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Add spatialdata notebook
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‎docs/notebooks/spatial_data_mouseliver.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {
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"nbsphinx": "hidden"
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},
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"source": [
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of a SpatialData object\n",
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"\n",
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"Data from https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/examples/transformations.ipynb"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"tags": []
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},
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"source": [
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"## Import dependencies"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"from os.path import join, isfile, isdir\n",
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"from urllib.request import urlretrieve\n",
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"import zipfile\n",
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"\n",
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"from vitessce import (\n",
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" VitessceConfig,\n",
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" ViewType as vt,\n",
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" CoordinationType as ct,\n",
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" CoordinationLevel as CL,\n",
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" SpatialDataWrapper,\n",
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" get_initial_coordination_scope_prefix\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"data_dir = \"data\"\n",
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"zip_filepath = join(data_dir, \"mouse_liver.spatialdata.zarr.zip\")\n",
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"spatialdata_filepath = join(data_dir, \"mouse_liver.spatialdata.zarr\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"if not isdir(spatialdata_filepath):\n",
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" if not isfile(zip_filepath):\n",
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" os.makedirs(data_dir, exist_ok=True)\n",
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" urlretrieve('https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zip', zip_filepath)\n",
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" with zipfile.ZipFile(zip_filepath,\"r\") as zip_ref:\n",
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" zip_ref.extractall(data_dir)\n",
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" os.rename(join(data_dir, \"data.zarr\"), spatialdata_filepath)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Configure Vitessce\n",
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"\n",
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"Vitessce needs to know which pieces of data we are interested in visualizing, the visualization types we would like to use, and how we want to coordinate (or link) the views."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"vc = VitessceConfig(\n",
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" schema_version=\"1.0.17\",\n",
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" name='SpatialData Demo (mouse_liver)',\n",
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")\n",
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"# Add data to the configuration:\n",
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"wrapper = SpatialDataWrapper(\n",
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" sdata_store=spatialdata_filepath,\n",
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" # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
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" table_path=\"tables/table\",\n",
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" image_path=\"images/raw_image\",\n",
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" labels_path=\"labels/segmentation_mask\",\n",
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" #shapes_path=\"shapes/nucleus_boundaries\",\n",
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" #points_path=\"points/transcripts\",\n",
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" obs_feature_matrix_path=\"tables/table/X\",\n",
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" obs_set_paths=[\"tables/table/obs/annotation\"],\n",
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" obs_set_names=[\"Annotation\"],\n",
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" region=\"nucleus_boundaries\",\n",
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" coordinate_system=\"global\",\n",
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" coordination_values={\n",
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" \"obsType\": \"cell\" \n",
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" }\n",
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")\n",
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"dataset = vc.add_dataset(name='Mouse Liver').add_object(wrapper)\n",
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"\n",
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"# Add views (visualizations) to the configuration:\n",
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"spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
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"feature_list = vc.add_view(vt.FEATURE_LIST, dataset=dataset)\n",
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"layer_controller = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
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"obs_sets = vc.add_view(vt.OBS_SETS, dataset=dataset)\n",
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"\n",
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"vc.link_views_by_dict([spatial, layer_controller], {\n",
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" 'imageLayer': CL([{\n",
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" 'photometricInterpretation': 'BlackIsZero',\n",
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" 'imageChannel': CL([{\n",
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" 'spatialChannelColor': [255, 255, 255],\n",
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" 'spatialChannelWindow': [0, 4000],\n",
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" }])\n",
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" }]),\n",
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"}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n",
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"\n",
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"vc.link_views_by_dict([spatial, layer_controller], {\n",
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" 'segmentationLayer': CL([{\n",
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" 'segmentationChannel': CL([{\n",
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" 'obsColorEncoding': 'cellSetSelection',\n",
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" }]),\n",
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" }]),\n",
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"}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
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"\n",
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"vc.link_views([spatial, layer_controller, feature_list, obs_sets], ['obsType'], [wrapper.obs_type_label])\n",
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"\n",
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"# Layout the views\n",
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"vc.layout(spatial | (feature_list / layer_controller / obs_sets));"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### Render the widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"vw = vc.widget(custom_js_url=\"http://localhost:3001/packages/main/dev/dist/index.js\")\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.14"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎src/vitessce/widget.py‎

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next_port = DEFAULT_PORT
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js_package_version = Unicode('3.5.4').tag(sync=True)
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js_package_version = Unicode('3.5.10').tag(sync=True)
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js_dev_mode = Bool(False).tag(sync=True)
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custom_js_url = Unicode('').tag(sync=True)
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plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
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store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
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def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.5.4', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=30000):
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def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.5.10', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=30000):
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"""
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Construct a new Vitessce widget.
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# Launch Vitessce using plain HTML representation (no ipywidgets)
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def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.5.4', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
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def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.5.10', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
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from IPython.display import display, HTML
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uid_str = "vitessce" + get_uid_str(uid)
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