29:null 2a:["$","title",null,{"children":"Webgen | ericr491 | Observable"}] 2f:[] 2d:{"id":"3b85afe5c44aeaeb","slug":"webgen","title":"Webgen","thumbnail":"19f011086a874cf9f159969fe2a97b665f259b7ffbcbfd7be582387fdc716843","access_level":"public","create_time":"$D2020-08-31T16:51:09.922Z","update_time":"$D2020-09-18T17:40:42.886Z","view_time":null,"first_public_time":"$D2020-08-31T16:51:50.087Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"7e9c6da13068e72e","login":"ericr491","name":"","avatar_url":"https://avatars-next.observableusercontent.com/65ad77edc5b17fcf3050d9c0fde39324d5b7612c94f589f54fc3dcab21b2a864","tier":"starter_2024"},"version":175,"publish_version":175,"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":1,"collection":null,"type":"notebook","body":{"title":"Webgen","cells":[{"id":0,"value":"md`# Webgen`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":16,"value":"html`

Testing out making API calls to GDC Restful API

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":6,"value":"await fetch(\"https://api.gdc.cancer.gov/files/874e71e0-83dd-4d3e-8014-10141b49f12c\")\n.then(response => response.json());","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":83,"value":"html`

Performing API calls from firebrowse

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":127,"value":"html`

Deconstructing the fetched objects
Cohort = Cancer type
Gene = gene type
TCGA_participiant = Who's the data from
z-score and expression_log = actual numeric values used for violin and heat maps

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":49,"value":"param = {\n return {\n format: \"json\",\n gene: \"PSCA,BRCA2\",\n cohort: \"BLCA\",\n protocol: \"RSEM\",\n page: 1,\n page_size: 2000,\n sort_by: \"cohort\"\n }\n};","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":74,"value":"baseUrl = \"https://firebrowse.herokuapp.com\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":43,"value":"endUrl = {\n return 'http://firebrowse.org/api/v1/Samples/mRNASeq'\n};","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":53,"value":"queryUrl = {\n return new URLSearchParams(param).toString();\n};","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":71,"value":"await fetch(baseUrl + '?' + endUrl + '?' + queryUrl).then(response => response.json()).then(json => /* insert array mapping functions here */ json.mRNASeq);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":133,"value":"html`

An array of objects with participant as key and an array of expression_log2 and z-score

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":153,"value":"fetchedArray = fetch(baseUrl + '?' + endUrl + '?' + queryUrl).then(response => response.json()).then(json => json.mRNASeq);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":157,"value":"fetchedArray.map( (obj) => {\n let { tcga_participant_barcode : partId, expression_log2 : e_l2, [\"z-score\"] : z} = obj\n let p = {\n name: partId,\n data : [e_l2, z]\n } \n return p\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":145,"value":"test = () => [1,2,3]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":147,"value":"test()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":101,"value":"html`

Testing out Plotly

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":91,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":93,"value":"{\n let trace1 = {\n x: [1, 2, 3, 4],\n y: [10, 15, 13, 17],\n mode: 'lines+markers',\n name: 'Lines',\n line: {\n color: 'rgb(200, 100, 50)',\n width: 2\n }\n }\n\n let trace2 = {\n x: [2, 3, 4, 5],\n y: [16, 5, 11, 9],\n mode: 'lines',\n name: 'Lines2',\n line: {\n color: 'rgb(0,0,0)'\n }\n }\n \n let layout = {\n title:'Line Graph'\n }\n \n const div = document.createElement('div')\n Plotly.newPlot(div, [trace1, trace2],layout);\n return div\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":138,"value":"html`

Notes for me.