3e:null 3f:["$","title",null,{"children":"Synteny | christopher shaffer | Observable"}] 45:T44a,Plot.plot({ y: { label: "Genes In-Between" }, marks: [ Plot.barX( geneDistances[0], Plot.groupY( { x: "count" }, { y: "figure1Data", sort: { y: "y" }, title: (d) => d.figure1Data } ) ), Plot.ruleY([0]) ], caption: md`**Figure 1.** For the selected function pair (*${genesFunction1}* and *${genesFunction2}*), the total number of times that pair occurs in all cluster *${selectedCluster}* genomes at each distance is shown. Distances are measured as the number of genes in-between the selected genes, regardless of which selected gene occurs first in the genome. Adjacent genes in a genome have a value of 0. The results are order-independent, meaning that the number of genes in-between the selected genes will never be below 0. In cluster *${selectedCluster}*, *${ figureStats["Number of Unique Phages in Pair"] }* of the *${figureStats["Cluster Size"]}* genomes *(${( (figureStats["Number of Gene Pairs"] / figureStats["Cluster Size"]) * 100 ).toLocaleString()}%)* contain this pair.` })46:T53b,geneDistances = { // make an empty array to hold the calculated distances const figure1Array = []; const figure2Array = []; // geneDistances.function1Genes = []; // geneDistances.function2Genes = []; // get an array of phage names from the selected cluster const phageNames = phagesByCluster.map((d) => d.phagename); // loop over each phageName // for each phageName: for (const phageName of phageNames) { const function1Genes = genes.filter( (g) => g["Phage Name"] === phageName && g["Function"] === genesFunction1 ); const function2Genes = genes.filter( (g) => g["Phage Name"] === phageName && g["Function"] === genesFunction2 ); // geneDistances.function1Genes.push(function1Genes); // geneDistances.function2Genes.push(function2Genes); function1Genes.map((gene1) => { function2Genes.map((gene2) => { const figure1Data = Math.abs(gene1["Gene Name"] - gene2["Gene Name"]) - 1; const figure2Data = gene1["Gene Name"] < gene2["Gene Name"] ? gene2["Gene Name"] - gene1["Gene Name"] - 1 : gene2["Gene Name"] - gene1["Gene Name"] + 1; figure1Array.push({ gene1, gene2, figure1Data }); figure2Array.push({ gene1, gene2, figure2Data }); }); }); } return [figure1Array, figure2Array]; }47:[] 43:{"id":"e3726b5b637ce71f","slug":null,"title":"Synteny","thumbnail":"46d78770f15769cdcebdecbc107f4d33cd5f1c09c85a48d5cbf4c2be7444fc2c","access_level":"public","create_time":"$D2023-06-12T14:38:18.468Z","update_time":"$D2024-04-08T20:48:05.909Z","view_time":null,"first_public_time":"$D2023-06-12T14:38:18.468Z","has_unpublished_edits":null,"fork":{"id":"fcf8b81836e7b4be","slug":null,"title":"Synteny","owner":{"id":"2f98234bc0da6450","login":"bowers","name":"Bowers"}},"stars":0,"starred":false,"owner":{"type":"team","id":"fa036640d47dbb0d","login":"024d5b11114707b5","name":"christopher shaffer","avatar_url":"https://avatars-next.observableusercontent.com/560c8ae53f32731e7da960896659a2944d76939cb5229e6be66f419f032fa613","tier":"starter_2024","bio":"","following":false},"version":777,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"024d5b11114707b5","login":"024d5b11114707b5","name":"christopher shaffer","avatar_url":"https://avatars-next.observableusercontent.com/560c8ae53f32731e7da960896659a2944d76939cb5229e6be66f419f032fa613","tier":null,"bio":"just a user poking around on the site","following":false}],"members":[{"type":"individual","id":"024d5b11114707b5","login":"024d5b11114707b5","name":"christopher shaffer","avatar_url":"https://avatars-next.observableusercontent.com/560c8ae53f32731e7da960896659a2944d76939cb5229e6be66f419f032fa613","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Synteny","cells":[{"id":0,"value":"# Synteny","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":652,"value":"### Authors\n\nLauren Bruno, Sarah Donaire, Jasmine Kauffeld, Katelyn McHugh, and Steven G. Cresawn","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":142,"value":"terms","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":20,"value":"viewof formData = {\n let formData = \"Signed In\";\n formData = formWithSubmit(html`\n \n`);\n return formData;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":37,"value":"md`### *Welcome${user.name ? \", \" + user.name.split(\" \")[0] : \"\"}!* :)`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":161,"value":"This notebook provides two quantitative ways to think about synteny in phage genomes. The first of these, _synteny analysis_, reports the genomic spacing (measured as the number of in-between genes) between two selected gene functions. The second, _neighborhood analysis_, reports those gene functions that occur in an adjacent position (either the upstream or downstream gene) to a selected function. \n\nSuggestions for improvement are welcome. Just leave a public comment by selecting \"Add comment\" from the \"...\" menu in the left margin of any cell.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":164,"value":"First, select which data set you would like to use.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":58,"value":"viewof dataset = Inputs.select(user.datasets.sort(), {\n label: \"Select a data set\",\n value: \"Actino_Draft\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":158,"value":"## Synteny Analysis","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":166,"value":"Synteny analysis analyzes data at the cluster level. To get started, select a cluster from the menu below.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":60,"value":"viewof selectedCluster = Inputs.select(\n clusters.map((cluster) => cluster.name),\n { label: \"Select a cluster\", value: \"D\" }\n)\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":119,"value":"Lastly, select two functions below. The gene function menus show all unique functions from all phages in cluster _${selectedCluster}_. The results will produce a bar chart comparing distances between the gene functions in each of these phages. Be aware that the same function may be entered inconsistently in different phages. For instance \"terminase small subunit\" and \"small terminase subunit\" would show up separately in the menus.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":89,"value":"viewof genesFunction1 = Inputs.select(\n uniqueFunctions.sort((a,b) => a.localeCompare(b)),\n { label: \"Select Gene Function 1\"}\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":149,"value":"viewof genesFunction2 = Inputs.select(\n uniqueFunctions.filter(func2 => func2 != genesFunction1).sort((a,b) => a.localeCompare(b)),\n { label: \"Select Gene Function 2\" }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":284,"value":"$45","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":361,"value":"Plot.plot({\n y: { label: \"Genes In-Between\" },\n marks: [\n Plot.barX(\n geneDistances[1],\n Plot.groupY(\n { x: \"count\" },\n { y: \"figure2Data\", sort: { y: \"y\" }, title: (d) => d.figure2Data }\n )\n ),\n Plot.ruleY([0])\n ],\n caption: md`**Figure 2.** For the selected functions (*${genesFunction1}* and *${genesFunction2}*), the total number of times the pair occurs in all cluster *${selectedCluster}* at each distance is shown. Distances are measured as the number of genes in-between the selected genes. Adjacent genes in a genome have a value of 0. The results are order-dependent, meaning that the graph could produce a negative number based on the order in which the functions are selected.\n\nIn cluster *${selectedCluster}*, *${\n figureStats[\"Number of Unique Phages in Pair\"]\n }* of the *${figureStats[\"Cluster Size\"]}* genomes *(${(\n (figureStats[\"Number of Gene Pairs\"] / figureStats[\"Cluster Size\"]) *\n 100\n ).toLocaleString()}%)* contain this pair.\n`\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":454,"value":"**Table 1.** Comprehensive table of genes from cluster _${selectedCluster}_.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":230,"value":"viewof search1 = Inputs.search(genes, { label: \"Search any column\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":228,"value":"Inputs.table(search1, { width: { \"Phage Name\": 100, Function: 350 } })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":731,"value":"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":531,"value":"## Neighborhood Analysis\n\nSelect a gene function and see the functions of all adjacent genes (either upstream or downstream), as well as how many times they occur in adjacent genomes. This analysis uses all genes in the selected data set, not just those from a particular cluster.\n\n**Notes**:\n- Hover or tap (if using a touchscreen) on the bars to see the precise number of occurrences.\n- The *Actino_Draft* data set contains numerous instances of inconsistent terminology and typographical error. For instance, each of these is an annotated function in the database:\n - D-Ala D-Ala carboxypeptidase\n - D-Ala-D-Ala carboxypeptidase\n - D-ala D-ala carboxypeptidase\n - D-ala-D-ala carboxypeptidase\n - D-ala-D-ala-carboxypeptidase","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":547,"value":"viewof selectedFunction = Inputs.select(functions.sort())","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":732,"value":"functionFrequencies","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":735,"value":"Plot.plot({\n width: width,\n marginLeft: 200,\n marks: [\n Plot.barX(functionFrequencies, {\n x: \"frequency\",\n y: \"function\",\n fill: \"function\",\n sort: {y: \"x\", reverse: true, limit: 40}\n }),\n Plot.ruleX([0])\n ],\n color: { legend: true}\n})\n ","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":761,"value":"Plot.plot({\n width: width,\n marginLeft: 200,\n marks: [\n Plot.barX(functionFrequencies, {\n x: \"frequency\",\n y: \"function\",\n fill: \"function\",\n sort: {y: \"x\", reverse: true,}\n }),\n Plot.ruleX([0])\n ],\n color: { legend: true}\n})\n ","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":760,"value":"Plot.plot({\n width: width,\n marginLeft: 200,\n marks: [\n Plot.barX(functionFrequencies, {\n x: \"frequency\",\n y: \"function\",\n fill: \"function\",\n sort: {y: \"x\", reverse: true, limit:25\n \n }\n }),\n Plot.ruleX([0])\n ],\n color: { legend: false}\n})\n ","pinned":true,"hidden":true,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":743,"value":"Plot.plot({\n width,\n marginLeft: 10,\n y: {\n grid: true\n },\n marks: [\n Plot.barY(functionFrequencies, { x: \"function\", y: \"frequency\", sort: {x: \"y\", reverse: true}}),\n fill: \"function\",\n title: (d) => `${d.function}`\n }\n )\n ),\n Plot.ruleX([0])\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":538,"value":"Plot.plot({\n marginLeft: 350,\n marks: [\n Plot.barX(neighbors, {\n x: \"count\",\n y: \"function\",\n sort: { y: \"x\", reverse: true },\n title: (d) => d.function + \" : \" + d.count\n }),\n Plot.ruleX([0])\n ],\n caption: md`**Figure 3.** Neighbors of *${selectedFunction}* and the number of times they are adjacent in a genome.`\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"## Appendix\n\nThe cells below retrieve data from the Phamerator.org API and analyze the data in order to generate the above figures. Check them out if you want. If you break something, just reload the notebook. :)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":266,"value":"$46","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":504,"value":"figureStats = {\n let phageCount = phagesByCluster.length;\n let pairsCount = geneDistances[0].length;\n let uniquePhagesinPairs = Array.from(\n new Set(geneDistances[0].map((pair) => pair.gene1[\"Phage Name\"]))\n ).length;\n return {\n \"Cluster Size\": phageCount,\n \"Number of Gene Pairs\": pairsCount,\n \"Number of Unique Phages in Pair\": uniquePhagesinPairs\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":162,"value":"genefunctions = genesByCluster\n .filter((gene) => gene.genefunction != \"\")\n .map((gene) => gene.genefunction)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":684,"value":"functionFrequencies = {\n const counts = {};\n\n for (const geneFunction of genefunctions) {\n counts[geneFunction] = counts[geneFunction] ? counts[geneFunction] + 1 : 1;\n }\n return Object.entries(counts).map((e) => {\n return { function: e[0], frequency: e[1] };\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":692,"value":"functionFrequencies_table = functionFrequencies","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"functionFrequencies_table","database":"$undefined"},{"id":695,"value":"Plot.plot({\n marginLeft: 400,\n grid: true,\n width,\n height: Math.max(functionFrequencies_table.length * 10, 100),\n marks: [\n Plot.barX(functionFrequencies_table, {\n x: \"frequency\",\n y: \"function\",\n title: (d) => d.frequency,\n sort: { y: \"x\", reverse: true }\n }),\n Plot.ruleX([0])\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":180,"value":"uniqueFunctions = genefunctions.filter((element, index) => {\n return genefunctions.indexOf(element) === index;\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"import { formValue } from \"@mbostock/form-input\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":301,"value":"styles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":49,"value":"clusters = getPhameratorData(dataset, \"/clusters\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":267,"value":"phagesByCluster = getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedCluster}`,\n user.email,\n user.password\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":87,"value":"genesByCluster = getPhameratorData(\n dataset,\n `/genesbycluster/${selectedCluster}`,\n user.email,\n user.password\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":232,"value":"genes = {\n let genes = await getPhameratorData(\n dataset,\n `/genesbycluster/${selectedCluster}`,\n user.email,\n user.password\n );\n genes.sort((a, b) => {\n if (a.phageID === b.phageID) {\n return +a.name - +b.name;\n } else {\n return a.phageID < b.phageID;\n }\n });\n genes = genes.map((gene, index) => {\n // first the first gene, upstream gap is the distance from left end of genome\n const upstreamRightEnd =\n index === 0 || gene.phageID != genes[index - 1].phageID\n ? 1\n : d3.max([+genes[index - 1].start, +genes[index - 1].stop]);\n const leftEnd = d3.min([+gene.start, +gene.stop]);\n return {\n \"Phage Name\": gene.phageID,\n \"Gene Name\": +gene.name,\n Start: +gene.start,\n Stop: +gene.stop,\n Direction: gene.direction,\n Length: Math.abs(+gene.stop - +gene.start) + 1,\n \"Gap Size\": gene.gap,\n Phamily: +gene.phamName,\n Function: gene.genefunction === \"\" ? \"unknown\" : gene.genefunction\n };\n });\n\n return genes;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":561,"value":"functions = getPhameratorData(dataset, \"/functions\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":596,"value":"neighbors = getPhameratorData(\n dataset,\n `/neighbors/${selectedFunction}`,\n user.email,\n user.password\n).then((values) =>\n values.map((value) => {\n value.function === \"\" ? (value.function = \"NKF\") : null;\n return value;\n })\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":338,"value":"import { Plot } from \"@mkfreeman/plot-tooltip\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":657,"value":"import {\n terms,\n getPhameratorData,\n user,\n formWithSubmit,\n styles\n} with { formData } from \"@scresawn/phamerator-api-utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W47","stdlib":"1"}} 44:"$43:body"

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