29:null 2a:["$","title",null,{"children":"CDD Data for Group | Maddie Bendele | Observable"}] 2f:T43e,# A Comparative Analysis of Protein and Domain Conservation within Cluster Q Genomes Bacteriophage genomic data can be assembled into a hierarchy at a variety of levels. Broadly, genomes are grouped into clusters (and optionally subclusters) based on broad patterns of nucleotide sequence similarity. With more granularity, phage proteins are grouped into phamilies based on substantially conserved amino acid sequences. Within the proteins of a given phamily, patterns of conserved amino acid sequences are also detectable as matches to NCBI's database of conserved domains. These conserved domains represent the finest level of granularity in the currently established hierarchy. The conservation of protein phamilies and domains may provide clues as to which elements of a genome are essential to being a functional member of the genome's assigned cluster. Our work analyzes the conservation of phamilies and protein domains in the relatively homogeneous cluster Q with a focus on quantifying conservation. We subsequently hope to apply the metrics to other, more diverse clusters. 30:T464,# Question for Dr. Cresawn 1. (JK Answered) If we look at the Wishmaker conserved domains in this table (by filtering with phageId), can we be confident that these are the CDS with the highest probability to be the right one, or does this just include all conserved domains that are shown in Phamerator? So if there are 5 CDS seen in one gene, are those all placed into the database, or does it just add in the top pick? 1a. What about conserved domains at the end of the genome? 2. Is this the Biosymposium presentation too? 3. How can we save or make more graphs so that we don't need to keep going back and forth with filters? 4. With the data that we have, what would be a valuable comparison? 5. What platforms (notebooks, phamerator, PECAAN, etc) should we be using to compare the CDD data to? 6. What should the poster look like, what should each section include? Where do you see this going? 7. Can we work on this during a class period? 8. Could we use observable to turn the two datasets into SQL and then merge them into one database so that we can compare the conserved domains that show up in both clusters? 9. 31:T557,# Potential Figures 1. Heatmap of ** conservation scores ** across all phamily: This figure could show a heatmap of the conservation scores for all identified phamilies across the phage genomes analyzed. This figure can provide a more detailed view of the conservation scores for all phamilies and help identify patterns and clusters of conserved domains. 2. Bar chart of top 10 most conserved domains: This figure could show the conservation scores of the top 10 most conserved domains across the phage genomes analyzed. This figure can provide a quick overview of the most conserved domains and their relative conservation scores. 3. Number of phams in a cluster divided by the number of genomes or number of genes in that cluster. 4. Color code genes by how big the phamily they are in (greyscale encoding, darker rectangle, the bigger the gene family) # Conservation Scores Meaning A conservation score is a metric used to quantify the level of conservation of a conserved domain across multiple genomes. It indicates how frequently the conserved domain appears in the genomes being analyzed. It takes into account the presence or absence of the domain in each genome being analyzed and calculates the proportion of genomes in which the domain is present. The resulting value ranges from 0 (no genomes share the domain) to 1 (all genomes share the domain). 32:Tff8,function BubbleChart( clusterQandFdomainsTable, { name = ([x]) => x, // alias for label label = name, // given d in data, returns text to display on the bubble value = ([, y]) => y, // given d in data, returns a quantitative size group, // given d in data, returns a categorical value for color title, // given d in data, returns text to show on hover link, // given a node d, its link (if any) linkTarget = "_blank", // the target attribute for links, if any width = 640, // outer width, in pixels height = width, // outer height, in pixels padding = 3, // padding between circles margin = 1, // default margins marginTop = margin, // top margin, in pixels marginRight = margin, // right margin, in pixels marginBottom = margin, // bottom margin, in pixels marginLeft = margin, // left margin, in pixels groups, // array of group names (the domain of the color scale) colors = d3.schemeTableau10, // an array of colors (for groups) fill = "#ccc", // a static fill color, if no group channel is specified fillOpacity = 0.7, // the fill opacity of the bubbles stroke, // a static stroke around the bubbles strokeWidth, // the stroke width around the bubbles, if any strokeOpacity // the stroke opacity around the bubbles, if any } = {} ) { // Compute the values. const D = d3.map(clusterQgenes, (d) => d); const V = d3.map(clusterQgenes, value); const G = group == null ? null : d3.map(clusterQgenes, group); const I = d3.range(V.length).filter((i) => V[i] > 0); // Unique the groups. if (G && groups === undefined) groups = I.map((i) => G[i]); groups = G && new d3.InternSet(groups); // Construct scales. const color = G && d3.scaleOrdinal(groups, colors); // Compute labels and titles. const L = label == null ? null : d3.map(clusterQgenes, label); const T = title === undefined ? L : title == null ? null : d3.map(clusterQgenes, title); // Compute layout: create a 1-deep hierarchy, and pack it. const root = d3 .pack() .size([width - marginLeft - marginRight, height - marginTop - marginBottom]) .padding(padding)(d3.hierarchy({ children: I }).sum((i) => V[i])); const svg = d3 .create("svg") .attr("width", width) .attr("height", height) .attr("viewBox", [-marginLeft, -marginTop, width, height]) .attr("style", "max-width: 100%; height: auto; height: intrinsic;") .attr("fill", "currentColor") .attr("font-size", 10) .attr("font-family", "sans-serif") .attr("text-anchor", "middle"); const leaf = svg .selectAll("a") .clusterQgenes(root.leaves()) .join("a") .attr( "xlink:href", link == null ? null : (d, i) => link(D[d.clusterQgenes], i, clusterQgenes) ) .attr("target", link == null ? null : linkTarget) .attr("transform", (d) => `translate(${d.x},${d.y})`); leaf .append("circle") .attr("stroke", stroke) .attr("stroke-width", strokeWidth) .attr("stroke-opacity", strokeOpacity) .attr( "fill", G ? (d) => color(G[d.clusterQgenes]) : fill == null ? "none" : fill ) .attr("fill-opacity", fillOpacity) .attr("r", (d) => d.r); if (T) leaf.append("title").text((d) => T[d.clusterQgenes]); if (L) { // A unique identifier for clip paths (to avoid conflicts). const uid = `O-${Math.random().toString(16).slice(2)}`; leaf .append("clipPath") .attr("id", (d) => `${uid}-clip-${d.clusterQgenes}`) .append("circle") .attr("r", (d) => d.r); leaf .append("text") .attr( "clip-path", (d) => `url(${new URL(`#${uid}-clip-${d.clusterQgenes}`, location)})` ) .selectAll("tspan") .clusterQgenes((d) => `${L[d.clusterQgenes]}`.split(/\n/g)) .join("tspan") .attr("x", 0) .attr("y", (d, i, D) => `${i - D.length / 2 + 0.85}em`) .attr("fill-opacity", (d, i, D) => (i === D.length - 1 ? 0.7 : null)) .text((d) => d); } return Object.assign(svg.node(), { scales: { color } }); }33:[{"id":"d199bc31d7b4f6bacb51996118ffa219b6da886520e1b2c7f8c564c40e21acca698672d3eaf5ad620fb54738e861a55a3f5e4a538ff1abd2defef104e8724f5b","href":"https://static.observableusercontent.com/files/d199bc31d7b4f6bacb51996118ffa219b6da886520e1b2c7f8c564c40e21acca698672d3eaf5ad620fb54738e861a55a3f5e4a538ff1abd2defef104e8724f5b","name":"clusterFdomains.json","type":"application/json","lastModified":1680304879355.789,"size":11920170},{"id":"98435aac96ed4b72f1384742513d735993c1ec8cfd38a4f8e97c6845a19340ddfd862d44d2d67513eea45bbc2902668c46122f554414cd25c7fe662ac1492578","href":"https://static.observableusercontent.com/files/98435aac96ed4b72f1384742513d735993c1ec8cfd38a4f8e97c6845a19340ddfd862d44d2d67513eea45bbc2902668c46122f554414cd25c7fe662ac1492578","name":"clusterQdomains.json","type":"application/json","lastModified":1680304879355.789,"size":1462345}] 2d:{"id":"699db39bcb02352f","slug":null,"title":"CDD Data for Group","thumbnail":"f6a9aecd547e81d81eea96bfdbd53e712d7dd8565158c59ac0acd44fe818e4a8","access_level":"public","create_time":"$D2023-03-31T23:21:19.355Z","update_time":"$D2023-04-01T00:06:46.532Z","view_time":null,"first_public_time":"$D2023-03-31T23:21:19.355Z","fork":{"id":"bde45c9ff4642b6d","slug":null,"title":"CDD Data for Group","owner":{"id":"3e2509283042eb59","login":"icobb","name":"Isobel Cobb"}},"stars":0,"starred":false,"owner":{"type":"team","id":"f5a60deb983d2ac1","login":"mbendele","name":"Maddie Bendele","avatar_url":"https://avatars-next.observableusercontent.com/eda08aa21264f41360de6456790ae57ec6fa4ab04010c83e854f643516c54538","tier":"starter_2024"},"version":1339,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"24c6369a6fc83150","login":"mbendele","name":"Maddie Bendele","avatar_url":"https://avatars-next.observableusercontent.com/df056cb5c50bb95442f5984e912a3fdad13fb13fc423a0b8e54da82de553579a","tier":null}],"members":[{"type":"individual","id":"24c6369a6fc83150","login":"mbendele","name":"Maddie Bendele","avatar_url":"https://avatars-next.observableusercontent.com/df056cb5c50bb95442f5984e912a3fdad13fb13fc423a0b8e54da82de553579a","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"CDD Data for Group","cells":[{"id":0,"value":"# CDD Data for Group","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":47,"value":"$2f","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":50,"value":"# Cluster F Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3,"value":"clusterfdomains = FileAttachment(\"clusterFdomains.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"data1 = clusterfdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"data1","database":"$undefined"},{"id":11,"value":"Plot.plot({\n marginLeft: 150,\n insetLeft: 0,\n height: 3500,\ncolor: {\n legend: true\n },\n marks: [\n Plot.auto(data1, {x: {value: \"domainname\", reduce: \"count\"}, y: \"domainname\", color: \"description\"})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":52,"value":"# Cluster Q Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5,"value":"clusterqdomains = FileAttachment(\"clusterQdomains.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"data = clusterqdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"data","database":"$undefined"},{"id":1244,"value":"clusterQfunctions = getPhameratorData(\"Actino_Draft\", '/functions', user.email, user.password)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1274,"value":"phams = getPhameratorData(\"Actino_Draft\", '/phamilies', user.email, user.password)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1276,"value":"clusterQgenes = getPhameratorData(\"Actino_Draft\", `/genesbycluster/Q`,\n user.email,\n user.password)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1281,"value":"clusterFgenes = getPhameratorData(\"Actino_Draft\", `/genesbycluster/F`,\n user.email,\n user.password)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1279,"value":"clusterFphams = Array.from(new Set(clusterFgenes.map(d => +d.phamName)))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1282,"value":"clusterQphams = Array.from(new Set(clusterQgenes.map(d => +d.phamName)))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8,"value":"Plot.plot({\n marginLeft: 150,\n marginRight: 100,\n width: 1500,\n height: 5000,\ncolor: {\n legend: true\n },\n marks: [\n Plot.auto(data, {x: {value: \"domainname\", reduce: \"count\"}, y: \"phageID\", fy: \"description\", color: \"query_start\"})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":948,"value":"data2 = clusterqdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"data2","database":"$undefined"},{"id":951,"value":"fff = Plot.plot({\n marginLeft: 200,\n marginRight: 1,\n marginBottom: 100,\n width: 1000,\n color: {\n legend: false\n },\n marks: [\n Plot.auto(data2, {x: \"phageID\", y: \"domainname\", color: \"description\"})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"fff","database":"$undefined"},{"id":1068,"value":"fff1 = Plot.plot({\n marginLeft: 200,\n marginRight: 1,\n marginBottom: 100,\n width: 1000,\n color: {\n legend: true\n },\n marks: [\n Plot.auto(data2, {x: \"phageID\", y: \"domainname\", color: \"query_start\"})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"fff1","database":"$undefined"},{"id":1069,"value":"Plot.auto(data2, { x: \"phageID\", y: \"domainname\", color: \"DomainID\" }).plot({\n x: {tickRotate: -45},\n color: { legend: true },\n width: 1000,\n marginLeft: 200,\n marginRight: 1,\n marginBottom: 100\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":983,"value":"","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"","database":"var:clusterfdomains"},{"id":1087,"value":"clusterQandFdomains = clusterfdomains.concat(clusterqdomains)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1089,"value":"clusterQandFdomainsTable = clusterQandFdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"clusterQandFdomainsTable","database":"$undefined"},{"id":1091,"value":"Plot.plot({\n marginLeft: 200,\n color: {\n legend: true\n },\n marks: [\n Plot.auto(clusterQandFdomainsTable, {x: {value: \"domainname\", reduce: \"count\"}, y: \"domainname\", color: \"cluster\"})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1237,"value":"data3 = clusterQandFdomainsTable","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"data3","database":"$undefined"},{"id":1240,"value":"Plot.plot({\n marks: [\n Plot.auto(data3, {})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1202,"value":"Plot.plot({\n width: width,\n marginLeft: 100,\n marks: [\n Plot.barX(clusterQandFdomainsTable, {\n x: \"domainname\",\n y: \"cluster\",\n fill: \"domainname\"\n }),\n Plot.ruleX([0])\n ],\n color: { legend: true }\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":304,"value":"$30","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1078,"value":"$31","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":856,"value":"# Other Notebooks\n1. https://observablehq.com/d/297ef50dfe2a4fce\n2. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1246,"value":"import {\n terms,\n getPhameratorData,\n user,\n formWithSubmit,\n styles\n} with { formData } from \"@scresawn/phamerator-api-utilities\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1250,"value":"import {Plot} from \"@mkfreeman/plot-tooltip\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1262,"value":"viewof formData = {\n let formData = \"Signed In\";\n formData = formWithSubmit(html`\n \n`);\n return formData;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1264,"value":"styles","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1295,"value":"chart = BubbleChart(clusterQgenes, {\n label: (d) =>\n [\n ...d.id\n .split(\".\")\n .pop()\n .split(/(?=[A-Z][a-z])/g),\n d.value.toLocaleString(\"en\")\n ].join(\"\\n\"),\n value: (d) => d.value,\n group: (d) => d.id.split(\".\")[1],\n title: (d) => `${d.id}\\n${d.value.toLocaleString(\"en\")}`,\n link: (d) =>\n `https://github.com/prefuse/Flare/blob/master/flare/src/${d.id.replace(\n /\\./g,\n \"/\"\n )}.as`,\n width: 1152\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1288,"value":"$32","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1290,"value":"import { BubbleChart } from \"@d3/bubble-chart\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1300,"value":"phamsQ = clusterQgenes","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"phamsQ","database":"$undefined"},{"id":1335,"value":"import { Swatches } from \"@d3/color-legend\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1337,"value":"import { howto } from \"@d3/example-components\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 2e:"$2d:body"

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