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HuBMAP Partonomy Tree Visualization
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| { | |
| "$schema": "https://vega.github.io/schema/vega/v5.json", | |
| "width": 1200, | |
| "height": 2400, | |
| "padding": 5, | |
| "signals": [ | |
| { | |
| "name": "labels", | |
| "value": true, | |
| "bind": { | |
| "input": "checkbox" | |
| } | |
| }, | |
| { | |
| "name": "layout", | |
| "value": "tidy", | |
| "bind": { | |
| "input": "radio", | |
| "options": [ | |
| "tidy", | |
| "cluster" | |
| ] | |
| } | |
| }, | |
| { | |
| "name": "links", | |
| "value": "diagonal", | |
| "bind": { | |
| "input": "select", | |
| "options": [ | |
| "line", | |
| "curve", | |
| "diagonal", | |
| "orthogonal" | |
| ] | |
| } | |
| } | |
| ], | |
| "data": [ | |
| { | |
| "name": "tree", | |
| "url": "https://cdn.jsdelivr.net/gh/hubmapconsortium/hubmap-ontology/ontologies/partonomy/reifications/partonomy.jsonld", | |
| "transform": [ | |
| { | |
| "type": "project", | |
| "fields": [ | |
| "@id", | |
| { | |
| "expr": "if(isArray(datum.parent), datum.parent[0]['@id'], null)" | |
| }, | |
| { | |
| "expr": "datum['http://www.w3.org/2000/01/rdf-schema#label'][0]['@value']" | |
| }, | |
| { | |
| "expr": "if(isArray(datum['http://www.geneontology.org/formats/oboInOwl#id']), datum['http://www.geneontology.org/formats/oboInOwl#id'][0]['@value'], datum['@id'])" | |
| }, | |
| { | |
| "expr": "datum['http://www.geneontology.org/formats/oboInOwl#hasExactSynonym']" | |
| } | |
| ], | |
| "as": [ | |
| "iri", | |
| "parent", | |
| "name", | |
| "id", | |
| "altLabels" | |
| ] | |
| }, | |
| { | |
| "type": "stratify", | |
| "key": "iri", | |
| "parentKey": "parent" | |
| }, | |
| { | |
| "type": "tree", | |
| "method": { | |
| "signal": "layout" | |
| }, | |
| "size": [ | |
| { | |
| "signal": "height" | |
| }, | |
| { | |
| "signal": "width - 100" | |
| } | |
| ], | |
| "as": [ | |
| "y", | |
| "x", | |
| "depth", | |
| "children" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "links", | |
| "source": "tree", | |
| "transform": [ | |
| { | |
| "type": "treelinks" | |
| }, | |
| { | |
| "type": "linkpath", | |
| "orient": "horizontal", | |
| "shape": { | |
| "signal": "links" | |
| } | |
| } | |
| ] | |
| } | |
| ], | |
| "scales": [ | |
| { | |
| "name": "color", | |
| "type": "linear", | |
| "range": { | |
| "scheme": "magma" | |
| }, | |
| "domain": { | |
| "data": "tree", | |
| "field": "depth" | |
| }, | |
| "zero": true | |
| } | |
| ], | |
| "marks": [ | |
| { | |
| "type": "path", | |
| "from": { | |
| "data": "links" | |
| }, | |
| "encode": { | |
| "update": { | |
| "path": { | |
| "field": "path" | |
| }, | |
| "stroke": { | |
| "value": "#ccc" | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "type": "symbol", | |
| "from": { | |
| "data": "tree" | |
| }, | |
| "encode": { | |
| "enter": { | |
| "size": { | |
| "value": 100 | |
| }, | |
| "stroke": { | |
| "value": "#fff" | |
| } | |
| }, | |
| "update": { | |
| "x": { | |
| "field": "x" | |
| }, | |
| "y": { | |
| "field": "y" | |
| }, | |
| "fill": { | |
| "scale": "color", | |
| "field": "depth" | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "type": "text", | |
| "from": { | |
| "data": "tree" | |
| }, | |
| "encode": { | |
| "enter": { | |
| "text": { | |
| "field": "name" | |
| }, | |
| "fontSize": { | |
| "value": 9 | |
| }, | |
| "baseline": { | |
| "value": "middle" | |
| } | |
| }, | |
| "update": { | |
| "x": { | |
| "field": "x" | |
| }, | |
| "y": { | |
| "field": "y" | |
| }, | |
| "dx": { | |
| "signal": "datum.children ? -7 : 7" | |
| }, | |
| "align": { | |
| "signal": "datum.children ? 'right' : 'left'" | |
| }, | |
| "opacity": { | |
| "signal": "labels ? 1 : 0" | |
| } | |
| } | |
| } | |
| } | |
| ] | |
| } |
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