3e:null 3f:["$","title",null,{"children":"SEA-PHAGES Template with Examples | Ruth Plymale | Observable"}] 45:[] 43:{"id":"02b7c10060996d45","slug":null,"title":"SEA-PHAGES Template with Examples","thumbnail":"334174ada958b2d0a505d040f9c6572d6c643fe4e5d7be520bf23b4202770dfc","access_level":"public","create_time":"$D2023-06-03T21:15:31.803Z","update_time":"$D2023-06-03T21:15:31.803Z","view_time":null,"first_public_time":"$D2023-06-03T21:15:31.803Z","has_unpublished_edits":null,"fork":true,"stars":0,"starred":false,"owner":{"type":"team","id":"83778b8300efc286","login":"plymaler","name":"Ruth Plymale","avatar_url":"https://avatars-next.observableusercontent.com/d363778fc1540da610fbb8d403496b26a752af99a8a0ea6fb409d00e698364ec","tier":"starter_2024","bio":"","following":false},"version":500,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"8508630a82dae81d","login":"plymaler","name":"Ruth Plymale","avatar_url":"https://avatars-next.observableusercontent.com/d363778fc1540da610fbb8d403496b26a752af99a8a0ea6fb409d00e698364ec","tier":null,"bio":"","following":false}],"members":[{"type":"individual","id":"8508630a82dae81d","login":"plymaler","name":"Ruth Plymale","avatar_url":"https://avatars-next.observableusercontent.com/d363778fc1540da610fbb8d403496b26a752af99a8a0ea6fb409d00e698364ec","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"SEA-PHAGES Template with Examples","cells":[{"id":0,"value":"# SEA-PHAGES Template with Examples\n\nWe hope that this notebook will help you get started accessing SEA-PHAGES data in a data science context. What you choose to do with that is up to you, but it's at least a good starting point for building tools for data export, sequence analysis, annotation, and visualization. By using the notebook as a template, you will start with the following:\n- a working mechanism for signing in to Phamerator.org\n- a demonstration of how to retrieve data\n- menus that allow you and your users to make selections\n- a table with controls for filtering, sorting, and slicing data\n- a few examples of data visualization using the _Plot_ library\n\nTo get started, _**fork this notebook**_ by using the _Fork button_ or _Fork menu item_ at the top of this notebook.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":33,"value":"terms","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":353,"value":"md`### *Welcome${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":"$undefined"},{"id":18,"value":"viewof formData = {\n let formData = \"Signed In\";\n formData = formWithSubmit(html`\n \n`);\n return formData;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"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":"$undefined"},{"id":46,"value":"viewof selectedCluster = Inputs.select(\n clusters.map((c) => c.name),\n {\n label: \"Select a cluster\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"viewof selectedPhage = Inputs.select(phages.map((p) => p.phagename).sort(), {\n label: \"Select a phage\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":75,"value":"genes_table = genes","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"genes_table","database":"$undefined"},{"id":148,"value":"Plot.plot({\n caption: md`**Figure 1.** A genome map of phage **${selectedPhage}**. The vertical position of gene arrows is based on reading frame.`,\n height: 555,\n width,\n marginTop: 150,\n marginRight: 125,\n x: {\n type: \"linear\",\n domain: [0, genomeLength],\n nice: false,\n grid: true\n },\n y: { label: null, ticks: 0 },\n marks: [\n Plot.ruleY([0]),\n Plot.arrow(genes_table, {\n title: (g) => g.name,\n x1: \"start\",\n y1: (gene) =>\n (gene.stop % 3) + 1 + (gene.direction === \"forward\" ? 3 : 0),\n x2: \"stop\",\n y2: (gene) =>\n (gene.stop % 3) + 1 + (gene.direction === \"forward\" ? 3 : 0),\n stroke: (gene) => (gene.direction === \"forward\" ? \"blue\" : \"orange\"),\n bend: false\n }),\n Plot.text(genes_table, {\n x: \"midpoint\",\n y: (gene) => (gene.stop % 3) + 1 + (gene.direction === \"forward\" ? 3 : 0),\n text: (d) => d.genefunction,\n dy: -15,\n rotate: -15,\n textAnchor: \"start\"\n })\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":410,"value":"viewof scaleFactor = Inputs.range([1, 5], { value: 1, step: 0.1 })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":369,"value":"Plot.plot({\n caption: md`**Figure 2.** A genome map of phage **${selectedPhage}**. The vertical position of gene rectangles is based on reading frame.`,\n height: 300,\n width: width * scaleFactor,\n marginTop: 150,\n marginRight: 125,\n x: {\n type: \"linear\",\n domain: [0, genomeLength],\n nice: false,\n grid: true\n },\n y: { axis: null },\n marks: [\n // Plot.ruleY([0]),\n Plot.barX(genes_table, {\n x1: \"start\",\n x2: \"stop\",\n y: (gene) => (gene.stop % 3) + (gene.direction === \"forward\" ? 0 : 3),\n fill: \"phamColor\",\n // opacity: 0.5,\n stroke: \"gray\",\n strokeWidth: 1,\n title: (d) => d.name\n }),\n Plot.text(genes_table, {\n x: \"midpoint\",\n y: (gene) => (gene.stop % 3) + 1 + (gene.direction === \"forward\" ? 0 : 3),\n text: (d) => d.genefunction,\n dy: -45,\n rotate: -90,\n textAnchor: \"start\"\n }),\n Plot.ruleY([2.5], { stroke: \"lightgray\" })\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":320,"value":"Plot.plot({\n caption: md`**Figure 3.** A beeswarm plot of upstream gap sizes for the _${genes_table.length.toLocaleString()}_ genes in phage _${selectedPhage}_.`,\n height: 400,\n marks: [\n Plot.dot(\n genes,\n Plot.dodgeY({\n x: \"gap\",\n fill: \"phamColor\",\n stroke: \"gray\",\n title: (d) => d.gap\n })\n )\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":348,"value":"Plot.plot({\n caption: md`**Figure 4.** A tick chart of upstream gap sizes for the _${genes_table.length.toLocaleString()}_ genes in phage _${selectedPhage}_.`,\n\n marks: [\n Plot.tickX(genes_table, { x: \"gap\", opacity: 0.2, title: (d) => d.gap })\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":264,"value":"---\n## Data\n\nThe data in the cells below were downloaded using the Phamerator.org API based on what you have selected in the menus above.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":52,"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":"$undefined"},{"id":62,"value":"phages = getPhameratorData(dataset, `/phagesbycluster/${selectedCluster}`, user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"genes = getPhameratorData(\n dataset,\n `/genes/${selectedPhage}`,\n user.email,\n user.password\n).then((value) =>\n value.map((v) => {\n v.genefunction = v.genefunction === \"\" ? null : v.genefunction;\n return v;\n })\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":79,"value":"genes_table","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":183,"value":"genomeLength = getPhameratorData(\n dataset,\n `/genome/${selectedPhage}`,\n user.email,\n user.password\n).then((v) => v.genomelength)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":38,"value":"---\n\n## Appendix\n\nThe cells below are required.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":5,"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":"$undefined"},{"id":204,"value":"import { Plot } from \"@mkfreeman/plot-tooltip\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":21,"value":"styles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W45","stdlib":"1"}} 44:"$43:body"

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