2a:null 2b:["$","title",null,{"children":"PLCO SDK | ericr491 | Observable"}] 30:[] 2e:{"id":"31136e94f9770207","slug":"plco-sdk","title":"PLCO SDK","thumbnail":"a903014eb1b79ceb84ea2ad78bc08e2c7194701a1c2d0964a5456176fc050537","access_level":"public","create_time":"$D2021-06-28T22:34:38.994Z","update_time":"$D2021-08-06T22:57:51.138Z","view_time":null,"first_public_time":"$D2021-06-28T22:38:58.817Z","fork":{"id":"b238d7cb4c1c7dbf","slug":"plco-sdk","title":"PLCO SDK","owner":{"id":"be31c14f0c46ba8e","login":"enemeth19","name":"Erika Nemeth"}},"stars":2,"starred":false,"owner":{"type":"team","id":"7e9c6da13068e72e","login":"ericr491","name":"","avatar_url":"https://avatars-next.observableusercontent.com/65ad77edc5b17fcf3050d9c0fde39324d5b7612c94f589f54fc3dcab21b2a864","tier":"starter_2024"},"version":620,"publish_version":620,"role":null,"authored":false,"authors":[{"type":"individual","id":"cd3a30e19baa6e8f","login":"ericr491","name":"","avatar_url":"https://avatars-next.observableusercontent.com/65ad77edc5b17fcf3050d9c0fde39324d5b7612c94f589f54fc3dcab21b2a864","tier":null}],"members":[{"type":"individual","id":"cd3a30e19baa6e8f","login":"ericr491","name":"","avatar_url":"https://avatars-next.observableusercontent.com/65ad77edc5b17fcf3050d9c0fde39324d5b7612c94f589f54fc3dcab21b2a864","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"PLCO SDK","cells":[{"id":0,"value":"html`\n

PLCO SDK

\nA notebook to accompany our development of an SDK for usage of the PLCO API\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":240,"value":"html`\n

Step 0: Load SDK on your webpage.

If you want to use the SDK on webpage, simply add in the following in your html file.

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":264,"value":"''","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":100,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":45,"value":"html`\n

Step 1: Load SDK

First, let's load plco.js, a JS file contained in our GitHub repo

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":28,"value":"plco = require('https://episphere.github.io/plco/plco.js')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":421,"value":"md`Next, let's check if our dependicies are loaded in!`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":424,"value":"Plotly = plco.Plotly","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":426,"value":"localforage = plco.localForage","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":159,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":137,"value":"html`\n

Step 2: Check if API service is available

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":93,"value":"html`\n

ping

\nRetrieve status of API service\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":14,"value":"await plco.api.ping()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":151,"value":"html`\n

If response is \"true\", then we may proceed in using the SDK to retrieve data from the PLCO API

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":162,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":155,"value":"html`\n

Step 3: Browse data via the PLCO API

Example values are passed as arguments to each function below

Note: Any bolded blue text indicates an API endpoint term

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":82,"value":"html`\n

download

\nDownload the original association results for a phenotype\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":131,"value":"//await plco.api.download(\"phenotype_id:3080\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":165,"value":"html`\n

metadata

\nRetrieve metadata about each phenotype specified\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":168,"value":"await plco.api.metadata({ phenotype_id: 3080, sex: \"female\", ancestry: \"european\" })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":173,"value":"html`\n

participants

\nRetrieve single phenotype's aggregated participant data\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":176,"value":"await plco.api.participants({phenotype_id: 2250})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":555,"value":"html`\n

phenotypes

\nRetrieves a list of all phenotypes available\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":558,"value":"await plco.api.phenotypes()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":180,"value":"html`\n

summary

\nRetrieves variants for all chromosomes at a resolution of 400x800 bins across the entire genome and -log10(p) range. Each bin can contain multiple variants.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":185,"value":"await plco.api.summary({ phenotype_id: 3080, sex: \"female\", ancestry: \"european\", p_value_nlog_min: 4 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":187,"value":"html`\n

variants

\nRetrieves a list of variants by phenotype ID\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":200,"value":"await plco.api.variants({ phenotype_id: 3080, sex: \"female\", ancestry: \"european\", chromosome: 8, p_value_nlog_min: 4, limit: 10 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":79,"value":"html`\n

Some helper functions

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":70,"value":"await plco.api.get(\"metadata?phenotype_id=3080\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":73,"value":"await plco.api.parms2string()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":227,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":444,"value":"html`\n

Step 3.5: Explore phenotypes id

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":448,"value":"phenotypesData = await plco.explorePhenotypes(true)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":452,"value":"Fuse = require('https://cdn.jsdelivr.net/npm/fuse.js@6.4.6')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":457,"value":"html`Using Fuse.js to search through available phenotypes by name.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":463,"value":"fuse = new Fuse(phenotypesData, { keys: ['display_name'] })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":522,"value":"inputElement = {\n y;\n return document.getElementById(\"input\");\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":505,"value":"(inputElement.onchange = (e) =>\n (document.getElementById(\"paragraph\").innerHTML = JSON.stringify(\n fuse\n .search(inputElement.value)\n .slice(0, 8)\n .map(({ item }) => ({\n id: item.id,\n name: item.name,\n display_name: item.display_name,\n import_count: item.import_count\n }))\n )))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":551,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined"},{"id":548,"value":"html`Type out the name of the phenotype that you are looking for in the text box and hit ENTER
Please note that phenotypes with 'import_count' of null indiciates there are no data currently available for plotting.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":482,"value":"y = html`\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":509,"value":"html`

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":212,"value":"html`\n

Step 4: Browse data via pre-made plots

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":585,"value":"md`\n#### After changing the values below, please re-run the respective cells to update the values!\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":278,"value":"x = html`\n Select a phenotype_id.\n \n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":292,"value":"html`\n Select a sex.\n \n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":295,"value":"html`\n Select a ancestry.\n \n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":301,"value":"selectElements = {\n x;\n return document.getElementsByTagName('select');\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":577,"value":"phenotype_id = {\n x;\n return Number.parseInt(document.getElementById(\"select-phenotype-id\").value);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":317,"value":"sex = selectElements[0].value","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":335,"value":"ancestry = selectElements[1].value","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":298,"value":"html`\n

qqPlot

\n Quartile-quartile plot\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":342,"value":"qqPlotObj = await plco.plot.qq(\"qq\", phenotype_id, sex, ancestry, false)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":360,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":365,"value":"html`\n

pcaPlot

\n PCA plot\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":368,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":371,"value":"pcaObj = await plco.plot.pca(\"pca\", phenotype_id, sex, ancestry, false)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":386,"value":"html`\n

manhattanPlot

\n Manhattan plot\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":391,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":393,"value":"manhatObj = await plco.plot.manhattan(\n \"manhattan\",\n phenotype_id,\n sex,\n ancestry,\n 2,\n undefined,\n false\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":600,"value":"html`\n

Step 5: Use custom HTML elements to simplify plotting

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":605,"value":"plcoCustomEle = require(\"https://episphere.github.io/plco/plcoHTMLElements.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":616,"value":"You may need to zoom out to see the whole plot.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":607,"value":"","pinned":true,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2f:"$2e:body"