2d:null 2e:["$","title",null,{"children":"PLCO | Jonas Almeida | Observable"}] 33:T49b,plot1 = { let div = DOM.element('div'); let ip = DOM.element('input'); let p = DOM.element('p'); p.innerHTML = 'Chromossome: '; p.appendChild(ip); ip.value = 1; ip.type = 'number'; ip.style.width = '50px'; let divPlot = DOM.element('div'); // plot in this division div.appendChild(divPlot); div.appendChild(p); ip.onchange = _ => { if (ip.value < 1) { ip.value = 1; } else if (ip.value > 22) { ip.value = 22; } else { // prepare plotly let xx = breastCancerEuropean.data.filter(x => x[4] == ip.value); let trace = { x: xx.map(x => parseInt(x[5])), // position y: xx.map(x => parseFloat(x[6])), // -logp mode: 'markers', type: 'scatter', marker: { symbol: 3, size: 5 } }; let layout = { title: `Chromossome ${ip.value}`, xaxis: { title: 'position' }, yaxis: { title: '-log(p)' } }; Plotly.newPlot(divPlot, [trace], layout); } }; ip.onchange(); div.appendChild(p); //div.innerHTML = `# of records: ${breastCancerEastAsia.data.length}`; return div; }34:[] 31:{"id":"28f23c6cbdd8b966","slug":"plco","title":"PLCO","thumbnail":"c74be2da987d4e428f810d4c71ca8a6e7fa2f88d2b0bec922f71e3cece49ee5a","access_level":"public","create_time":"$D2021-02-02T21:36:03.166Z","update_time":"$D2021-12-09T15:56:28.233Z","view_time":null,"first_public_time":"$D2021-02-02T21:36:04.748Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"0f2e596d5bd6ef6e","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":"starter_2024"},"version":233,"publish_version":233,"role":null,"authored":false,"authors":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null}],"members":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":2,"collection":null,"type":"notebook","body":{"title":"PLCO","cells":[{"id":65,"value":"md`\n# PLCO\nExploring DCEG's PLCO project by operating its APIs (for the time being you need to be in NIH's network to access them).\n\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":0,"value":"md`## Breast Cancer\nLet's start by checking the status of the system with a quick call for ${breastCancerEuropean.data.length} variands for breast cancer in east asia women:\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":62,"value":"breastCancerEuropean = (await fetch(\n 'https://exploregwas-dev.cancer.gov/plco-atlas/api/summary?phenotype_id=3080&sex=female&ancestry=european&p_value_nlog_min=2&raw=true'\n)).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":94,"value":"md`### Screening one Chromossome at the time\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":104,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":205,"value":"md`\n## Q&A\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":210,"value":"md`\n### QQPlot - how come for all p's we don't have a lot more values\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"md`\nFor example, for phenotype 3080 (breast cancer), east asian women, we get a maximum of ${breastCancerEastAsian.data.length} datapoints\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":216,"value":"breastCancerEastAsian = (\n await fetch(\n \"https://exploregwas-dev.cancer.gov/plco-atlas/api/summary?phenotype_id=3080&sex=female&ancestry=east_asian&p_value_nlog_min=-10000&raw=true\"\n )\n).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":227,"value":"md`\nBut for the same cohort, in QQ plot at https://exploregwas-dev.cancer.gov/plco-atlas, we only get\n`","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":232,"value":"breastCancerEastAsianQQ = (\n await fetch(\n \"https://exploregwas-dev.cancer.gov/plco-atlas/points?phenotype_id=3080&sex=female&ancestry=east_asian&raw=true\"\n )\n).json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"md`\n## Methods\nStarting with PLCO episphere library.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"//plco = require('http://localhost:8000/plco/plco.js')\nplco = require('https://episphere.github.io/plco/plco.js')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":141,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W34","stdlib":"1","titling":"auto"}} 32:"$31:body"