T13:20:43.963Z","view_time":null,"first_public_time":null,"has_unpublished_edits":null,"fork":true,"stars":1,"starred":false,"owner":{"type":"team","id":"006a48c0ba2fb93a","login":"cresawn-labs","name":"Cresawn Labs","avatar_url":"https://avatars-next.observableusercontent.com/c72c7e544a40cf2c2a6283afb916fc12c08a80e14df5153e0ad6dcad90f5b3c9","tier":"pro_2024"},"version":1718,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"9f316fa2aba52cf9","login":"scresawn","name":"Steven Cresawn","avatar_url":"https://avatars-next.observableusercontent.com/e2727956835daa3b5e9995b66c1111489c2e403c176b4fb761ec6ad64b97786b","tier":null}],"members":[{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null,"role":"editor"},{"type":"individual","id":"24c6369a6fc83150","login":"mbendele","name":"Maddie Bendele","avatar_url":"https://avatars-next.observableusercontent.com/df056cb5c50bb95442f5984e912a3fdad13fb13fc423a0b8e54da82de553579a","tier":null,"role":"editor"},{"type":"individual","id":"9f316fa2aba52cf9","login":"scresawn","name":"Steven Cresawn","avatar_url":"https://avatars-next.observableusercontent.com/e2727956835daa3b5e9995b66c1111489c2e403c176b4fb761ec6ad64b97786b","tier":null,"role":"editor"},{"type":"team","id":"006a48c0ba2fb93a","login":"cresawn-labs","name":"Cresawn Labs","avatar_url":"https://avatars-next.observableusercontent.com/c72c7e544a40cf2c2a6283afb916fc12c08a80e14df5153e0ad6dcad90f5b3c9","tier":"pro_2024","role":"viewer"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":14,"collection":null,"type":"notebook","body":{"title":"Phamerator Map","cells":[{"id":0,"value":"# Phamerator Map","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1717,"value":"terms","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":297,"value":"viewof dataset = Inputs.select(user.datasets.sort(), {\n label: \"Data set\",\n value: \"Actino_Draft\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":832,"value":"viewof selectedCluster = \nInputs.select(\n clusters.map((c) => c.name),\n {\n label: \"Select a cluster\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":745,"value":"viewof program = Inputs.select(['blastn', 'tblastx'], {label: \"Select a program\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":606,"value":" viewof width = Inputs.range([500, 5000], {label: \"Width\", step: 100, value: 1000})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":717,"value":"viewof verticalSpacing = Inputs.range([70, 300], {\n label: \"Vertical spacing\",\n step: 10,\n value: 100\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1320,"value":"viewof Form3 = { \n const inputs = (\n Inputs.form({\n radios: Inputs.radio([\"Select phages by cluster\", \"Select phages from any cluster\"], {value: \"Select phages by cluster\"})\n\n }));\n return inputs\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":726,"value":"menus = html`\n \n \n \n \n \n \n \n \n

Select phages	Drag to reorder the phages
${viewof Form}\n	${viewof reorderPhages}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":536,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1452,"value":"## Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1132,"value":"phamilies = getPhameratorData(dataset, '/phamilies', user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":735,"value":"phages = {let result = [];\n await getPhameratorData(dataset, \"/genomes\", user.email, user.password).then(arr => {\n for (let phage of arr) {\n phage.cluster === \"\" ? phage.cluster = \"Singletons\" : null\n phage.phagename = phage.phagename.replace(\"_Draft\", \"\")\n result.push(phage)\n }\n })\n return result.sort((a,b) => a.phagename < b.phagename ? -1 : 1)}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1315,"value":"phagesByCluster ={\n let result = [];\n await getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedCluster}`,\n user.email,\n user.password\n ).then(arr => {\n for (let phage of arr) {\n phage.cluster === \"\" ? phage.cluster = \"Singletons\" : null\n // phage.phagename = phage.phagename.replace(\"_Draft\", \"\")\n result.push(phage)\n }\n })\n return result}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":737,"value":"genomes = {\n let genomes = [];\n for await (let phage of reorderPhages) {\n let genome = await getPhameratorData(dataset, `/genome/${phage}`, user.email, user.password)\n for await (let gene of genome.genes) {\n gene.phamSize = phamilies.filter(d => d.PhamID === +gene.phamName)[0].size;\n }\n \n genomes.push(genome)\n } \n \n return Promise.all(genomes);\n}\n\n ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":739,"value":"genomePairs = {\n let genomePairs = []\n for (let i = 0 ; i < genomes.length - 1; i++) {\n genomePairs.push({query : genomes[i], subject: genomes[i+1]})\n }\n return genomePairs;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":741,"value":"blastData = {\n // create a place to store the final result\n let data = [];\n\n // for each pair, asynchronously call the blast* function and then wait for the yielded value to be an object (value) with\n // value.loading being false (aka it's done) and value.error being false (aka no errors)\n // then push the value object into an array along with the query and subject phage names\n await Promise.all(genomePairs.map(async (pair) => {\n for await (const value of blast(program, pair.query.sequence, pair.subject.sequence)) {\n if (!value.loading && !value.error) data.push({query: pair.query.phagename, subject: pair.subject.phagename, ...value});\n }\n }))\n return data;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1060,"value":"hsps = parsedData.map(d => d.hsps).flat()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1645,"value":"hspsTable = hsps","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"hspsTable","database":"$undefined"},{"id":743,"value":"parsedData = blastData.map(d => parseBlastResults(d)).flat()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":834,"value":"clusters = getPhameratorData(dataset, \"/clusters\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1679,"value":"genesByCluster = {\n \n let genesByCluster = await getPhameratorData(dataset, `/genesbycluster/${selectedCluster}`, user.email, user.password)\n return genesByCluster;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"## Appendix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1692,"value":"d3.interpolateWarm(colorScale(0.00001))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1037,"value":"colorScale = d3.scaleSequential().domain([0, 1e-4]).range([0,1])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1030,"value":"function saturate(color, k = 1) {\n const {l, c, h} = d3.lch(color);\n return d3.lch(l, c + 18 * k, h);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":530,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":78,"value":"height = 25 + (reorderPhages.length * verticalSpacing)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":60,"value":"xScale = d3\n .scaleLinear()\n .domain([0, genomeLength])\n .range([margin.left, width - margin.right])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"xAxis = (g) =>\n g\n .attr(\"transform\", `translate(0,${height - margin.bottom})`)\n .call(d3.axisBottom(xScale))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":73,"value":"yAxis = (g) =>\n g.attr(\"transform\", `translate(${margin.left},0)`).call(d3.axisLeft(yScale))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"yScale = d3\n .scaleOrdinal()\n .domain([\"forwardOdd\", \"forwardEven\", \"reverseOdd\", \"reverseEven\"])\n .range([\n height - margin.bottom - geneHeight * 4,\n height - margin.bottom - geneHeight * 3,\n height - margin.bottom - geneHeight * 2,\n height - margin.bottom - geneHeight\n ])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":24,"value":"geneHeight = 12.5","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"genomeLength = {\n let lengths = [];\n for (let phage of reorderPhages) {\n let genome = await getPhameratorData(\n dataset,\n `/genome/${phage}`,\n user.email,\n user.password\n )\n lengths.push(genome.genomelength);\n }\nreturn d3.max(lengths)\n }","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":76,"value":"margin = ({ top: 20, right: 30, bottom: 30, left: 40 })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":230,"value":"styles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1703,"value":"reorderPhages","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":722,"value":"viewof reorderPhages = {\n let data = [];\n let orderPhage = [];\n let phageData = d3.group(Form.selectedPhages, (d) => d.phagename);\n for (let phage of phageData) {\n data.push({ phageID: phage[0], clusterInfo: phage[1] });\n }\n data.sort((a, b) => {\n if (a.clusterInfo.clusterSubcluster < b.clusterInfo.clusterSubcluster)\n return -1;\n else if (a.clusterInfo.clusterSubcluster > b.clusterInfo.clusterSubcluster)\n return 1;\n else if (a.phageID < b.phageID) return -1;\n else return 1;\n });\n orderPhage = selectOrder(data.map((d) => `${d.phageID} `));\n\n if (orderPhage.length === 0) {\n return displayCaution(\n \"Please select a phage from the menu to the left.\"\n );\n } else {\n return orderPhage;\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":827,"value":"viewof Form = { \n if (Form3.radios.includes(\"Select phages by cluster\")){\n const inputs = (\n Inputs.form({\n selectedPhages: Inputs.select(phagesByCluster, {format: x => `${x.phagename} (${x.cluster})`, multiple: true}),\n checkbox: Inputs.checkbox([\"phamilies\",\"gene functions\",\"show cluster\", \"reformat silly gene names\"])\n\n }));\n return inputs\n}\n else if (Form3.radios.includes(\"Select phages from any cluster\")){\n const inputs = (\n Inputs.form({\n selectedPhages: Inputs.select(phages, {format: x => `${x.phagename} (${x.cluster})`, multiple: true}),\n checkbox: Inputs.checkbox([\"phamilies\", \"gene names\", \"gene functions\",\"show cluster\", \"reformat silly gene names\"])\n\n }));\n return inputs\n\n}}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1201,"value":"legendScale = d3.scaleSequential(d3.interpolateWarm).domain([0,1e-4])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1213,"value":"legendTitle = \"BLAST Expect (E) value\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1220,"value":"legendBarHeight = 15","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1607,"value":"## Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":305,"value":"import {\n terms,\n getPhameratorData,\n user,\n formWithSubmit,\n styles\n} with { formData } from \"@cresawn-labs/phamerator-api-utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":731,"value":"import {selectOrder} from \"@cresawn-labs/reorder-a-list\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":733,"value":"import {blast, parseBlastResults } from \"d9fb4709bc7dbda2\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":728,"value":"import { displayCaution } from \"@mkfreeman/utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1191,"value":"import { legend } with { legendTitle as title, legendScale as colorScale, legendBarHeight as barHeight } from \"f663b3ea6130a8f3\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W35","stdlib":"1","titling":"auto"}} 32:"$31:body"