3e:null 3f:["$","title",null,{"children":"A Comparative Analysis of Protein and Domain Conservation within Cluster Q Genomes | Isobel Cobb | Observable"}] 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43:{"id":"d88a20407fb97991","slug":null,"title":"A Comparative Analysis of Protein and Domain Conservation within Cluster Q Genomes","thumbnail":"943bb8d41e7de4f2491e390ea40fe6815c7acd351f0194bb61b5e944fb9ecc45","access_level":"public","create_time":"$D2023-04-03T13:46:51.787Z","update_time":"$D2023-04-23T02:04:17.082Z","view_time":null,"first_public_time":"$D2023-04-03T13:46:51.787Z","has_unpublished_edits":null,"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":"3e2509283042eb59","login":"icobb","name":"Isobel 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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"}],"comments":[{"id":"20ad4996e0712cd1","reply_to_id":null,"content":"This is a test to look at the x axis and load the SVG","create_time":"$D2023-04-03T15:06:10.432Z","update_time":null,"resolved":true,"user":{"type":"individual","id":"2d6b5bbb66e9af61","login":"icobb","name":"Isobel Cobb","avatar_url":"https://avatars-next.observableusercontent.com/7b05262d8809fccadb2a7d8df2214cd26ac3ad57393de009a985fb8257469bfe","tier":null}},{"id":"ec2d8e20a003d04f","reply_to_id":null,"content":"This is the same thing as above, it just has the x-axis showing and the X and Y axis are flipped.","create_time":"$D2023-04-03T15:06:49.475Z","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}}],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"A Comparative Analysis of Protein and Domain Conservation within Cluster Q Genomes","cells":[{"id":47,"value":"# A Comparative Analysis of Protein and Domain Conservation within Cluster Q Genomes ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2757,"value":" ## Abstract \nBacteriophage 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.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$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","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2243,"value":"# Domains+Genes+Phams Combined with SQL\n\n**Description:** You can use these tables to match the phams that are unique to each cluster to their annotated gene function and conserved domains. You can also see the frequency of a pham in within the phages of the cluster. \n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2342,"value":"## Cluster Q Phams, Genes, and Domains","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2696,"value":"SELECT DISTINCT phamName, genefunction, PhamFrequency FROM clusterQgenes\nINNER JOIN QfunctionFrequencies\n ON clusterQgenes.genefunction = QfunctionFrequencies.QFunction\nINNER JOIN QphamsFrequencies\n ON clusterQgenes.phamName = QphamsFrequencies.Qpham\nORDER BY phamName","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"ClusterQGDF_Table","database":"var:DBClusterQ_PFDG"},{"id":3143,"value":"Sunburst(dataFlare, {\n // path: (d) => d.name, // e.g. flare/animate/Easing\n label: (d) => d.name, // display text\n value: (d) => d?.value, // angle of each arc\n title: (d, n) => [n.id, n.value.toLocaleString()].join(\"\\n\"), // hover text\n width: 1500,\n height: 1500\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":3303,"value":"**Figure 1.** This is a sunburst diagram that displays phamilies that are unique to cluster Q in the center ring and annotated gene function on the outer ring. This figure displays a serious issue with the Actinobacteriophage Database when it comes to phage genome annotation. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2740,"value":"## Cluster F Phams, Genes, and Domains","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2614,"value":"SELECT phamName, genefunction, PhamFrequency FROM clusterFgenes\nINNER JOIN FFunctionFrequencies\n ON clusterFgenes.genefunction = FFunctionFrequencies.Ffunction\nINNER JOIN FphamsFrequencies\n ON clusterFgenes.phamName = FphamsFrequencies.Fpham\nORDER BY phamName","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"ClusterFGDF_Table","database":"var:DBClusterF_PFDG"},{"id":3216,"value":"SELECT DISTINCT phamName, PhamFrequency, genefunction FROM clusterFgenes\nINNER JOIN FFunctionFrequencies\n ON clusterFgenes.genefunction = FFunctionFrequencies.Ffunction\nINNER JOIN FphamsFrequencies\n ON clusterFgenes.phamName = FphamsFrequencies.Fpham\nORDER BY phamName","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"ClusterFGDF_Table2","database":"var:DBClusterF_PFDG"},{"id":3344,"value":"SELECT DISTINCT phamName, PhamFrequency FROM clusterFgenes\n\nINNER JOIN FphamsFrequencies\n ON clusterFgenes.phamName = FphamsFrequencies.Fpham\nORDER BY phamName","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"ClusterFGDF_Table1","database":"var:DBClusterF_PFDG"},{"id":3223,"value":"Sunburst(dataFlare2, {\n // path: (d) => d.name, // e.g. flare/animate/Easing\n label: (d) => d.name, // display text\n value: (d) => d?.value, // angle of each arc\n title: (d, n) => [n.id, n.value.toLocaleString()].join(\"\\n\"), // hover text\n width: 1600,\n height: 1600\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2743,"value":"## Cluster Q Combined Data Tables\n**Description:** This will have everything from the gene, phamily, and domain tables.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2331,"value":"SELECT * FROM phams, clusterQgenes, clusterqdomains \n WHERE phams.PhamID = clusterQgenes.phamName \n AND clusterqdomains.geneID = clusterQgenes.geneID;","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"clusterQcombined_SQL","database":"var:combinedDB"},{"id":2747,"value":"## Cluster F Combined Data Tables\n**Description:** This will have everything from the gene, phamily, and domain tables.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2349,"value":"SELECT * FROM clusterFphams, clusterFgenes, clusterfdomains \n WHERE clusterFphams.PhamilyName = clusterFgenes.phamName \n AND clusterfdomains.geneID = clusterFgenes.geneID ","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"clusterFcombined_SQL","database":"var:combinedDB"},{"id":2750,"value":"# Shared Phams in both Q and F\n**Description:** The first table lists the phams that are seen in both Q and F. The second table shows the functions of these phams.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3117,"value":"SELECT * FROM phams \n INNER JOIN clusterFphams\n ON phams.phamID = clusterFphams.PhamilyName\n INNER JOIN clusterQphams \n ON phams.phamID = clusterQphams.PhamilyName","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"SharedPhamsInQandF_SQL","database":"var:combinedDB"},{"id":2471,"value":"SELECT DISTINCT phamID, clusterFgenes.geneFunction AS FGeneFunc, clusterQgenes.geneFunction AS QGeneFunc, FROM phams \nINNER JOIN clusterFphams\nON phams.phamID = clusterFphams.PhamilyName\nINNER JOIN clusterQphams \nON phams.phamID = clusterQphams.PhamilyName\nINNER JOIN clusterQgenes\nON phams.PhamID = clusterQgenes.phamName\nINNER JOIN clusterFgenes\nON phams.PhamID = clusterFgenes.phamName\nWHERE FGeneFunc != '' and QGeneFunc != '';","pinned":false,"hidden":false,"mode":"sql","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"SharedPhamFunctions_SQL","database":"var:combinedDB"},{"id":2303,"value":"# Pham Bubble Charts\n_ **Interpreting These Figures:** These are bubble charts for phamilies that are unique to Cluster Q and Cluster F. The top number inside the bubble represents the phamily name and the bottom number represents the number of genes in that phamily. Smaller bubbles indicate a small group of genes that make up the phamiliy and large bubbles indicate a higher number of genes in the phamily. The color is associated with the pham in Phamerator. _\n\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2306,"value":"clusterfbubblechart = FileAttachment(\"ClusterFBubbleChart.png\").image()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2308,"value":"** Figure 4.** Cluster F contains 218 phages that are typically 104.2 genes in length. Due to it's large sample size and larger genome, it makes sense that there is a larger number of phamilies that are unique to cluster F phages.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2357,"value":"clusterqphambubblechart = FileAttachment(\"ClusterQPhamBubbleChart.png\").image()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2355,"value":"** Figure 4.** Cluster Q contains 21 phages with an average genome length of 81 genes. This cluster contains a smaller amount of phamilies that are unique to it which is synonymous with a smaller genome. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1424,"value":"# Comparing Domains in Cluster F and Q\n**Description:** The following bar charts display the conserved domains on the y axis and the phageID on the x axis. The point of these charts are to help visualize how often a conserved domain shows up in either a cluster Q or cluster F phage. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3070,"value":"**_set height to 3500 to bring back normal size_**","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1068,"value":"Plot.plot({\n marginLeft: 150,\n width: 2000,\n height: 400,\ncolor: {\n legend: true\n },\n marks: [\n Plot.auto(clusterQandFdomains, {x: \"phageID\", y: \"domainname\", color: \"cluster\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1430,"value":"# Cluster F Bar Chart","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3043,"value":"**_delete the height constraints to make it the right size (this is just so it's easier to scroll through the document)_**","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3050,"value":"Plot.plot({\n width: 1500,\n height: 400,\ncolor: {\n legend: true\n },\n marks: [\n Plot.auto(clusterfdomains, {x: \"phageID\", y: \"domainname\", color: \"cluster\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2541,"value":"** Figure 2. ** This bar chart displays the cluster F phageID on the X axis and the conserved domain name on the Y axis. This figure shows what conserved domains are conserved in all cluster F phages and what conserved domains are not. This can help us determine which conserved domains and associated genes we should focus on to determine if they are an essential component of what makes this a functional cluster F phage. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1506,"value":"# Cluster Q Bar Chart ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3041,"value":"**_delete the height constraints to make it the right size (this is just so it's easier to scroll through the document)_**","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1505,"value":"Plot.plot({\n marginLeft: 150,\n width: 1200,\n height: 400,\nmarks: [\n Plot.auto(clusterqdomains, {x: \"phageID\", y: \"domainname\", color: \"#ff8c38\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2544,"value":"** Figure 3. ** This bar chart displays the cluster F phageID on the X axis and the conserved domain name on the Y axis. This figure shows what conserved domains are conserved in all cluster Q phages and what conserved domains are not. This chart shows us that the majority of conserved domains in cluster Q are conserved in every cluster Q phage, and therefore essential to what makes each phage a functional cluster Q phage. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2319,"value":"# Phamerator Genome Maps\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2291,"value":"clusterF_greyscalePhameratorMap = FileAttachment(\"Cluster F_Greyscale Phamerator Map.svg\").image()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2293,"value":"** Figure 5. ** This is a greyscale Phamerator genome map that indicates phamily abundance in Cluster F phages (does not show all phages). The genes are color coded by phamily abundance where darker grey indicates a higher phamily abundance and lighter grey indicates a low phamily abundance. Phamily abundance means the number of genes that are in a phamily. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2260,"value":"# Protein Function Bar Chart","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2280,"value":"**Description.** You are now viewing a graph of the top 20 protein functions in cluster _${selectedCluster}_ phages. Be aware that some functions may be listed multiple times due to inconsistent data entry and lack of a standardized naming system. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2264,"value":"### Select a dataset and cluster ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2262,"value":"viewof dataset = Inputs.select(user.datasets.sort(), {\n label: \"Select a data set\",\n value: \"Actino_Draft\"\n})\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2266,"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","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2274,"value":"Plot.plot({\n width: width,\n marginLeft: 250,\n marks: [\n Plot.barX(functionFrequencies, {\n x: \"frequency\",\n y: \"function\",\n fill: \"frequency\",\n sort: {y: \"x\", reverse: true, limit: 20},\n stroke: \"frequency\",\n title: (d) => `${d.frequency}`\n }),\n Plot.ruleX([0])\n ],\n \n color: { scheme: \"Purples\" }\n})\n ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":3283,"value":"**Figure 3.** This is a bar chart of the top 20 protein functions and their frequency in _cluster ${selectedCluster}_ phages.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1839,"value":"# Appendix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2722,"value":"## Database Information\n* _PFDG means Pham, Function, Domain, Gene_\n* _combinedDB is almost all of our tables_","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2653,"value":"DBClusterF_PFDG = DuckDBClient.of({ clusterFphams, FfunctionFrequencies, clusterfdomains, clusterFgenes, FphamsFrequencies})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2714,"value":"DBClusterQ_PFDG = DuckDBClient.of({ clusterQphams, QfunctionFrequencies, clusterqdomains, clusterQgenes, QphamsFrequencies})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2207,"value":"combinedDB = DuckDBClient.of({ clusterFgenes, clusterfdomains, clusterQgenes, clusterqdomains, clusterQphams, clusterFphams, phams, FfunctionFrequencies, clusterQandFdomains})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2566,"value":"## Domain Data\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3,"value":"clusterfdomains = FileAttachment(\"clusterFdomains.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"clusterqdomains = FileAttachment(\"clusterQdomains.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1087,"value":"clusterQandFdomains = clusterfdomains.concat(clusterqdomains)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2502,"value":"## Cluster Q and F Phams and Genes for All Above Tables\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","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":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$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","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1282,"value":"clusterQphams = Array.from(new Set(clusterQgenes.map(d => +d.phamName))).map(d => {return {\"PhamilyName\": d}})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$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","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$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":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2598,"value":"clusterFfunctions = clusterFgenes\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":"$undefined"},{"id":2687,"value":"clusterQfunctions = clusterQgenes\n.filter((gene)=> gene.genefunction != \"\")\n.map((gene) => gene.genefunction)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2604,"value":"FfunctionFrequencies = {\n const counts = {};\n\n for (const clusterFfunction of clusterFfunctions) {\n counts[clusterFfunction] = counts[clusterFfunction] ? counts[clusterFfunction] + 1 : 1;\n }\n return Object.entries(counts).map((e) => {\n return { Ffunction: 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":"$undefined"},{"id":2691,"value":"QfunctionFrequencies = {\n const counts = {};\n\n for (const clusterQfunction of clusterQfunctions) {\n counts[clusterQfunction] = counts[clusterQfunction] ? counts[clusterQfunction] + 1 : 1;\n }\n return Object.entries(counts).map((e) => {\n return {Qfunction: e[0], frequency: e[1] };\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2868,"value":"clusterFphamFreqs = clusterFgenes\n.filter((pham)=> pham.phamName != \"\")\n.map((pham) => pham.phamName)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2871,"value":"FphamsFrequencies = {\n const counts = {};\n\n for (const clusterFphamFreq of clusterFphamFreqs) {\n counts[clusterFphamFreq] = counts[clusterFphamFreq] ? counts[clusterFphamFreq] + 1 : 1;\n }\n return Object.entries(counts).map((e) => {\n return { Fpham: e[0], PhamFrequency: e[1] };\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2892,"value":"clusterQphamFreqs = clusterQgenes\n.filter((pham)=> pham.phamName != \"\")\n.map((pham) => pham.phamName)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2896,"value":"QphamsFrequencies = {\n const counts = {};\n\n for (const clusterQphamFreq of clusterQphamFreqs) {\n counts[clusterQphamFreq] = counts[clusterQphamFreq] ? counts[clusterQphamFreq] + 1 : 1;\n }\n return Object.entries(counts).map((e) => {\n return {Qpham: e[0], PhamFrequency: e[1]};\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2987,"value":"## Sunburst","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3145,"value":"dataFlare = ({\n name: \"Phamilies In Cluster Q\",\n children: d3\n .groups(ClusterQGDF_Table , (d) => d.phamName)\n .map((d) => {\n return {\n name: d[0],\n // value: 1\n children: d[1].map((e) => {\n return { name: e.genefunction.replaceAll(\"-\", \"_\"), value: e.PhamFrequency };\n })\n };\n })\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":3213,"value":"dataFlare2 = ({\n name: \"Phamilies In Cluster F\",\n children: d3\n .groups(ClusterFGDF_Table2 , (d) => d.phamName)\n .map((d) => {\n return {\n name: d[0],\n // value: 1\n children: d[1].map((e) => {\n return { name: e.genefunction.replaceAll(\"-\", \"_\"), value: e.PhamFrequency };\n })\n };\n })\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2250,"value":"## Cluster Information for Protein Function Graph\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2252,"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":"$undefined"},{"id":2254,"value":"genesByCluster = getPhameratorData(\n dataset,\n `/genesbycluster/${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":"$undefined"},{"id":2256,"value":"genefunctions = genesByCluster\n .filter((gene) => gene.genefunction != \"\")\n .map((gene) => gene.genefunction)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2258,"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":"$undefined"},{"id":2248,"value":"## Phamerator API","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$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":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1250,"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":"$undefined"},{"id":1264,"value":"styles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":3005,"value":"import {Sunburst} from \"@d3/sunburst\"","pinned":true,"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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