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serohub.mjs
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serohub.mjs
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function saveFile(txt=':-)',fileName="hello.txt") { // x is the content of the file
var bb = new Blob([txt]);
var url = URL.createObjectURL(bb);
var a = document.createElement('a')
a.href=url;
if (fileName){
if(typeof(fileName)=="string"){ // otherwise this is just a boolean toggle or something of the sort
a.download=fileName;
}
a.click() // then download it automatically
}
return a
}
console.log(`seroHub ES6 module imported at,\n${Date()}`)
let Plotly
/*
try{
Plotly = (await import("https://esm.sh/[email protected]")).default
} catch(err){
Plotly = await require("https://cdn.plot.ly/plotly-2.34.0.min.js")
}
*/
if(typeof(define)=='undefined'){
Plotly = (await import("https://esm.sh/[email protected]")).default
}else{
define(['https://cdn.plot.ly/plotly-2.34.0.min.js'],[function(mod){Plotly=mod}])
}
console.log(`ploting with`,Plotly)
//const Plotly = (await import("https://episphere.github.io/plotly/esm.mjs")).esm
const localForage = (await import('https://esm.run/[email protected]/src/localforage.js')).default
const url = 'https://episphere.github.io/serohub/seroprevalence.json.zip'
let seroHub={
loadedAt:Date(),
loadedFrom:url,
Plotly:Plotly
}
let dt = await localForage.getItem('seroHub_Prevalence')
//if(true){
if(!dt){
const loadZip = (await import('https://episphere.github.io/serohub/loadZip.mjs'))
dt = await loadZip.loadZippedFiles(url)
localForage.setItem('seroHub_Prevalence',dt)
}
seroHub.seroprevalence=dt['seroprevalence.json']
// add row number
seroHub.seroprevalence.seroprevalences.forEach((x,i)=>{seroHub.seroprevalence.seroprevalences[i].row=i+1})
// list variables
seroHub.variables = Object.keys(seroHub.seroprevalence.seroprevalences[0])
// extract values of an attribute
seroHub.values=function(variable='age'){
if(typeof(variable)=='number'){
variable = seroHub.variables[variable]
}
console.log(`reading variable "${variable}"`)
return seroHub.seroprevalence.seroprevalences.map(row=>row[variable])
}
// unique values for a variable
seroHub.uniqueValues=function(variable='age'){
if(typeof(variable)=='number'){
variable = seroHub.variables[variable]
}
console.log(`unique values for "${variable}"`)
return [... new Set(seroHub.seroprevalence.seroprevalences.map(row=>row[variable]))]
}
// Plots
seroHub.plotSeroprevalence=function(div=seroHubDiv){ // values vs time
if(!div){
div = document.createElement('div')
document.body.appendChild(div)
}
console.log('ploting at ',div)
// start and end of each collection
// let xx = seroHub.seroprevalence.seroprevalences.map(x=>[Date.parse(x.collection_start),Date.parse(x.collection_end)])
let xx = seroHub.seroprevalence.seroprevalences.map(x=>[x.collection_start,x.collection_end])
let yy = seroHub.seroprevalence.seroprevalences.map(x=>[x.seroprevalence,x.seroprevalence])
let traces=xx.slice(0,1000).map((z,i)=>{
return {
x:[xx[i][0],xx[i][1]],
y:[yy[i][0],yy[i][1]]
}
})
let layout = {
title:'test plot',
width:1000,
height:1000
}
Plotly.newPlot(div,traces,layout)
}
seroHub.byGroup = function(xx,attr,vals){
if(typeof(xx)=='string'){ // in case this is already about seroHub, this will be the attribute
vals=attr
attr=xx
xx=seroHub.seroprevalence.seroprevalences
}
if(!xx){xx=seroHub.seroprevalence.seroprevalences}
if(!attr){attr='antigen_target'}
if(!vals){vals = seroHub.uniqueValues(attr)}
let grp = {}
vals.sort().forEach(v=>{
grp[v]=xx.filter(x=>(x[attr]==v))
})
return grp
}
seroHub.plotByGroup = function(div,grps=seroHub.byGroup(),divData){
if(!div){ //main div
div = document.createElement('div')
document.body.appendChild(div)
}
if(!divData){
divData = document.createElement('div')
div.parentElement.appendChild(divData)
divData.innerHTML='Summary row information pops up when you mouse hover the plot above. When you click, the corresponding full entry will be displayed here.'
}
let traces = []
Object.keys(grps).forEach((grp,i)=>{
traces.push({
x:grps[grp].map(x=>x['collection_midpoint']),
y:grps[grp].map(x=>x['seroprevalence']),
text:grps[grp].map(x=>`row: ${x.row}, state:${x.collection_state}, age: ${x.age})`),
type:'scatter',
name:grp,
mode:'markers',
marker:{
opacity:0.5,
symbol:['circle-open','square-open','cross-open','hexagon-open','triangle-up-open','triangle-down-open','triangle-left-open','triangle-right-open','diamond-open'][i], //seroHub.Plotly.PlotSchema.get().traces.scatter.attributes.marker.symbol.values
size:7,
}
})
})
let layout = {
title:`Prevalence over time, by antigen target`,
width:1000,
height:1000,
xaxis:{
title:`Midpoint collection date`
},
yaxis:{
title:`Prevalence`
},
}
Plotly.newPlot(div,traces,layout)
.then(function(gd) {
gd.on('plotly_click',
function(data) {
// Function to execute on hover
// console.log(data);
//divData.innerHTML=seroHub.seroprevalence.seroprevalences[parseInt('row 35957 (California, age: )'.match(/row ([0-9]+)/)[1])].row
let i = grps[data.points[0].fullData.name][data.points[0].pointIndex].row-1
// divData.innerHTML=JSON.stringify(seroHub.seroprevalence.seroprevalences[i],null,3)
divData.innerHTML='' // clear
let taRow = document.createElement('textarea')
let btDownload = document.createElement('button')
let rowFileName = document.createElement('input')
rowFileName.id="rowFileName"
//console.log(btDownload)
btDownload.id="btDownload"
btDownload.innerHTML='download entry'
divData.appendChild(btDownload)
divData.appendChild(rowFileName)
taRow.id="taRow"
taRow.style.backgroundColor='white'
taRow.style.color='navy'
taRow.style.fontSize=10
divData.appendChild(taRow)
taRow.style.width='100%'
taRow.style.height='100em'
taRow.value=JSON.stringify(seroHub.seroprevalence.seroprevalences[i],null,3)
rowFileName.value=`row_${seroHub.seroprevalence.seroprevalences[i].row}.json`
btDownload.onclick=function(){
saveFile(JSON.stringify(seroHub.seroprevalence.seroprevalences[i]),rowFileName.value)
//console.table(taRow.value)
}
});
})
//.then(function(gd) {
// gd.on('plotly_click',
// function(data) {console.log(data)})})
}
//serohub.dt = seroHub.seroprevalence.seroprevalences // array
/*
serohub.group = function(xx=seroHub.seroprevalence.seroprevalences,attr='antigen_target',vals){
if(!vals){
vals = seroHub.uniqueValues(attr)
}
vals
return grp
}
*/
export{
seroHub
}