29:null 2a:["$","title",null,{"children":"CDD Data for Group | Isobel Cobb | 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:T558,# 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). 31:[{"id":"7e16b339710c17e13db747b078f8467c4f13e696971c594c564251a670e095c1b480a9d523e5b3973db4d67d6115926be96c1b91f320e84f498cff3d9a31f3fa","href":"https://static.observableusercontent.com/files/7e16b339710c17e13db747b078f8467c4f13e696971c594c564251a670e095c1b480a9d523e5b3973db4d67d6115926be96c1b91f320e84f498cff3d9a31f3fa","name":"Greyscale Phamerator Map_Cluster F.svg","type":"image/svg+xml","lastModified":1680646924979.12,"size":619341},{"id":"03dda6f659395547b622e73df70537bf09477e8a5dac40f8a65bedf09baadca1ca68011195af6a55ff4aee826aecc33cadada5629bed82ca23ec2632973edd81","href":"https://static.observableusercontent.com/files/03dda6f659395547b622e73df70537bf09477e8a5dac40f8a65bedf09baadca1ca68011195af6a55ff4aee826aecc33cadada5629bed82ca23ec2632973edd81","name":"Greyscale Phamerator Map_Cluster Q.svg","type":"image/svg+xml","lastModified":1680646952599.18,"size":2292714},{"id":"98435aac96ed4b72f1384742513d735993c1ec8cfd38a4f8e97c6845a19340ddfd862d44d2d67513eea45bbc2902668c46122f554414cd25c7fe662ac1492578","href":"https://static.observableusercontent.com/files/98435aac96ed4b72f1384742513d735993c1ec8cfd38a4f8e97c6845a19340ddfd862d44d2d67513eea45bbc2902668c46122f554414cd25c7fe662ac1492578","name":"clusterQdomains.json","type":"application/json","lastModified":1680266798029.533,"size":1462345},{"id":"d199bc31d7b4f6bacb51996118ffa219b6da886520e1b2c7f8c564c40e21acca698672d3eaf5ad620fb54738e861a55a3f5e4a538ff1abd2defef104e8724f5b","href":"https://static.observableusercontent.com/files/d199bc31d7b4f6bacb51996118ffa219b6da886520e1b2c7f8c564c40e21acca698672d3eaf5ad620fb54738e861a55a3f5e4a538ff1abd2defef104e8724f5b","name":"clusterFdomains.json","type":"application/json","lastModified":1680266798106.03,"size":11920170}] 2d:{"id":"bde45c9ff4642b6d","slug":null,"title":"CDD Data for Group","thumbnail":"72db76e7bdbcc6586c060fd06267ef6cce56070c16cbdbe6e14c91e57cbfc581","access_level":"public","create_time":"$D2023-03-31T12:46:23.081Z","update_time":"$D2023-04-06T02:44:48.481Z","view_time":null,"first_public_time":"$D2023-03-31T12:46:23.081Z","fork":false,"stars":2,"starred":false,"owner":{"type":"team","id":"3e2509283042eb59","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":"starter_2024"},"version":3090,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null}],"members":[{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null,"role":"editor"},{"type":"individual","id":"24c6369a6fc83150","login":"mbendele","name":"Maddie Bendele","avatar_url":"https://avatars-next.observableusercontent.com/df056cb5c50bb95442f5984e912a3fdad13fb13fc423a0b8e54da82de553579a","tier":null,"role":"editor"},{"type":"individual","id":"9f316fa2aba52cf9","login":"scresawn","name":"Steven Cresawn","avatar_url":"https://avatars-next.observableusercontent.com/e2727956835daa3b5e9995b66c1111489c2e403c176b4fb761ec6ad64b97786b","tier":null,"role":"editor"},{"type":"individual","id":"cb7ded4a1c316f71","login":"zshiff02","name":"Zelda","avatar_url":"https://avatars-next.observableusercontent.com/29ce3190c8bd7d97a9f638ae7a13cd9dbcf41f6028155c086d3367a37b729e86","tier":null,"role":"editor"}],"comments":[{"id":"feefc6c0f265ba0c","reply_to_id":null,"content":"3. How can we save or make more graphs so that we don't need to keep going back and forth with filters?","create_time":"$D2023-03-31T14:10:59.243Z","update_time":null,"resolved":true,"user":{"type":"individual","id":"cb7ded4a1c316f71","login":"zshiff02","name":"Zelda","avatar_url":"https://avatars-next.observableusercontent.com/29ce3190c8bd7d97a9f638ae7a13cd9dbcf41f6028155c086d3367a37b729e86","tier":null}},{"id":"ec7db9dbca184ddd","reply_to_id":null,"content":"add {legend: true} into color to see the legend","create_time":"$D2023-04-04T03:53:11.371Z","update_time":null,"resolved":false,"user":{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null}},{"id":"2b355857158f9463","reply_to_id":null,"content":"I get this error when I try to add in the phams\n\ncombinedDB = TypeError: Cannot read properties of null (reading 'length')","create_time":"$D2023-04-04T04:04:00.216Z","update_time":null,"resolved":true,"user":{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null}},{"id":"6cc8032648de5032","reply_to_id":null,"content":"make a database with Q and F phams","create_time":"$D2023-04-05T00:35:37.697Z","update_time":null,"resolved":true,"user":{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null}}],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":3,"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":1262,"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","output":"$undefined","database":"$undefined"},{"id":50,"value":"# Cluster F Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3,"value":"clusterfdomains = FileAttachment(\"clusterFdomains.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"clusterfdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1975,"value":"## Cluster F Search","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1969,"value":"viewof searchF = Inputs.search(clusterfdomains, {label: \"Search any column\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1972,"value":"Inputs.table(searchF, { width: { \"Domain Name\": 100, Function: 350 } })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","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":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"clusterqdomains","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1984,"value":"## Cluster Search Q\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1978,"value":"viewof searchQ = Inputs.search(clusterqdomains, { label: \"Search any column\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1981,"value":"Inputs.table(searchQ, { width: { \"Domain Name\": 100, Function: 350 } })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1958,"value":"# Cluster Q and F Combined Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1087,"value":"clusterQandFdomains = clusterfdomains.concat(clusterqdomains)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1957,"value":"clusterQandFdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2006,"value":"## Cluster D and F Combined Search","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1963,"value":"viewof searchDF = Inputs.search(clusterQandFdomains, { label: \"Search any column\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1965,"value":"Inputs.table(searchDF, { width: { \"Domain Name\": 100, Function: 350 } })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1742,"value":"# Cluster Q and F Phams and Genes ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1274,"value":"phams = getPhameratorData(\"Actino_Draft\", '/phamilies', user.email, user.password)","pinned":false,"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":false,"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":false,"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))).map(d => {return {\"PhamilyName\": d}})","pinned":false,"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))).map(d => {return {\"PhamilyName\": d}})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2289,"value":"# Domains+Genes Combined with SQL","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2034,"value":"combinedDB = DuckDBClient.of({ clusterFgenes, clusterfdomains, clusterQgenes, clusterqdomains, clusterQphams, clusterFphams, phams, functionFrequencies})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2550,"value":"phams","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2715,"value":"SELECT * FROM phams, clusterQgenes, clusterqdomains \n WHERE phams.PhamID = clusterQgenes.phamName \n AND clusterqdomains.geneID = clusterQgenes.geneID;","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"DBclusterQdomains","database":"var:combinedDB"},{"id":2721,"value":"SELECT *FROM clusterFphams, clusterFgenes, clusterfdomains \n WHERE clusterFphams.PhamilyName = clusterFgenes.phamName \n AND clusterfdomains.geneID = clusterFgenes.geneID;","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"DBclusterFdomains","database":"var:combinedDB"},{"id":2937,"value":"SELECT * FROM phams, clusterFgenes, clusterfdomains \n WHERE phams.PhamID = clusterFgenes.phamName \n AND clusterfdomains.geneID = clusterFgenes.geneID AND PhamID Like '399'\n","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"DBclusterFdomains1","database":"var:combinedDB"},{"id":2826,"value":"DBclusterFdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2920,"value":"SELECT * FROM 'phams'","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"","database":"var:combinedDB"},{"id":2698,"value":"# Conserved Domain and Pham Frequency","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2623,"value":"SELECT domainname, COUNT(*) AS mostFrequentFDomains \nFROM clusterFdomains\n INNER JOIN \"clusterFgenes\"\n ON clusterfdomains.geneID = clusterFgenes.geneID\nGROUP BY domainname;","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"FDomainFreq","database":"var:combinedDB"},{"id":2695,"value":"SELECT domainname, COUNT(*) AS mostFrequentQDomains \nFROM clusterQdomains\n INNER JOIN \"clusterQgenes\"\n ON clusterqdomains.geneID = clusterQgenes.geneID\nGROUP BY domainname;","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"QDomainFreq","database":"var:combinedDB"},{"id":2729,"value":"SELECT phamName, COUNT(*) AS QphamFrequency\nFROM clusterQgenes\nGROUP BY phamName\n ORDER BY QphamFrequency DESC\n LIMIT 73","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"QPhamFreq","database":"var:combinedDB"},{"id":2748,"value":"SELECT phamName, COUNT(*) AS FphamFrequency\nFROM clusterFgenes\nGROUP BY phamName\n ORDER BY FphamFrequency DESC\n LIMIT 73\n\n","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"FPhamFreq1","database":"var:combinedDB"},{"id":2907,"value":"SELECT DISTINCT * FROM phams \n INNER JOIN clusterFphams\n ON phams.phamID = clusterFphams.PhamilyName\n INNER JOIN clusterQphams\n ON phams.phamID = clusterQphams.PhamilyName\n ","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"","database":"var:combinedDB"},{"id":2959,"value":"","pinned":true,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","output":"","database":"var:combinedDB"},{"id":1424,"value":"# Comparing Domains in Cluster F and Q\n1. The first chart below is a bubble chart to compare the domains between the two cluster (you can remove the facet X to combine)\n2. looking at cluster F\n3. looking at cluster Q","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1428,"value":"Data table to look at specific conserved domains","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1430,"value":"# Cluster F Bubble Chart (same as above, just smaller)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1906,"value":"clusterFdomainsChart1 = Plot.plot({\n marginLeft: 150,\n width: 1500,\n height: 4000,\ncolor: {\n legend: true\n },\n marks: [\n Plot.auto(clusterfdomains, {x: \"phageID\", y: \"domainname\", color: \"cluster\"})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"clusterFdomainsChart1","database":"$undefined"},{"id":1506,"value":"# Cluster Q Bubble Chart ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1505,"value":"Plot.plot({\n marginLeft: 150,\n width: 1500,\n color: {\n legend: true\n },\n marks: [\n Plot.auto(clusterqdomains, {x: \"phageID\", y: \"domainname\", color: \"cluster\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1091,"value":"Plot.plot({\n marginLeft: 150,\n width: 1500,\n height: 4000,\ncolor: {\n legend: true\n },\n marks: [\n Plot.auto(clusterQandFdomains, {x: \"phageID\", y: \"domainname\", color: \"cluster\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2308,"value":"# Figures with Gene+Domain Data Combined","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2127,"value":"Plot.plot({\n marks: [\n Plot.auto(clusters, {})\n ]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2271,"value":"# Protein Function Bar Chart\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2249,"value":"You are now viewing a graph of the top 20 protein functions in cluster _${selectedCluster}_ phages. Be aware that some functions may be listed multiple times due to inconsistent data entry and lack of a standardized naming system. \n\n### Select a dataset and cluster","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2225,"value":"viewof dataset = Inputs.select(user.datasets.sort(), {\n label: \"Select a data set\",\n value: \"Actino_Draft\"\n})\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2227,"value":"viewof selectedCluster = Inputs.select(\n clusters.map((cluster) => cluster.name),\n { label: \"Select a cluster\", value: \"Q\" }\n)\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2236,"value":"Plot.plot({\n width: width,\n marginLeft: 250,\n marks: [\n Plot.barX(functionFrequencies, {\n x: \"frequency\",\n y: \"function\",\n fill: \"function\",\n sort: {y: \"x\", reverse: true, limit: 20}\n }),\n Plot.ruleX([0])\n ],\n color: {}\n})\n ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2520,"value":"phams","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2571,"value":"# SVG Files with Phamerator\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2573,"value":"greyscalePhameratorMap_clusterF = FileAttachment(\"Greyscale Phamerator Map_Cluster F.svg\").image()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2575,"value":"greyscalePhameratorMap_clusterQ = FileAttachment(\"Greyscale Phamerator Map_Cluster Q.svg\").image()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3080,"value":"DBclusterFdomains","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1078,"value":"$30","pinned":false,"hidden":false,"mode":"md","author":"$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":"$undefined"},{"id":2262,"value":"# Appendix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2299,"value":"## Protein Function Stuffs","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2230,"value":"clusters = getPhameratorData(dataset, \"/clusters\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2242,"value":"genesByCluster = getPhameratorData(\n dataset,\n `/genesbycluster/${selectedCluster}`,\n user.email,\n user.password\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2240,"value":"genefunctions = genesByCluster\n .filter((gene) => gene.genefunction != \"\")\n .map((gene) => gene.genefunction)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2238,"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":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2293,"value":"## Phamerator API","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1246,"value":"import {\n terms,\n getPhameratorData,\n user,\n formWithSubmit,\n styles\n} with { formData } from \"@scresawn/phamerator-api-utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1250,"value":"import {Plot} from \"@mkfreeman/plot-tooltip\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1264,"value":"styles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W31","stdlib":"1","titling":"auto"}} 2e:"$2d:body"

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