2a:null 2b:["$","title",null,{"children":"Hilbert Genome | Alex Reynolds | Observable"}] 30:T46e,chromosomeSizes = [ { "name": 1, "size": 248956422 }, { "name": 2, "size": 242193529 }, { "name": 3, "size": 198295559 }, { "name": 4, "size": 190214555 }, { "name": 5, "size": 181538259 }, { "name": 6, "size": 170805979 }, { "name": 7, "size": 159345973 }, { "name": 8, "size": 145138636 }, { "name": 9, "size": 138394717 }, { "name": 10, "size": 133797422 }, { "name": 11, "size": 135086622 }, { "name": 12, "size": 133275309 }, { "name": 13, "size": 114364328 }, { "name": 14, "size": 107043718 }, { "name": 15, "size": 101991189 }, { "name": 16, "size": 90338345 }, { "name": 17, "size": 83257441 }, { "name": 18, "size": 80373285 }, { "name": 19, "size": 58617616 }, { "name": 20, "size": 64444167 }, { "name": 21, "size": 46709983 }, { "name": 22, "size": 50818468 }, { "name": "X", "size": 156040895 }, { "name": "Y", "size": 57227415 } ]31:T15b4,plotMarks = async () => { let marks = []; switch (dataMark.name) { case "Epilogos": { marks.push( Plot.cell(csamples, { x: "x", y: "y", fill: "fill", inset: 0 }) ); break; } case "DHS Domains": { marks.push( Plot.cell(csamples, { x: "x", y: "y", fill: "fill", inset: 0 }) ); break; } case "Lines": { marks.push( Plot.line(csamples, { x: "x", y: "y", stroke: "name", strokeOpacity: dataMarkLineHighlight[0] === "All" ? 1 : 0.25, strokeWidth: 3 }) ); break; } default: { break; } } // per-chromosome labels // marks.push( // Plot.dot(chromosomes, { // x: (d) => // getHilbertXY(d.offset + d.size / 2, { // baseOrder, // viewOrder: sampleOrder // })[0], // y: (d) => // getHilbertXY(d.offset + d.size / 2, { // baseOrder, // viewOrder: sampleOrder // })[1], // // x: d => baseHilbert.getXyAtVal(d.offset + d.size/2)[0], // // y: d => baseHilbert.getXyAtVal(d.offset + d.size/2)[1], // r: 10, // strokeWidth: 1, // fill: "white", // stroke: "black" // }) // ); // marks.push( // Plot.text(chromosomes, { // text: (d) => d.name + "", // x: (d) => // getHilbertXY(d.offset + d.size / 2, { // baseOrder, // viewOrder: sampleOrder // })[0], // y: (d) => // getHilbertXY(d.offset + d.size / 2, { // baseOrder, // viewOrder: sampleOrder // })[1], // // x: d => baseHilbert.getXyAtVal(d.offset + d.size/2)[0], // // y: d => baseHilbert.getXyAtVal(d.offset + d.size/2)[1], // fontWeight: "bold" // }) // ); // query pins and tooltip functionality // marks.push( // Plot.dot(pinLocations, { // x: (d) => // getHilbertXY( // chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, // { baseOrder, viewOrder: sampleOrder } // )[0], // y: (d) => // getHilbertXY( // chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, // { baseOrder, viewOrder: sampleOrder } // )[1], // r: 33, // fill: (d) => "black", // opacity: (d) => // dataMarkPinHighlight === "All" || // (d.type === "query" && dataMarkPinHighlight === "Query") || // (d.type === "hit" && dataMarkPinHighlight === "Hit") // ? 1 // : 0.25 // }) // ); if (dataMarkPinHighlight[0] !== "None") { marks.push( Plot.dot(pinLocations, { x: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[0], y: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[1], r: 32, fill: (d) => "#44444400", stroke: "black", opacity: (d) => dataMarkPinHighlight[0] === "All" || (d.type === "query" && dataMarkPinHighlight[0] === "Query") || (d.type === "hit" && dataMarkPinHighlight[0] === "Hit") ? 1 : 0 }) ); marks.push( Plot.dot(pinLocations, { x: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[0], y: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[1], r: 30, fill: (d) => (d.type === "query" ? "#ff000000" : "#eeeeee44"), opacity: (d) => dataMarkPinHighlight[0] === "All" || (d.type === "query" && dataMarkPinHighlight[0] === "Query") || (d.type === "hit" && dataMarkPinHighlight[0] === "Hit") ? 1 : 0 }) ); marks.push( Plot.text(pinLocations, { x: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[0], y: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[1], fill: (d) => (d.type === "query" ? "#000000" : "#000000"), fontWeight: "700", fontSize: (d) => (d.type === "query" ? "1.75em" : "2.25em"), text: (d) => d.type, // `${d.origin.toUpperCase()}\n${d.type}`, opacity: (d) => dataMarkPinHighlight[0] === "All" || (d.type === "query" && dataMarkPinHighlight[0] === "Query") || (d.type === "hit" && dataMarkPinHighlight[0] === "Hit") ? 1 : 0 }) ); marks.push( Plot.tooltip(pinLocations, { x: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[0], y: (d) => getHilbertXY( chromosomes[chromosomeNameToIndex[d.chrom]].offset + d.pos, { baseOrder, viewOrder: sampleOrder } )[1], // content: (d) => pinLocationTooltip(d), stroke: "white" }) ); } return marks; }32:Tb8a,// sample (num) points from the (order) curve makePointsSample = ({ order, // order of the hilbert space we want to sample num, // number of points we want to return start = 0, // first point in linear space end = num, // last point in linear space chrom // chromosome name } = {}) => { // console.log(`order ${order} | num ${num}`); let hilbert = d3hilbert.hilbert().order(order); const states = 18; let s = d3.scaleLinear().domain([0, num]).range([start, end]); if (dataMark.name === "Epilogos") { if (dataMarkEpilogosHighlight[0] === "All") { return d3.range(num).map((i) => { // let p = Math.floor(i / num * Math.pow(4, order)); let p = Math.floor(s(i)); let xy = hilbert.getXyAtVal(p); let state = epilogosData[chrom][i]; // Math.floor(Math.random() * states); let fill = stateMetadata[state][1]; return { x: xy[0], y: xy[1], i, p, state, fill }; }); } else { const stateToPreserveDefaultOpacity = parseInt(dataMarkEpilogosHighlight[2]) - 1; return d3.range(num).map((i) => { // let p = Math.floor(i / num * Math.pow(4, order)); let p = Math.floor(s(i)); let xy = hilbert.getXyAtVal(p); let state = epilogosData[chrom][i]; // Math.floor(Math.random() * states); let fill = addAlpha( stateMetadata[state][1], stateToPreserveDefaultOpacity === state ? 1 : 0.1 ); return { x: xy[0], y: xy[1], i, p, state, fill }; }); } } else if (dataMark.name === "DHS Domains") { if (dataMarkDHSDomainHighlight[0] === "All") { return d3.range(num).map((i) => { // let p = Math.floor(i / num * Math.pow(4, order)); let p = Math.floor(s(i)); let xy = hilbert.getXyAtVal(p); let state = dhsDomainData[chrom][i]; // Math.floor(Math.random() * states); let fill = dhsDomainMetadata[state][1]; return { x: xy[0], y: xy[1], i, p, state, fill }; }); } else { const dhsDomainToPreserveDefaultOpacity = parseInt(dataMarkDHSDomainHighlight[2]) - 1; return d3.range(num).map((i) => { // let p = Math.floor(i / num * Math.pow(4, order)); let p = Math.floor(s(i)); let xy = hilbert.getXyAtVal(p); let state = dhsDomainData[chrom][i]; // Math.floor(Math.random() * states); let fill = addAlpha( dhsDomainMetadata[state][1], dhsDomainToPreserveDefaultOpacity === state ? 1 : 0.1 ); return { x: xy[0], y: xy[1], i, p, state, fill }; }); } } else { return d3.range(num).map((i) => { // let p = Math.floor(i / num * Math.pow(4, order)); let p = Math.floor(s(i)); let xy = hilbert.getXyAtVal(p); let state = epilogosData[chrom][i]; // Math.floor(Math.random() * states); let fill = stateMetadata[state][1]; return { x: xy[0], y: xy[1], i, p, state, fill }; }); } }33:T4ef,function renderCurve(data, { opacity = d => d.scores, color = d3.scaleOrdinal().range(d3.schemeTableau10), width = 800, height = width, order = 6, scale = d3.scaleLinear().domain([0, Math.sqrt(Math.pow(4, order))]).range([0, width]), rw = width / Math.sqrt(Math.pow(4, order)) } = {}) { let canvas = html`

` canvas.width = width canvas.height = height let ctx = canvas.getContext("2d") ctx.fillStyle = "#F0F0F0"; ctx.fillRect(0, 0, canvas.width, canvas.height); let path = d3.line() .x(d => scale(d.x)) .y(d => scale(d.y)) .context(ctx) for(let d of data) { // First fill with a solid white // ctx.globalAlpha = 1 ctx.fillStyle = "lightgray"//color(d.name); // TODO: generalize this ctx.fillRect(scale(d.x), scale(d.y), rw - 6, rw - 6) } for(let d of overlay) { // First fill with a solid white // ctx.globalAlpha = 1 ctx.fillStyle = "steelblue"//color(d.name); // TODO: generalize this ctx.fillRect(scale(d.x)-2, scale(d.y)-2, 4, 4) } ctx.strokeStyle = "steelblue" ctx.beginPath() path(overlay) ctx.stroke() return Object.assign(canvas, { scale, rw }) }36:T8c6,function pinPlot(innerColor, outerColor, strokeColor, scale, uid) { const width = 100; const height = 128; let svg = ``.replace(/(\r\n|\n|\r)/gm, ""); return html`${svg}`; 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2e:{"id":"ff59ee3a053d0779","slug":"hilbert-genome-r2","title":"Hilbert Genome","thumbnail":"535f10bdbd9f53982e32f35adfb347661f0b44ed162350b45ed3485431716c42","access_level":"public","create_time":"$D2022-07-29T16:11:46.096Z","update_time":"$D2022-12-22T06:53:05.756Z","view_time":null,"first_public_time":"$D2022-12-09T21:39:59.811Z","has_unpublished_edits":null,"fork":{"id":"158c1dc85eedbdeb","slug":"hilbert-genome-test","title":"Hilbert Genome","owner":{"id":"c37303cdd0850875","login":"alexpreynolds","name":"Alex Reynolds"}},"stars":0,"starred":false,"owner":{"type":"team","id":"c37303cdd0850875","login":"alexpreynolds","name":"Alex Reynolds","avatar_url":"https://avatars-next.observableusercontent.com/d65c5655ec5460fd3f3e991b39388f7f7bc6fd994a450ca1cd6723004caa728c","tier":"starter_2024"},"version":4788,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"2e14005bda844aa3","login":"alexpreynolds","name":"Alex Reynolds","avatar_url":"https://avatars-next.observableusercontent.com/d65c5655ec5460fd3f3e991b39388f7f7bc6fd994a450ca1cd6723004caa728c","tier":null}],"members":[{"type":"individual","id":"2e14005bda844aa3","login":"alexpreynolds","name":"Alex Reynolds","avatar_url":"https://avatars-next.observableusercontent.com/d65c5655ec5460fd3f3e991b39388f7f7bc6fd994a450ca1cd6723004caa728c","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Hilbert Genome","cells":[{"id":0,"value":"md`# Hilbert Genome\n\nTrying to understand how to place all of the chromosomes on the 4^16 Hilbert space.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":398,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":439,"value":"Plot.plot({\n marks: [\n Plot.barX(chromosomeSizes, { x: \"size\", fill: \"name\", stroke: \"white\" }),\n Plot.text(\n chromosomeSizes,\n Plot.stackX({ text: (d) => \"\" + d.name, x: \"size\", z: \"name\", dy: -15 })\n ),\n Plot.text(\n chromosomeSizes,\n Plot.stackX({\n text: (d) => numf(d.size),\n x: \"size\",\n z: \"name\",\n dy: 15,\n dx: 0,\n rotate: 45,\n textAnchor: \"start\"\n })\n )\n ],\n color: { type: \"ordinal\", scheme: \"tableau10\" },\n x: {\n axis: null\n // tickRotate: 55\n },\n width,\n height: 140,\n marginTop: 20,\n marginBottom: 100,\n marginRight: 50,\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":662,"value":"chromosomes = {\n let offset = 0;\n return chromosomeSizes.map(d => {\n let c = {\n ...d,\n offset: offset\n }\n offset += d.size// + perChromosomeOffset\n // if(d.name == 8) offset += 36000000//1200000000\n return c\n })\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4161,"value":"viewof dataMark = Inputs.select(dataMarkClasses, {\n label: \"Selected data mark\",\n format: (x) => x.name,\n value: dataMarkClasses.find((m) => m.name === \"Lines\")\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4604,"value":"viewof dataMarkPinHighlight = Inputs.select(dataMarkPinHighlightMetadata, {\n label: \"Highlight pin elements\",\n format: (d) => d[0],\n value: dataMarkPinHighlightMetadata.find((d) => d[0] === \"All\")\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4599,"value":"viewof dataMarkLineHighlight = Inputs.select(dataMarkLineHighlightMetadata, {\n label: \"Highlight line elements\",\n format: (d) => d[0],\n value: dataMarkLineHighlightMetadata.find((d) => d[0] === \"All\")\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4495,"value":"viewof dataMarkEpilogosHighlight = Inputs.select(\n dataMarkEpilogosHighlightMetadata,\n {\n label: \"Highlight epilogos state\",\n format: (d) => d[0],\n value: dataMarkEpilogosHighlightMetadata.find((d) => d[0] === \"All\")\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4581,"value":"viewof dataMarkDHSDomainHighlight = Inputs.select(\n dataMarkDHSDomainHighlightMetadata,\n {\n label: \"Highlight DHS domain category\",\n format: (d) => d[0],\n value: dataMarkDHSDomainHighlightMetadata.find((d) => d[0] === \"All\")\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4232,"value":"viewof pinUrl = Inputs.text({\n label: \"Pin URL\",\n placeholder: \"Enter URL for query and hit pins\",\n value:\n \"https://resources.altius.org/~areynolds/public/observable/hilbert-genome-test/pin_test.080122.bed\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4357,"value":"viewof sampleOrder = Inputs.range([6, 9], {\n label: \"Sample order\",\n step: 1,\n value: 8\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":590,"value":"Plot.plot({\n color: plotColor(),\n marks: await plotMarks(),\n x: plotChannel(),\n y: plotChannel(),\n marginLeft: margins.l,\n marginTop: margins.t,\n marginBottom: margins.b,\n marginRight: margins.r,\n width: plotWidth,\n height: plotHeight,\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4200,"value":"plotColor = () => {\n let color = {};\n switch (dataMark.name) {\n case \"Epilogos\":\n color = {\n type: \"identity\",\n domain: stateMetadataColorList,\n range: stateMetadataColorList\n };\n break;\n case \"DHS Domains\":\n color = {\n type: \"identity\",\n domain: dhsDomainMetadataColorList,\n range: dhsDomainMetadataColorList\n };\n break;\n case \"Lines\":\n color = {\n type: \"categorical\",\n scheme: \"tableau10\"\n };\n break;\n default:\n break;\n }\n return color;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4238,"value":"plotChannel = () => {\n // defaults\n let channel = {\n axis: false\n };\n switch (dataMark.name) {\n case \"Epilogos\":\n channel.type = \"band\";\n break;\n case \"DHS Domains\":\n channel.type = \"band\";\n break;\n case \"Lines\":\n default:\n channel.type = \"point\";\n break;\n }\n return channel;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4398,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4174,"value":"dataMark.name","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4163,"value":"dataMarkClasses = [\n { name: \"Lines\" },\n { name: \"Epilogos\" },\n { name: \"DHS Domains\" }\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3942,"value":"plotWidth = 1024","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3946,"value":"plotHeight = 1024","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3318,"value":"margins = {\n return { l: 40, r: 40, b: 40, t: 40 };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":425,"value":"adding up the lengths of each chromosome: ${numf(chromosomeSize)}. \nfull extent of hilbert space at 16th order: ${numf(fullSize)}. \namount of free space: ${numf(fullSize - chromosomeSize)}.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":406,"value":"chromosomeSize = d3.sum(chromosomes, d => d.size)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":431,"value":"baseOrder = Math.log(chromosomeSize) / Math.log(4)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":680,"value":"baseHilbert = d3hilbert.hilbert().order(baseOrder)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":412,"value":"fullSize = Math.pow(4, baseOrder)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":418,"value":"fullSize - chromosomeSize","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1003,"value":"// just for the above plot to demonstrate the base order hilbert curve\nsampleOrder","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":578,"value":"// we create some sample points for each chromosome and render it in the same color\ncsamples = makeChromosomeSamples({\n baseOrder: baseOrder,\n viewOrder: sampleOrder,\n totalSamples: 8192 * sampleOrder\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":788,"value":"makeChromosomeSamples = function ({ baseOrder, viewOrder, totalSamples } = {}) {\n let offset = 0;\n let baseToView = (i) => Math.floor(i / Math.pow(4, baseOrder - viewOrder));\n return chromosomes.flatMap((d) => {\n // console.log(\n // `chromosome ${JSON.stringify(\n // d\n // )} | viewOrder ${viewOrder} | totalSamples ${totalSamples} | chromosomeSize ${chromosomeSize} | ${Math.floor(\n // (totalSamples * d.size) / chromosomeSize\n // )}`\n // );\n let UCSC_chromosome_name = `chr${d.name}`;\n let points = makePointsSample({\n order: viewOrder,\n num: Math.floor((totalSamples * d.size) / chromosomeSize),\n start: baseToView(d.offset),\n end: baseToView(d.offset + d.size),\n chrom: UCSC_chromosome_name\n }).map((p) => {\n return {\n ...p,\n name: d.name\n };\n });\n return points;\n });\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":481,"value":"$32","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4313,"value":"epilogosDataZips = {\n return {\n 7: FileAttachment(\n \"hilbert-genome@3.epilogos.Boix_et_al_833_sample.hg38.18.All_833_biosamples.S1.7.8192.zip\"\n ).zip(),\n 8: FileAttachment(\n \"hilbert-genome@4.epilogos.Boix_et_al_833_sample.hg38.18.All_833_biosamples.S1.8.8192.zip\"\n ).zip(),\n 9: FileAttachment(\n \"hilbert-genome@3.epilogos.Boix_et_al_833_sample.hg38.18.All_833_biosamples.S1.9.8192.zip\"\n ).zip()\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4431,"value":"epilogosDataZip = epilogosDataZips[sampleOrder]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4315,"value":"epilogosData = epilogosDataZip.file(\"data.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4570,"value":"dhsDomainDataZips = {\n return {\n 7: FileAttachment(\n \"hilbert-genome.dhs_domains.WM20201125.hg38.17.multiDHS_domains.S1.7.8192.zip\"\n ).zip(),\n 8: FileAttachment(\n \"hilbert-genome.dhs_domains.WM20201125.hg38.17.multiDHS_domains.S1.8.8192.zip\"\n ).zip(),\n 9: FileAttachment(\n \"hilbert-genome.dhs_domains.WM20201125.hg38.17.multiDHS_domains.S1.9.8192.zip\"\n ).zip()\n };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4566,"value":"dhsDomainDataZip = dhsDomainDataZips[sampleOrder]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4568,"value":"dhsDomainData = dhsDomainDataZip.file(\"data.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4492,"value":"addAlpha = function (color, opacity) {\n // coerce values so ti is between 0 and 1.\n var _opacity = Math.round(Math.min(Math.max(opacity || 1, 0), 1) * 255);\n return color + _opacity.toString(16).toUpperCase();\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4606,"value":"dataMarkPinHighlightMetadata = [...pinMetadata]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4608,"value":"pinMetadata = [\n [\"All\", null, \"0\"],\n [\"Query\", null, \"1\"],\n [\"Hit\", null, \"2\"],\n [\"None\", null, \"3\"]\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4595,"value":"dataMarkLineHighlightMetadata = [...lineMetadata]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4592,"value":"lineMetadata = [\n [\"All\", null, \"0\"],\n [\"None\", null, \"1\"]\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4496,"value":"dataMarkEpilogosHighlightMetadata = [[\"All\", null, \"0\"], ...stateMetadata]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4155,"value":"// $ awk -vFS=\"\\t\" -vOFS=\"\" '{ print \"[\\\"\",$4\"\\\", \",\"\\\"\",$5,\"\\\", \\\"\",$2,\"\\\"],\" }' <(tail -n+2 /home/jquon/epilogos/data/state_metadata/human/Boix_et_al_833_sample/hg38/18/metadata.tsv)\nstateMetadata = [\n [\"Active TSS\", \"#ff0000\", \"1\"],\n [\"Flanking TSS\", \"#ff4500\", \"2\"],\n [\"Flanking TSS Upstream\", \"#ff4500\", \"3\"],\n [\"Flanking TSS Downstream\", \"#ff4500\", \"4\"],\n [\"Strong transcription\", \"#008000\", \"5\"],\n [\"Weak transcription\", \"#006400\", \"6\"],\n [\"Genic Enhancer 1\", \"#c2e105\", \"7\"],\n [\"Genic Enhancer 2\", \"#c2e105\", \"8\"],\n [\"Active Enhancer 1\", \"#ffc34d\", \"9\"],\n [\"Active Enhancer 2\", \"#ffc34d\", \"10\"],\n [\"Weak Enhancer\", \"#ffff00\", \"11\"],\n [\"ZNF genes + repeats\", \"#66cdaa\", \"12\"],\n [\"Heterochromatin\", \"#8a91d0\", \"13\"],\n [\"Bivalent/Poised TSS\", \"#cd5c5c\", \"14\"],\n [\"Bivalent Enhancer\", \"#bdb76b\", \"15\"],\n [\"Repressed PolyComb\", \"#808080\", \"16\"],\n [\"Weak Repressed PolyComb\", \"#c0c0c0\", \"17\"],\n [\"Quiescent/Low\", \"#ffffff\", \"18\"]\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4205,"value":"stateMetadataColorList = stateMetadata.map((d) => d[1])","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4579,"value":"dataMarkDHSDomainHighlightMetadata = [[\"All\", null, \"0\"], ...dhsDomainMetadata]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4548,"value":"// /net/seq/data/projects/Index/DHS_components_to_multivec/src/Constants.components.json\ndhsDomainMetadata = [\n [\"Tissue-invariant\", \"#eeeeee\", \"1\"],\n [\"Stromal A\", \"#bb2dd4\", \"2\"],\n [\"Embryonic\", \"#05C1D9\", \"3\"],\n [\"Stromal B\", \"#7A00FF\", \"4\"],\n [\"Lymphoid\", \"#FE8102\", \"5\"],\n [\"Renal / cancer\", \"#4A6876\", \"6\"],\n [\"Placental / trophoblast\", \"#FFE500\", \"7\"],\n [\"Neural\", \"#0467FD\", \"8\"],\n [\"Cardiac\", \"#07AF00\", \"9\"],\n [\"Organ development / renal\", \"#692108\", \"10\"],\n [\"Pulmonary development\", \"#B9461D\", \"11\"],\n [\"Musculoskeletal\", \"#4C7D14\", \"12\"],\n [\"Digestive\", \"#009588\", \"13\"],\n [\"Vascular / endothelial\", \"#414613\", \"14\"],\n [\"Myeloid / erythroid\", \"#FF0000\", \"15\"],\n [\"Cancer / epithelial\", \"#08245B\", \"16\"],\n [\"None\", \"#ffffff\", \"17\"]\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4573,"value":"dhsDomainMetadataColorList = dhsDomainMetadata.map((d) => d[1])","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":848,"value":"chromosomes[23]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2466,"value":"chromosomeNameToIndex = {\n return {\n chr1: 0,\n chr2: 1,\n chr3: 2,\n chr4: 3,\n chr5: 4,\n chr6: 5,\n chr7: 6,\n chr8: 7,\n chr9: 8,\n chr10: 9,\n chr11: 10,\n chr12: 11,\n chr13: 12,\n chr14: 13,\n chr15: 14,\n chr16: 15,\n chr17: 16,\n chr18: 17,\n chr19: 18,\n chr20: 19,\n chr21: 20,\n chr22: 21,\n chrX: 22,\n chrY: 23\n };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":829,"value":"{\n let h = d3hilbert.hilbert().order(viewOrder)\n let c = chromosomes[0]\n \n let s = d3.scaleLinear()\n .domain([0, 1000]) \n .range([c.offset, c.offset + c.size]);\n \n let p = Math.floor(s(900))\n let xy = h.getXyAtVal(p);\nreturn xy\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":609,"value":"// viewof perChromosomeOffset = Inputs.range([0, 52597000], { label: \"per chromosome offset\", step: 1000, value: 0})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":696,"value":"## View Curve\nWe want to aggregate metrics on the base curve at lower orders of the Hilbert curve. We'll want to be able to translate between coordinates in the view curve and the base curve.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":435,"value":"viewof viewOrder = Inputs.range([3, 16], {step: 0.1, value: 7, label: \"Hilbert curve order\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":495,"value":"the current view order (4^${viewOrder}) \n- each step of the hilbert curve represents ${numf(viewToBase(1))} basepairs.\n- has ${numf(Math.pow(4, viewOrder))} steps\n- ${numf(Math.pow(2, viewOrder))} blocks per side\n- at ${canvasWidth} pixels wide, thats ${Math.floor(canvasWidth/Math.pow(2, viewOrder))} pixels per block\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":772,"value":"viewHilbert = d3hilbert.hilbert().order(viewOrder)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":749,"value":"## View Canvas\n\nWe want a consistent way to render a curve and place annotations on it","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4745,"value":"baseOrder","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4747,"value":"viewOrder","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4751,"value":"viewTestOrder2 = 7","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":768,"value":"viewTestData = makeChromosomeSamples({\n baseOrder,\n viewOrder,\n totalSamples: 8192 * viewOrder\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4770,"value":"Math.max(\n ...viewTestData.map((o) => {\n return o.x;\n })\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":785,"value":"Plot.plot({\n marks: [\n Plot.line(viewTestData, { x: \"x\", y: \"y\", stroke: \"name\", strokeWidth: 2 }),\n ],\n x: { axis: false, type: \"point\" },\n y: { axis: false, type: \"point\" },\n color: { type: \"ordinal\", scheme: \"tableau10\" },\n marginLeft: 20,\n marginTop: 20,\n marginBottom: 20,\n marginRight: 20,\n width: 650,\n height: 650\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":782,"value":"view = renderCurve(viewTestData, {\n order: viewOrder\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":738,"value":"canvasWidth = 800","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":753,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":991,"value":"function getHilbertXY(i, {\n baseOrder,\n viewOrder\n} = {}) {\n let baseToOrder = (i) => Math.floor(i / Math.pow(4, baseOrder - viewOrder))\n let hilbert = d3hilbert.hilbert().order(viewOrder);\n return hilbert.getXyAtVal(baseToOrder(i));\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1300,"value":"function getXYHilbert({x,y}, {\n baseOrder,\n viewOrder\n} = {}) {\n let viewToBase = (i) => i * (Math.pow(4, baseOrder - viewOrder))\n let hilbert = d3hilbert.hilbert().order(viewOrder);\n \n return viewToBase(hilbert.getValAtXY(x,y));\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":484,"value":"// given a step in the view curve, get the basepair coordinate where it starts\nviewToBase = (i) => i * (Math.pow(4, baseOrder - viewOrder))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":485,"value":"// given a basepair coordinate we can map it to the view order\nbaseToView = (i) => Math.floor(i / Math.pow(4, baseOrder - viewOrder))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1481,"value":"### Playground Wouter","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1353,"value":"function TESTgetHilbertXY(i, order=3) {\n let hilbert = d3hilbert.hilbert().order(order);\n return hilbert.getXyAtVal(i);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1400,"value":"function TESTgetXYHilbert(x, y, order=3) {\n let hilbert = d3hilbert.hilbert().order(order);\n let scale = Math.pow(2, order)\n return hilbert.getValAtXY(x/scale, y/scale);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1382,"value":"//ord = 3\nord = Math.log(Math.ceil(Math.pow(2, baseOrder)))/Math.log(2) // attempt to make 2**ord an integer","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1834,"value":"Math.pow(2, ord)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1358,"value":"// First item (0)\nxy_first = TESTgetHilbertXY(0, ord)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1364,"value":"// Last item (63 for ord=3)\nxy_last = TESTgetHilbertXY(Math.pow(4,ord)-1, ord)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1402,"value":"val_first = TESTgetXYHilbert(xy_first[0], xy_first[1], ord)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1407,"value":"val_last = TESTgetXYHilbert(xy_last[0], xy_last[1], ord)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1754,"value":"TESTgetXYHilbert(Math.pow(2,ord)-1, 0, ord) // does not look right for non-integer ord, should give ~4**ord","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1610,"value":"//rotate/flip a quadrant appropriately\nfunction rot(n, xy, rx, ry) {\n if (ry == 0) {\n if (rx == 1) {\n xy[0] = (n - 1 - xy[0]);\n xy[1] = (n - 1 - xy[1]);\n }\n\n //Swap x and y\n xy.push(xy.shift());\n }\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1613,"value":"// https://github.com/vasturiano/d3-hilbert/blob/17b1e7aae40b08d6e769fb98c4d6196ad57899b3/src/hilbert.js#L21\n// Note: this function will start breaking down for n > 2^26 (MAX_SAFE_INTEGER = 2^53)\n// x,y: cell coordinates, n: sqrt of num cells (square side size)\nfunction point2Distance(x, y, n) {\n var rx, ry, d = 0,\n xy = [x, y];\n\n for (var s = n / 2; s >= 1; s /= 2) {\n rx = (xy[0] & s) > 0;\n ry = (xy[1] & s) > 0;\n d += s * s * ((3 * rx) ^ ry);\n //rot(s, xy, rx, ry); // used in d3 Hilbert code\n rot(n, xy, rx, ry); // consistent with Wikipedia code\n }\n return d;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1614,"value":"// https://github.com/vasturiano/d3-hilbert/blob/17b1e7aae40b08d6e769fb98c4d6196ad57899b3/src/hilbert.js#L35\n// d: distance, n: sqrt of num cells (square side size)\nfunction distance2Point(d, n) {\n var rx, ry, t = d,\n xy = [0, 0];\n\n for (var s = 1; s < n; s *= 2) {\n rx = 1 & (t / 2);\n ry = 1 & (t ^ rx);\n rot(s, xy, rx, ry);\n\n xy[0] += (s * rx);\n xy[1] += (s * ry);\n t /= 4;\n }\n return xy;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1674,"value":"xy_first_raw = distance2Point(0, Math.pow(2,ord))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1617,"value":"xy_last_raw = distance2Point(Math.pow(4,ord)-1, Math.pow(2,ord))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1665,"value":"val_first_raw = point2Distance(xy_first[0], xy_first[1], Math.pow(2,ord))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1633,"value":"val_last_raw = point2Distance(xy_last[0], xy_last[1], Math.pow(2,ord))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1103,"value":"## Semantic scales\n- 1bp = genetic variation and association with traits/diseases\n- 10bp = transcription factor binding site and their footprint\n- 100bp = accessible / regulatory element\n- 1,000bp = promoter region\n- 10,000bp = gene\n- 100,000bp = Topological Associated Domain\n- 1,000,000bp = Lamina Associated Domain","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":863,"value":"## Zoom to bounds\nWant to try calculating bounding box of a start, end in base space and zooming the canvas to that.\nso that you could give start and end of a chromosome and it would be fit to the screen (at whatever view order you want)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1113,"value":"* base order = base coordinate system (single basepair for one hilbert step)\n* base coordinates = projection = 2d hilbert coordinates at base order\n * x and y are between 0 and ~${Math.round(Math.sqrt(fullSize))}\n* aggregate order = aggregation for visualized data\n* bounding box = expressed in base coordinates, or base pairs?\n* view coordinates = mapping from base coordinates to pixels, or screen coordinates\n\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1155,"value":"function get2D(i, {\n} = {}) {\n return baseHilbert.getXyAtVal(i);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1330,"value":"TODO: try this with lower orders to see if we can work","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1328,"value":"fullSize","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1217,"value":"getHilbertXY(fullSize - 1, { baseOrder, viewOrder })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1324,"value":"side = Math.sqrt(Math.pow(4, viewOrder))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1315,"value":"vhilbert = d3hilbert.hilbert().order(viewOrder);","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1319,"value":"numf(vhilbert.getValAtXY(65534/side, 0/side))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1307,"value":"getXYHilbert({x: 65533, y: 0}, { baseOrder, viewOrder: 16 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1179,"value":"baseExtent = get2D(fullSize - 1)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1293,"value":"numf(get1D({x: 55954, y: 40721}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1172,"value":"numf(get1D({x: 65534, y: 0}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1170,"value":"function get1D({x,y}, {\n} = {}) {\n let side = Math.round(Math.sqrt(fullSize))\n return baseHilbert.getValAtXY(x / side, y / side);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1245,"value":"numf(get1D({x:12, y:0}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1107,"value":"function getBounds2D(start, end, { \n} = {}) {\n let top, left, bottom, right;\n return { top, right, bottom, left }\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1142,"value":"function getBounds1D(bbox, { \n} = {}) {\n let x, y;\n \n let { top, right, bottom, left } = bbox\n return { x, y }\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1846,"value":"points3 = makePoints(3)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1869,"value":"hilbert3 = d3hilbert.hilbert().order(3)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1889,"value":"$34","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2060,"value":"testAggregateOrder = testOrder - testAggreageOrderOffset","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1933,"value":"testSize = Math.floor(.74 * Math.pow(4,testOrder)) // the # of \"basepairs\" for our test","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1920,"value":"testPoints = testScaled(testOrder, testSize)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2184,"value":"testPoints.get1D({x:0.0625, y:0})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2094,"value":"baseIndex = 75","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2082,"value":"bp = testPoints[baseIndex]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2125,"value":"testPoints.get1D(bp)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2080,"value":"// this gets us the hilbert coordinate, still need to get back the base coordinate from that\nhp = getXYHilbert(bp, { baseOrder: testOrder, viewOrder: testOrder })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2087,"value":"// would need to find closest point to the base hilbert point\n// we can count on the base coordinate going to a unique hilbert 1d coordinate\n// but we cant count on the inverse\ntestPoints.scale.invert(hp) ","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2118,"value":"testPoints.invert.get(hp)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1925,"value":"testPoints2 = testScaled(testAggregateOrder, testSize)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1908,"value":"viewof testOrder = Inputs.range([3, 8], { step: 1, label: \"test base order\"}) // our \"base order\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2067,"value":"viewof testAggreageOrderOffset = Inputs.range([0, 3], { step: 1, label: \"offset base order\"}) // ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2027,"value":"renderDoubleCurve(testPoints2, testPoints, { order: testAggregateOrder })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2277,"value":"renderDoubleCurve(testScaled(testAggregateOrder, testSize, true), testScaled(testOrder, testSize, true), { order: testAggregateOrder })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2025,"value":"$35","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1895,"value":"// plotHilbert(testPoints, { text: false, r: 1 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1928,"value":"// plotHilbert(testPoints2, { text: false, r: 3, fillOpacity: 0.15, strokeWidth: 1, fill: \"steelblue\"})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1953,"value":"// Plot.plot({\n// marks: [\n// Plot.cell(testPoints2, Plot.group({ fill: \"count\"}, { x: \"x\", y: \"y\"})),\n// Plot.rect(testPoints2, Plot.group({ fill: \"count\", x1: \"min\", x2: \"max\", y1: \"min\", y2: \"max\"}, { x: \"x\", y: \"y\"})),\n// Plot.text(testPoints2, Plot.group({ text: \"count\"}, { x: \"x\", y: \"y\"})),\n// Plot.line(testPoints, { x: \"x\", y: \"y\", stroke: \"steelblue\", strokeWidth: 1 }),\n// Plot.dot(testPoints, { x: \"x\", y: \"y\", stroke: \"steelblue\", r: 2, fill: \"steelblue\" }),\n// ],\n// color: { scheme: \"blues\", range: [0.15, 0.27]},\n// marginLeft: 40,\n// marginTop: 40,\n// marginBottom: 40,\n// marginRight: 40,\n// width: 650,\n// height: 650\n// });","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1987,"value":"import { spot } from \"@enjalot/plot-spot\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1994,"value":"// spot(testPoints, Plot.bin({ fill: \"count\", x1: d => d, x2: \"max\", y1: \"min\", y2: \"max\"}, { x: \"x\", y: \"y\", thresholds: Math.pow(2, testOrder - 1)}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1901,"value":"Math.pow(4, testOrder)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1872,"value":"bh3 = basepoints3.map(d => {\n let h = hilbert3.getXyAtVal(bscale(d))\n return { x: h[0], y: h[1], i: d, b: bscale(d) }\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1885,"value":"real3 = 45","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1861,"value":"basepoints3 = d3.range(real3)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1863,"value":"bscale = d3.scaleLinear().domain([0, real3]).range([0, Math.pow(4,3)])","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1866,"value":"bscale(40)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1848,"value":"d3.extent(points3, d => d.x)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1832,"value":"plotHilbert(points3)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1879,"value":"plotHilbert(bh3)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1830,"value":"function plotHilbert(points, { \n text = true,\n r = 9,\n stroke = \"steelblue\",\n fill = \"white\",\n fillOpacity = 1,\n strokeWidth = 3\n} = {}) {\n return Plot.plot({\n marks: [\n Plot.line(points, { x: \"x\", y: \"y\", stroke, strokeWidth }),\n Plot.dot(points, { x: \"x\", y: \"y\", stroke, r, fill, fillOpacity }),\n text ? Plot.text(points, { x: \"x\", y: \"y\", text: \"i\", dx: 0, textAnchor: \"middle\", fontSize: 9, fill: stroke }) : null\n ],\n x: { axis: false, type: \"point\" },\n y: { axis: false, type: \"point\" },\n // color: { type: \"ordinal\", scheme: \"tableau10\" },\n marginLeft: 20,\n marginTop: 20,\n marginBottom: 20,\n marginRight: 20,\n width: 650,\n height: 650\n // style: {\n // background: \"#eee\"\n // }\n });\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1148,"value":"scale and transform \n```\npixelX = k * baseX + tx \npixelY = k * baseY + ty \n```","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":420,"value":"numf = d3.format(\",d\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":534,"value":"import { Scrubber } from \"@mbostock/scrubber\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":536,"value":"// viewof asamples = Scrubber(d3.range(4096).slice(2800), { label: \"samples\", delay: 60 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"viewof order = Inputs.range([1, 4], { step: 1, value: 3, label: \"Order\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":147,"value":"Plot.plot({\n marks: [\n Plot.line(points, { x: \"x\", y: \"y\", stroke }),\n Plot.dot(points, { x: \"x\", y: \"y\", r: 10, fill: \"white\", stroke }),\n Plot.text(points, { x: \"x\", y: \"y\", text: \"i\", dx: 0, textAnchor: \"middle\", fontSize: 9, fill: stroke })\n ],\n x: { axis: false, type: \"point\" },\n y: { axis: false, type: \"point\" },\n marginLeft: 20,\n marginTop: 20,\n marginBottom: 20,\n marginRight: 20,\n width: 650,\n height: 650\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":198,"value":"// stroke = colors[order - 1]\nstroke = colors2[3]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":136,"value":"points = makePoints(order)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":236,"value":"makePoints = (order) => {\n let hilbert = d3hilbert.hilbert().order(order)\n return d3.range(Math.pow(4, order)).map(i => {\n let xy = hilbert.getXyAtVal(i)\n return { x: xy[0], y: xy[1], i }\n })\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":356,"value":"## Stacking Plots\nWhen you stack several orders of Hilbert curves on top of each other the pattern between orders can be a bit clearer. It helped me to notice the multiples of 4, and how each level \"up\" creates 4 corners of a box surrounding a point at the level below.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"html``","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":250,"value":"makeMarks = (order) => [\n Plot.line(makePoints(order), { x: \"x\", y: \"y\", stroke: colors[order - 1] }),\n Plot.dot(makePoints(order), { x: \"x\", y: \"y\", r: 10, fill: \"white\", stroke: colors[order - 1] }),\n Plot.text(makePoints(order), { x: \"x\", y: \"y\", text: \"i\", dx: 0, textAnchor: \"middle\", fontSize: 9, fill: colors[order - 1] })\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":362,"value":"This is just for fun 💅","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":242,"value":"options = ({ \n x: { axis: false, type: \"point\" },\n y: { axis: false, type: \"point\" },\n marginLeft: 20,\n marginTop: 20,\n marginBottom: 20,\n marginRight: 20,\n width: chartSize,\n height: chartSize\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":260,"value":"chartSize = width","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":210,"value":"md`[NYC subway colors](https://www.6sqft.com/did-you-know-the-mta-uses-pantone-colors-to-distinguish-train-lines/)`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":221,"value":"colors = [yellow, orange, blue, green, brown]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":312,"value":"colors2 = [red,yellow, orange, purple, lightgreen, brown]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"blue = \"#0039A6\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":215,"value":"red = \"#EE352E\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":217,"value":"green = \"#00933C\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":310,"value":"lightgreen = \"#6CBE45\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":223,"value":"brown = \"#996633\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":228,"value":"yellow = \"#FCCC0A\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":231,"value":"orange = \"#FF6319\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":307,"value":"purple = \"#B933AD\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2348,"value":"## Location Pin\nThe following provides code for generating a locational pin with desired appearance.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2358,"value":"pinPlot(pinColors.variant, pinColors.query, pinStrokeColor, pinScale, \"foo\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2417,"value":"pinPlotDataUrl(pinColors.gene, pinColors.query, pinStrokeColor, pinScale, \"uid\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2354,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2415,"value":"function pinPlotDataUrl(innerColor, outerColor, strokeColor, scale, uid) {\n return `data:image/svg+xml;utf8,${encodeURIComponent(\n pinPlot(innerColor, outerColor, strokeColor, scale, uid).outerHTML\n )}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2591,"value":"pinStrokeColor = \"#666666\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2439,"value":"pinScale = 0.33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2402,"value":"pinColors = {\n return {\n origin: {\n gene: \"#ff0000\",\n variant: \"#2f9aa0\"\n },\n type: {\n query: \"#eb8055\",\n hit: \"#e8fa5b\"\n }\n };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3020,"value":"pinLocationTooltip = function (d) {\n return `${d.type} | ${d.origin} | foo`;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2821,"value":"async function pinLocationsByUrl(url) {\n let results = [];\n const pinTestResponse = await axios({\n method: \"get\",\n url: url,\n data: {}\n }).then((result) => {\n const lines = result.data.split(\"\\n\");\n lines.forEach((l) => {\n const fields = l.split(\"\\t\");\n if (fields.length === 5) {\n const uid = uuidv4();\n const chrom = fields[0];\n const name = fields[0].replace(\"chr\", \"\");\n const chromName = isNaN(name) ? name : parseInt(name);\n results.push({\n chrom: chrom,\n chromName: chromName,\n start: parseInt(fields[1]),\n stop: parseInt(fields[2]),\n pos: parseInt(\n parseInt(fields[1]) +\n (parseInt(fields[2]) - parseInt(fields[1])) / 2\n ),\n type: fields[3],\n origin: fields[4],\n uid: uid\n });\n }\n });\n return results;\n });\n return await pinTestResponse;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2951,"value":"function uuidv4() {\n return ([1e7] + -1e3 + -4e3 + -8e3 + -1e11).replace(/[018]/g, (c) =>\n (\n c ^\n (crypto.getRandomValues(new Uint8Array(1))[0] & (15 >> (c / 4)))\n ).toString(16)\n );\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2413,"value":"pinLocations = pinLocationsByUrl(pinTestUrl)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2863,"value":"pinLocationsByUrl(pinTestUrl)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2813,"value":"pinTestUrl = `https://epilogos.altius.org:9001/${encodeURIComponent(pinUrl)}`","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2396,"value":"function pinLocationsTest() {\n const locations = [\n {\n chrom: \"chr1\",\n pos: 0,\n type: \"query\",\n origin: \"gene\"\n },\n {\n chrom: \"chr8\",\n pos: 0,\n type: \"hit\",\n origin: \"variant\"\n },\n {\n chrom: \"chr11\",\n pos: 0,\n type: \"hit\",\n origin: \"gene\"\n }\n ];\n return locations;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2942,"value":"md`**Sandbox**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2816,"value":"pinTestResponse = axios({\n method: \"get\",\n url: pinTestUrl,\n data: {}\n}).then((result) => result.data)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2919,"value":"getHilbertXY(chromosomes[chromosomeNameToIndex[\"chrX\"]].offset + 156040893, {\n baseOrder,\n viewOrder: sampleOrder\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2976,"value":"md`**Tooltip**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3003,"value":"import { addTooltip } from \"@alexpreynolds/experimental-plot-tooltip-01\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3006,"value":"Plot = require(\"@observablehq/plot\").then(addTooltip)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"md `**Dependencies**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2809,"value":"axios = require(\"https://cdn.jsdelivr.net/npm/axios/dist/axios.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":24,"value":"d3hilbert = require('d3-hilbert')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4334,"value":"hilbertGenomeEpilogosBoix_et_al_833_sampleHg3818Al = FileAttachment(\n \"hilbert-genome@4.epilogos.Boix_et_al_833_sample.hg38.18.All_833_biosamples.S1.8.8192.zip\"\n).zip()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W37","stdlib":"1"}} 2f:"$2e:body"