31:T5a9,getPgsFiles = function(trait){ let traitFilesArr = [] let assocPgsIdsArr = [] // get trait files that match selected trait from drop down traitFiles.filter(tfile => { if(trait.includes(tfile["trait_categories"][0])){ traitFilesArr.push(tfile ) } }) // get pgs scoring files if trait data found, unless type "associated_pgs_ids" if ( traitFilesArr[0]['trait_categories'] != undefined){ var pgsIds = traitFilesArr.flatMap( x => x.associated_pgs_ids).sort().filter((v,i) => traitFilesArr.flatMap( x => x.associated_pgs_ids).sort().indexOf(v) == i) assocPgsIdsArr = scoringFiles.filter(x => pgsIds.includes(x.id)) // } // filter results by number of SNPs var assocPgsIdsArrSubset = assocPgsIdsArr.filter(function (el) { return el.variants_number <= pgsVariantsNumber }); let data = assocPgsIdsArrSubset.map( o => preferredOrder(o,[ "id","trait_efo", "variants_number","weight_type", "trait_reported", "name", "publication", "matches_publication", "samples_variants", "samples_training", "trait_additional", "method_name", "method_params", "variants_interactions", "variants_genomebuild", "ancestry_distribution", "date_release", "ftp_harmonized_scoring_files","ftp_scoring_file", "license"])) // if (data.length == 0){ // data.push({"id":`no pgs files with less than ${pgsVariantsNumber} SNPs`}) // return data // } return data }32:[] 2f:{"title":"PGS_catalog2","cells":[{"id":0,"value":"# PGS_catalog2","pinned":false,"hidden":false,"mode":"md"},{"id":1534,"value":"pgs23 = await import('https://episphere.github.io/diseasome/sdk.js')","pinned":true,"hidden":false,"mode":"ojs"},{"id":751,"value":"pgsVariantsNumber = 2","pinned":true,"hidden":false,"mode":"ojs"},{"id":1673,"value":"{\nvar layout = {\n title: 'Counts of PGS Catalog Scoring Files by Trait',\n margin: {\n l: 250,\n r: 20,\n // t: 100,\n b: 70\n }\n}\nvar data = \n[\n {\n x: traitTotals.map(x=>x.count),\n y: traitTotals.map(x=>x.trait),\n type: 'bar',\n orientation: 'h'\n }\n]\n \n const myDiv = DOM.element(\"div\");\n Plotly.newPlot(myDiv, data, layout);\n return myDiv\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1602,"value":"traitTotals = {\n let traitTotals = []\n let allTraits = Array.from(new Set( traitFiles.flatMap(x => x[\"trait_categories\"]).sort().filter(e => \n e.length).map(JSON.stringify)), JSON.parse)\n let allScores = traits.map( x => getPgsFiles(x)) \n \n allTraits.map(( x, i)=> {\n let counts = {}\n counts[\"trait\"]= x\n counts[\"count\"]= allScores[i].length\n traitTotals.push(counts)\n })\n return traitTotals.sort((a,b) => a.count - b.count)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":998,"value":"## _(1) Filter disease by trait, pgs id, synonym, or mapped terms_","pinned":false,"hidden":false,"mode":"md"},{"id":755,"value":"Trait_synonyms and trait_mapped_terms are not as comprehensive (not available for all PGS scores)","pinned":false,"hidden":false,"mode":"md"},{"id":8,"value":" viewof trait = Inputs.select(\n Array.from(new Set( traitFiles.flatMap(x => x[\"trait_categories\"]).sort().filter(e => e.length).map(JSON.stringify)), JSON.parse)\n , {width: 620, value: \"Cancer\", label: \"Select trait\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1576,"value":"### `Found ${tableData.length} PGS catalog scoring files with =< ${pgsVariantsNumber} for ${trait}!`","pinned":false,"hidden":false,"mode":"md"},{"id":403,"value":"viewof pgs = Inputs.table(tableData , {value: tableData.filter((_, i) => [0,1].includes(i)),multiple: true,required: false},)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1591,"value":"tableData = getPgsFiles(trait)","pinned":true,"hidden":false,"mode":"ojs"},{"id":1113,"value":"$${textcolor(\"PGS ids matching selected trait categories: \", d3.schemeTableau10[3])}","pinned":false,"hidden":false,"mode":"md"},{"id":681,"value":"pgsIds = pgs.map(x => x.id)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1013,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":1003,"value":"## _(2) Or filter by The Experimental Factor Ontology Term ([EFO](https://www.ebi.ac.uk/efo/)) _","pinned":false,"hidden":false,"mode":"md"},{"id":1011,"value":"consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabularies.","pinned":false,"hidden":false,"mode":"md"},{"id":1015,"value":"viewof disease_ontology_term = Inputs.select(\n //efoIds from pgs catalog scoring files only\n scoringFilesEfoIds, {value: \"EFO:0000712\", width: 620, label: \"Select by EFO term\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":1185,"value":"$${textcolor(\"PGS ids matching selected EFO term: \", d3.schemeTableau10[3])}","pinned":false,"hidden":false,"mode":"md"},{"id":1312,"value":"viewof pgs2 = Inputs.table(tableDataEfo , {value: tableDataEfo.filter((_, i) => [0,1,4].includes(i)),multiple: true,required: false},)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1322,"value":"pgsIds2 = pgs2.map(x => x.id)","pinned":true,"hidden":false,"mode":"ojs"},{"id":1164,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":1200,"value":"### TODO: ","pinned":false,"hidden":false,"mode":"md"},{"id":1707,"value":"Get efos, with names and make bar plot of counts like with trait names","pinned":false,"hidden":false,"mode":"md"},{"id":1522,"value":"//in first selection, fixed trait drop down, but synonym breaks sometimes (old version below with map, not flatMap)\n // viewof trait = Inputs.select(\n // Array.from(new Set( traitFiles.map(x => x[type]).sort().filter(e => e.length).map(JSON.stringify)), JSON.parse)\n // , {width: 620, value: \"Cancer\", label: \"Select trait\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1161,"value":"$${textcolor(\"(1) filter efo terms without a pgs match, (2) edit the file to address scorefiles and efo terms with 2 terms and (3) get more efo terms (>4,000)\", d3.schemeTableau10[2])}","pinned":false,"hidden":false,"mode":"md"},{"id":1203,"value":"includesBlanckOntologyTerms = ontologyTerms._embedded.terms.map(x => x.obo_id).sort() // only 1,000 terms out of 4,000","pinned":true,"hidden":false,"mode":"ojs"},{"id":996,"value":"pgsWithtwoOrMoreEfos = scoringFiles.filter(file=> file.trait_efo.length > 1)","pinned":true,"hidden":false,"mode":"ojs"},{"id":690,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":18,"value":"## Appendix","pinned":false,"hidden":false,"mode":"md"},{"id":1671,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":1174,"value":"function textcolor(content, style = {}) {\n function yiq(color) {\n const {r, g, b} = d3.rgb(color);\n return (r * 299 + g * 587 + b * 114) / 1000 / 255; // returns values between 0 and 1\n }\n const {\n background,\n color = yiq(background) >= 0.6 ? \"#111\" : \"white\", \n padding = \"0 5px\",\n borderRadius = \"4px\",\n fontWeight = 800,\n ...rest\n } = typeof style === \"string\" ? {background: style} : style;\n return htl.html`${content}`;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1584,"value":"traits = Array.from(new Set( traitFiles.flatMap(x => x[\"trait_categories\"]).sort().filter(e => e.length).map(JSON.stringify)), JSON.parse)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1035,"value":"d3 = require('d3')","pinned":false,"hidden":false,"mode":"ojs"},{"id":1023,"value":"import {fetchp} from \"@tomlarkworthy/fetchp\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":518,"value":"async function fetchAll2(url, maxPolls = null) {\n const allResults = []\n\n if (maxPolls == null) maxPolls = Infinity\n \n for (let i = 0; i < maxPolls; i++) {\n const offset = i * 100\n let queryUrl = `${url}?limit=100&offset=${offset}`\n \n const results = (await (await fetch(queryUrl)).json()).results\n results.forEach(result => allResults.push(result))\n \n if (results.length < 100) {\n break \n }\n }\n return allResults\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1066,"value":"async function fetchAllOntology(url, maxPolls = null) {\n const allResults = []\n\n if (maxPolls == null) maxPolls = Infinity\n \n for (let i = 0; i < maxPolls; i++) {\n const offset = i * 500\n let queryUrl = `${url}?limit=500&offset=${offset}`\n \n const results = (await (await fetchp(queryUrl)).json()).results\n results.forEach(result => allResults.push(result))\n \n if (results.length < 10000) {\n break \n }\n }\n \n return allResults\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1078,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":73,"value":"traitCount= await (await(fetch('https://www.pgscatalog.org/rest/trait/all'))).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":525,"value":"traitFiles = fetchAll2('https://www.pgscatalog.org/rest/trait/all')","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"scoresCount = (await (await fetch('https://www.pgscatalog.org/rest/score/all')).json())","pinned":false,"hidden":false,"mode":"ojs"},{"id":522,"value":"scoringFiles = fetchAll2('https://www.pgscatalog.org/rest/score/all')","pinned":false,"hidden":false,"mode":"ojs"},{"id":817,"value":"function preferredOrder(obj, order) {\n var newObject = {};\n for(var i = 0; i < order.length; i++) {\n if(obj.hasOwnProperty(order[i])) {\n newObject[order[i]] = obj[order[i]];\n //console.log(obj[order[i]])\n }\n }\n return newObject;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1586,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":1400,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":1402,"value":"_Get unique EFOs from PGS catalog scoring files_","pinned":false,"hidden":false,"mode":"md"},{"id":1059,"value":"ontologyTerms = await (await(fetch('https://www.ebi.ac.uk/ols/api/ontologies/efo/terms?page=1&size=2000'))).json()//await (await(fetchp('https://www.ebi.ac.uk/ols/api/ontologies/efo'))).json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":1361,"value":"scoringFilesEfoIds = [...new Set(scoringFiles.flatMap(x => x.trait_efo.map(y=> {return y.id.replace(/_/g,':')})).sort())]\n// ontologyTermsEfoIds = ontologyTerms[\"_embedded\"][\"terms\"].map(x => x.obo_id).sort()","pinned":true,"hidden":false,"mode":"ojs"},{"id":1412,"value":"_Return PGS scoring files from selected drop down EFO id_","pinned":false,"hidden":false,"mode":"md"},{"id":1103,"value":" tableDataEfo = {\n let ids = []\n scoringFiles.flatMap((x,i) => x.trait_efo.map(pgs=>{\n if(pgs.id===disease_ontology_term.replace(/:/g,'_')){ids.push(x)\n }}))\nlet data = ids.map( o => \npreferredOrder(o,[\"id\",\"variants_number\",\"trait_reported\",\"name\",\"ftp_scoring_file\",\"ftp_harmonized_scoring_files\",\"publication\",\"matches_publication\",\"samples_variants\",\"samples_training\",\"trait_additional\",\"trait_efo\",\"method_name\",\"method_params\", \"variants_interactions\",\"variants_genomebuild\",\"weight_type\",\"acestry_distribution\",\n\"date_release\",\"license\"])).filter(function (el) {\n return el.variants_number <= pgsVariantsNumber\n})\n if (data.length == 0){\n data.push({\"id\":`no pgs files with less than ${pgsVariantsNumber} SNPs`})\n return data\n }\n return data\n }","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}