| license: MIT | |
| height: 700 | |
| scrolling: no | |
| border: yes |
Report for HuBMAP Data that have CCF "rui locations". See https://hubmapconsortium.github.io/ccf/ for more information.
To access your data, grab your API key and set it using localStorage.setItem('HUBMAP_KEY', 'my-key-goes-here') from the developer console and refresh. Note that keys expire and may cause the query to fail after a while. In that case, simply update the key above or delete it via the developer console.
| <!doctype html> | |
| <html lang="en"> | |
| <head> | |
| <title>HuBMAP CCF Registrations</title> | |
| <script src="https://cdn.jsdelivr.net/npm/vega@5"></script> | |
| <script src="https://cdn.jsdelivr.net/npm/vega-lite@4"></script> | |
| <script src="https://cdn.jsdelivr.net/npm/vega-embed@6"></script> | |
| </head> | |
| <body> | |
| <div id="visualization" style="width: 920px; height: 600px;"></div> | |
| <script type="text/javascript"> | |
| const searchUri = "https://search.api.hubmapconsortium.org/entities/search"; | |
| // const searchUri = 'https://search-api.dev.hubmapconsortium.org/entities/search'; | |
| const postData = { | |
| "credentials": "omit", | |
| "headers": { "Content-type": "application/json" }, | |
| "body": "{\"version\":true,\"size\":10000,\"_source\":{\"excludes\":[\"donor\",\"immediate_ancestors\",\"immediate_descendants\",\"ancestor_ids\",\"descendant_ids\"]},\"stored_fields\":[\"*\"],\"script_fields\":{},\"docvalue_fields\":[],\"query\":{\"exists\":{\"field\":\"rui_location\"}}}", | |
| "method": "POST" | |
| }; | |
| if (localStorage.getItem('HUBMAP_KEY')) { | |
| postData.headers.Authorization = 'Bearer ' + localStorage.getItem('HUBMAP_KEY'); | |
| } | |
| fetch("vis.vl.json").then((result) => result.json()).then((spec) => | |
| fetch(searchUri, postData).then((result) => result.json()).then((jsonData) => { | |
| // Embed the graph data in the spec for ease of use from Vega Editor | |
| spec.datasets = { | |
| data: jsonData.hits.hits.map(n => Object.assign({}, n._source, { | |
| rui_location: JSON.parse(n._source.rui_location) | |
| })) | |
| }; | |
| console.log(spec.datasets.data); | |
| return vegaEmbed("#visualization", spec, { "renderer": "svg", "actions": true }); | |
| }) | |
| ).then((results) => { | |
| console.log("Visualization successfully loaded"); | |
| }); | |
| </script> | |
| </body> | |
| </html> |
| { | |
| "$schema": "https://vega.github.io/schema/vega-lite/v4.json", | |
| "description": "Report for HuBMAP CCF Registrations", | |
| "autosize": {"type": "fit", "resize": true}, | |
| "config": {"view": {"strokeOpacity": 0}, "style": {"guide-label": {"width": 10}}}, | |
| "vconcat": [ | |
| { | |
| "hconcat": [ | |
| { | |
| "mark": {"type": "bar", "tooltip": {"content": "data"}}, | |
| "data": {"name": "data"}, | |
| "transform": [ | |
| {"calculate": "datum.origin_sample.organ", "as": "organ"} | |
| ], | |
| "encoding": { | |
| "x": {"aggregate": "count", "field": "organ"}, | |
| "y": {"field": "organ", "type": "nominal", "sort": "y", "title": "Organ Code"} | |
| } | |
| }, | |
| { | |
| "mark": {"type": "bar", "tooltip": {"content": "data"}}, | |
| "data": {"name": "data"}, | |
| "transform": [ | |
| {"calculate": "datum.origin_sample.organ", "as": "organ"}, | |
| {"calculate": "datum.rui_location.ccf_annotations.length > 0 ? 1 : 0", "as": "num_as"} | |
| ], | |
| "encoding": { | |
| "x": {"aggregate": "sum", "field": "num_as", "title": "# Samples with Anatomical Structures"}, | |
| "y": {"field": "organ", "type": "nominal", "sort": "y", "title": "Organ Code"} | |
| } | |
| } | |
| ] | |
| } | |
| ] | |
| } |