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clear notebooks
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@manzt
manzt committed Nov 20, 2024
1 parent 217eb93 commit f5372fc
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Showing 2 changed files with 28 additions and 802 deletions.
203 changes: 20 additions & 183 deletions notebooks/example.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "2a014a14-3d7c-4288-8534-df01d7bf2432",
"metadata": {},
"outputs": [],
Expand All @@ -12,57 +12,10 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"id": "61233841",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Track({\n",
" color: Color({\n",
" shorthand: 's1:N'\n",
" }),\n",
" data: {'type': 'csv', 'url': 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt', 'chromosomeField': 'c2', 'genomicFields': ['s1', 'e1', 's2', 'e2']},\n",
" height: 130,\n",
" mark: 'withinLink',\n",
" opacity: OpacityValue({\n",
" value: 0.2\n",
" }),\n",
" stroke: StrokeValue({\n",
" value: 'black'\n",
" }),\n",
" strokeWidth: StrokeWidthValue({\n",
" value: 0.5\n",
" }),\n",
" width: 600,\n",
" x: X({\n",
" domain: GenomicDomain({\n",
" chromosome: '1',\n",
" interval: [103900000, 104100000]\n",
" }),\n",
" shorthand: 's1:G'\n",
" }),\n",
" x1: X1({\n",
" domain: GenomicDomain({\n",
" chromosome: '1'\n",
" }),\n",
" shorthand: 's2:G'\n",
" }),\n",
" x1e: X1e({\n",
" shorthand: 'e2:G'\n",
" }),\n",
" xe: Xe({\n",
" shorthand: 'e1:G'\n",
" })\n",
"})"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"csvData = gos.csv(\n",
" url=\"https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt\",\n",
Expand All @@ -87,141 +40,15 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"id": "88f3a522",
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"\n",
"<!DOCTYPE html>\n",
"<html>\n",
"<head>\n",
" <style>.error { color: red; }</style>\n",
" <link rel=\"stylesheet\" href=\"https://unpkg.com/higlass@1.11/dist/hglib.css\">\n",
"</head>\n",
"<body>\n",
" <div id=\"jupyter-gosling-b21fb3e30816413d991b4879dae37703\"></div>\n",
" <script type=\"module\">\n",
"\n",
" async function loadScript(src) {\n",
" return new Promise(resolve => {\n",
" const script = document.createElement('script');\n",
" script.onload = resolve;\n",
" script.src = src;\n",
" script.async = false;\n",
" document.head.appendChild(script);\n",
" });\n",
" }\n",
"\n",
" async function loadGosling() {\n",
" // Manually load scripts from window namespace since requirejs might not be\n",
" // available in all browser environments.\n",
" // https://github.com/DanielHreben/requirejs-toggle\n",
" if (!window.gosling) {\n",
" window.__requirejsToggleBackup = {\n",
" define: window.define,\n",
" require: window.require,\n",
" requirejs: window.requirejs,\n",
" };\n",
" for (const field of Object.keys(window.__requirejsToggleBackup)) {\n",
" window[field] = undefined;\n",
" }\n",
"\n",
" // load dependencies sequentially\n",
" const sources = [\n",
" \"https://unpkg.com/react@17/umd/react.production.min.js\",\n",
" \"https://unpkg.com/react-dom@17/umd/react-dom.production.min.js\",\n",
" \"https://unpkg.com/pixi.js@6/dist/browser/pixi.min.js\",\n",
" \"https://unpkg.com/gosling.js@0.9.4/dist/gosling.js\",\n",
" ];\n",
"\n",
" for (const src of sources) await loadScript(src);\n",
"\n",
" // restore requirejs after scripts have loaded\n",
" Object.assign(window, window.__requirejsToggleBackup);\n",
" delete window.__requirejsToggleBackup;\n",
" }\n",
" return window.gosling;\n",
" };\n",
"\n",
" var el = document.getElementById('jupyter-gosling-b21fb3e30816413d991b4879dae37703');\n",
" var spec = {\"tracks\": [{\"data\": {\"type\": \"csv\", \"url\": \"https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt\", \"chromosomeField\": \"c2\", \"genomicFields\": [\"s1\", \"e1\", \"s2\", \"e2\"]}, \"height\": 130, \"mark\": \"withinLink\", \"width\": 600, \"color\": {\"field\": \"s1\", \"type\": \"nominal\"}, \"opacity\": {\"value\": 0.2}, \"stroke\": {\"value\": \"black\"}, \"strokeWidth\": {\"value\": 0.5}, \"x\": {\"domain\": {\"chromosome\": \"1\", \"interval\": [103900000, 104100000]}, \"field\": \"s1\", \"type\": \"genomic\"}, \"x1\": {\"domain\": {\"chromosome\": \"1\"}, \"field\": \"s2\", \"type\": \"genomic\"}, \"x1e\": {\"field\": \"e2\", \"type\": \"genomic\"}, \"xe\": {\"field\": \"e1\", \"type\": \"genomic\"}}], \"title\": \"Basic Marks: Bar\", \"subtitle\": \"Tutorial Examples\"};\n",
" var opt = {\"padding\": 0, \"theme\": null};\n",
"\n",
" loadGosling()\n",
" .then(gosling => gosling.embed(el, spec, opt))\n",
" .catch(err => {\n",
" el.innerHTML = `<div class=\"error\">\n",
" <p>JavaScript Error: ${error.message}</p>\n",
" <p>This usually means there's a typo in your Gosling specification. See the javascript console for the full traceback.</p>\n",
"</div>`;\n",
" throw error;\n",
" });\n",
" </script>\n",
"</body>\n",
"</html>"
],
"text/plain": [
"View({\n",
" subtitle: 'Tutorial Examples',\n",
" title: 'Basic Marks: Bar',\n",
" tracks: [Track({\n",
" color: Color({\n",
" field: 's1',\n",
" type: 'nominal'\n",
" }),\n",
" data: {'type': 'csv', 'url': 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt', 'chromosomeField': 'c2', 'genomicFields': ['s1', 'e1', 's2', 'e2']},\n",
" height: 130,\n",
" mark: 'withinLink',\n",
" opacity: OpacityValue({\n",
" value: 0.2\n",
" }),\n",
" stroke: StrokeValue({\n",
" value: 'black'\n",
" }),\n",
" strokeWidth: StrokeWidthValue({\n",
" value: 0.5\n",
" }),\n",
" width: 600,\n",
" x: X({\n",
" domain: GenomicDomain({\n",
" chromosome: '1',\n",
" interval: [103900000, 104100000]\n",
" }),\n",
" field: 's1',\n",
" type: 'genomic'\n",
" }),\n",
" x1: X1({\n",
" domain: GenomicDomain({\n",
" chromosome: '1'\n",
" }),\n",
" field: 's2',\n",
" type: 'genomic'\n",
" }),\n",
" x1e: X1e({\n",
" field: 'e2',\n",
" type: 'genomic'\n",
" }),\n",
" xe: Xe({\n",
" field: 'e1',\n",
" type: 'genomic'\n",
" })\n",
" })]\n",
"})"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"metadata": {},
"outputs": [],
"source": [
"# just render a view (not a mutable object)\n",
"track.view(title=\"Basic Marks: Bar\", subtitle=\"Tutorial Examples\")"
"view = track.view(title=\"Basic Marks: Bar\", subtitle=\"Tutorial Examples\", id=\"aa\")\n",
"w = view.widget()\n",
"w"
]
},
{
Expand All @@ -230,6 +57,16 @@
"id": "7a82cfcc",
"metadata": {},
"outputs": [],
"source": [
"view.id"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "05d7ecf9-d336-4daa-8d49-447d062f7236",
"metadata": {},
"outputs": [],
"source": []
}
],
Expand All @@ -249,7 +86,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
"version": "3.12.7"
}
},
"nbformat": 4,
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