30:[] 2e:{"title":"Webgen","cells":[{"id":0,"value":"md`# Webgen\nCompanion notebook to [web4bio.github.io/webgen](http://web4bio.github.io/webgen), Stony Brook University's Vertically Integrated Project (VIP) on WebGenomics.\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":170,"value":"html`

Next Step

\nFor next week (Feb22) discuss with potential collaborators what answers to these three questions interest you and describe your project:\n

Goal
Motivation/drive
Data

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":178,"value":"html`

Your Q&A:

If GDC is down, is there an alternative API?

\nThis should be exceedingly rare but yes, there are other APIs for cancer genomics data, cbio for instance. For an example of a JS client side implementation see github.com/mathbiol/cbio.\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":4,"value":"html`

Getting Started

\nLet's start with the demo API call at GDC documentation, and assign the real-time result fetched to a variable called demoData:`","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"demoData=(await fetch('https://api.gdc.cancer.gov/files/d853e541-f16a-4345-9f00-88e03c2dc0bc?pretty=true')).json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":19,"value":"html`Next, let's have a look at the Network tab of GDC portal and find how is the project data used to assemble the user interface being called from GDC. A little probing should lead you to 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 (go ahead click on it!). We'll now assign it to a variable called projectData. Look at the edit to make sure you know how the data is being retrieved. For a bit of alarm, note also how you can engage the data before you fecth it :-O! For example, I could note here that at ${Date()} there are ${projectData.data.hits.length} projects. There is something fishy going on with JS, how could it know ?! Let's discuss this next Friday.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":21,"value":"projectData=(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()","pinned":false,"hidden":false,"mode":"ojs"},{"id":330,"value":"html`

Methods

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":333,"value":"md`\n# OncoJS\nRichard threw this hot potato\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":336,"value":"loli=require('@oncojs/lolliplot')","pinned":false,"hidden":false,"mode":"ojs"},{"id":47,"value":"html`

Data

\nWe'll use api.gdc.cancer.gov as our \"hard disk\". We already know from the previous section how do get the list of projects. Let's now revisit that data structure to build the full map of cancer types described in The Cancer Genome Atlas (TCGA) by getting the values directly from GDC's API. Remember to check the code by clicking on the three dots to the left of the list below and chosing \"edit\".\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":52,"value":"{\n let div = DOM.element('div')\n div.innerHTML='

TCGA cancer project types ()

'\n let ol=DOM.element('ol')\n div.appendChild(ol)\n let caseCount=0\n projectData.data.hits.forEach(function(prj,i){\n let ul=DOM.element('ul')\n let li = DOM.element('li')\n li.innerHTML=`${prj.id}: ${prj.name} (${prj.summary.case_count})`\n caseCount=caseCount+prj.summary.case_count\n ol.appendChild(li)\n li.appendChild(ul)\n prj.disease_type.forEach(function(dtp){\n let li = DOM.element('li')\n li.style.fontSize='small'\n li.innerHTML=dtp\n ul.appendChild(li)\n })\n div\n //if(i==1){debugger}\n })\n div.querySelector('#caseCountSpan').textContent=caseCount\n return div\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":117,"value":"md`...`","pinned":false,"hidden":false,"mode":"ojs"},{"id":100,"value":"html`\n

Miscelaneous Notes

Calling from regular command line is a little more convoluted than from Observable. For example, fetching status would look someiting like\n

\n\n(async function(){ \n\treturn await (await fetch('https://api.gdc.cancer.gov/status')).json()\n})() .then(x=>console.log('response:',JSON.stringify(x,null,3)))\n\n

\ninstead of simply:\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":123,"value":"status = (await fetch('https://api.gdc.cancer.gov/status')).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":130,"value":"x=[1,2,3]","pinned":false,"hidden":false,"mode":"ojs"},{"id":157,"value":"note = notifications","pinned":false,"hidden":false,"mode":"ojs"},{"id":132,"value":"md`## Notifications\nfor Anuki`","pinned":false,"hidden":false,"mode":"ojs"},{"id":136,"value":"notifications = (await fetch(url)).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":142,"value":"url = 'https://api.gdc.cancer.gov/v0/notifications'","pinned":false,"hidden":false,"mode":"ojs"},{"id":144,"value":"{\n return {\n a:1,\n b:2,\n url:'https://api.gdc.cancer.gov/v0/notifications'\n }\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":184,"value":"factorial = (x) => {\n let _fac = (x) => {\n return (x<=1)? 1 : x * _fac(x-1)\n }\n return(_fac(x))\n }","pinned":true,"hidden":false,"mode":"ojs"},{"id":189,"value":"function fac(n,c,i){\n i=i||n;\n c=c||1;\n if(i==1){\n return c\n }else{\n return fac(n,c*i,i-1)\n }\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":193,"value":"fac(3)","pinned":false,"hidden":false,"mode":"ojs"},{"id":203,"value":"malesUrl='https://api.gdc.cancer.gov/files?from=0&size='+n","pinned":false,"hidden":false,"mode":"ojs"},{"id":312,"value":"html`Give this one a thought - I'm defining n, the number os files I want plotted, after the url is composed. Give it a try, change the value of n:`","pinned":false,"hidden":false,"mode":"ojs"},{"id":309,"value":"n=300","pinned":false,"hidden":false,"mode":"ojs"},{"id":205,"value":"dt = (await fetch(malesUrl)).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":224,"value":"dataPlot={\n let dtt={}\n let y = dt.data.hits.map(x=>{\n if(!dtt[x.data_type]){\n dtt[x.data_type]=0\n }\n dtt[x.data_type]+=1\n \n })\n return dtt\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":242,"value":"plotly=require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":274,"value":"Object.keys(dataPlot).map(tp=>dataPlot[tp])","pinned":false,"hidden":false,"mode":"ojs"},{"id":284,"value":"{\n let si = DOM.element('input')\n si.type='range'\n return si\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":246,"value":"plot= {\n let div = DOM.element('div')\n let trace={\n x:Object.keys(dataPlot),\n y:Object.keys(dataPlot).map(tp=>dataPlot[tp]),\n type:'bar'\n }\n return plotly.plot(div,[trace])\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":338,"value":"plotIt=async function(trace,layout){\n if(typeof(plotly)==\"undefined\"){\n let plotly= await require(\"https://cdn.plot.ly/plotly-latest.min.js\")\n }\n let div = DOM.element('div')\n trace=trace||false\n return plotly.plot(div,trace,layout)\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":340,"value":"plotIt([{\n x:['Spring','Summer','Fall','Winter'],\n y:[50,80,60,20],\n type:'bar',\n name:'Stony Brook'\n },\n {\n x:['Spring','Summer','Fall','Winter'],\n y:[80,90,100,70],\n type:'bar',\n name:'Houston'\n }])","pinned":true,"hidden":false,"mode":"ojs"},{"id":378,"value":"plotRichard=function(x,y,type,name){\n return plotIt(\n [{\n x:x,\n y:y,\n name:name,\n type:type\n }]\n )\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":382,"value":"plotRichard(['lala','lele'],[4,5],'bar','Richard Plot Demo')","pinned":false,"hidden":false,"mode":"ojs"},{"id":370,"value":"plotIt({\n x:['Spring','Summer','Fall','Winter'],\n y:[50,90,60,20],\n type:'bar'\n })","pinned":false,"hidden":false,"mode":"ojs"},{"id":354,"value":"lala = window.lili || 666666","pinned":true,"hidden":false,"mode":"ojs"},{"id":363,"value":"lili=9","pinned":false,"hidden":false,"mode":"ojs"},{"id":318,"value":"html`

Another example, calling data from the departent of heath of NY state

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":303,"value":"LunCancerMemorial2015='https://health.data.ny.gov/resource/82xm-y6g8.json?hospital_county=Manhattan&ccs_diagnosis_description=Cancer%20of%20bronchus;%20lung&facility_name=Memorial%20Hospital%20for%20Cancer%20and%20Allied%20Diseases'","pinned":false,"hidden":false,"mode":"ojs"},{"id":305,"value":"lundDt=(await fetch(LunCancerMemorial2015)).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":307,"value":"title=\"DeepLearned prediction of length of stay for lung cancre patienst in the state of New York\"","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W30","stdlib":"1","titling":"auto"}