Published
Edited
Oct 25, 2019
md`### Ki Oh
#### This Observable Notebook is a documentation of the progress in this project`
md `### Load other people's modules`
projectData_ugly=(await fetch('https://api.gdc.cancer.gov/projects?fields=disease_type,name,program.name,project_id,summary.case_count&from=0&size=1000&sort=disease_type:asc')).json()
betterFetch = async function(url,body) {
let fetchData = {
method: 'POST',
body: JSON.stringify(body),
headers:{'Content-Type':'application/json'}
}
let tmpData=(await fetch(url, fetchData)).json()
return(tmpData)
}
projectData = {
let url = 'https://api.gdc.cancer.gov/projects'
let body = ({
'fields': "disease_type,name,program.name,project_id,summary.case_count",
'from': 0,
'size': 1000
})
return(await betterFetch(url,body))
}
getCaseCounts = function(projectData) {
let caseCounts=[];
projectData.data.hits.forEach(function(prj,i){
// for each hit (project)
caseCounts = caseCounts.concat({
"label" : prj.id,
"y" : prj.summary.case_count,})
})
return caseCounts
};
getSortedHistData = function(hitdata) {
let histData={}
hitdata.map(x=>{
if(!histData[x]){
histData[x]=0
}
histData[x]+=1
})
let histSorted = Object.keys(histData)
.sort(function(a,b){return histData[b]-histData[a]})
.reduce(function (acc, key) {
acc[key] = histData[key];
return acc;
}, {})
return(histSorted)
}
PrintTCGA = function(projectData) {
let div = DOM.element('div') // set up the main object
div.innerHTML='<h3 style="color:green">TCGA Project types in GDC (<span id="caseCountSpan"></span>)</h3>'
let ol=DOM.element('ol') // set up the sub-object which will contain our data
div.appendChild(ol)
let caseCount=0
projectData.data.hits.forEach(function(prj,i){
// for each hit (project)
if ((/TCGA/.test(prj.id))) {
//if (true) {
let li = DOM.element('li') // build up the header "li"
li.innerHTML=`<b style="color:blue">${prj.id}</b>: ${prj.name}
(<span style="color:green">${prj.summary.case_count}</span>)`
caseCount=caseCount+prj.summary.case_count
ol.appendChild(li) // append the header "li" to the larger object "ol"
let ul = DOM.element('ul') // build up the bullets "ul"
prj.disease_type.forEach(function(dtp){
// for each disease_type
let li = DOM.element('li')
li.style.fontSize='small'
li.innerHTML=dtp
ul.appendChild(li) // append one bullet "li" to the list of bullets "ul"
})
li.appendChild(ul) // append the bullets "ul" to the header "li"
}
})
div.querySelector('#caseCountSpan').textContent=caseCount
return div
};
caseCounts = getCaseCounts(projectData)
{
let plotData = {
labels: caseCounts.map(x=>x["label"]),
values: caseCounts.map(x=>x["y"]),
type: 'pie',
}
let layout = {
autosize:true
}
const div = DOM.element('div')
Plotly.newPlot(div, [plotData],layout);
return div
}
Plotly = require("https://cdn.plot.ly/plotly-latest.min.js")
require('@oncojs/lolliplot')
hosturl = 'https://firebrowse.herokuapp.com'
endpointurl = "http://firebrowse.org/api/v1/Samples/mRNASeq"
queryJSON = {
let queryJSON = {
format: 'json',
gene: 'PSCA',
cohort: 'BLCA',
protocol: 'RSEM',
page: 1,
page_size: 250,
sort_by: 'cohort'
}
return queryJSON
}
queryurl = "format=json&gene=PSCA&cohort=BLCA&protocol=RSEM&page=1&page_size=250&sort_by=cohort"
queryurl =jq.param(queryJSON)
One platform to build and deploy the best data apps
Experiment and prototype by building visualizations in live JavaScript notebooks. Collaborate with your team and decide which concepts to build out.
Use Observable Framework to build data apps locally. Use data loaders to build in any language or library, including Python, SQL, and R.
Seamlessly deploy to Observable. Test before you ship, use automatic deploy-on-commit, and ensure your projects are always up-to-date.