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‎docs/notebooks/widget_plugin_spatial-query.ipynb‎

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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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"execution_count": 1,
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"metadata": {
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"tags": []
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},
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"outputs": [],
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"source": [
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"#!pip install \"vitessce[all]==3.3.0\" esbuild_py anndata\n",
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"!pip install \"mlxtend~=0.23.0\"\n",
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"#!pip install \"mlxtend~=0.23.0\"\n",
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"#!pip install -i \"https://test.pypi.org/simple/\" SpatialQuery\n",
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"!pip install \"SpatialQuery @ git+https://github.com/ShaokunAn/Spatial-Query@main\""
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"#!uv pip install \"pybind11\"\n",
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"#!uv pip install \"SpatialQuery @ git+https://github.com/ShaokunAn/Spatial-Query@main\""
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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": 1,
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"ename": "ImportError",
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"evalue": "dlopen(/Users/mkeller/research/dbmi/vitessce/vitessce-python/.venv/lib/python3.10/site-packages/SpatialQueryEliasFanoDB.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace '__ZNSt3__113__hash_memoryEPKvm'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[2], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mSpatialQuery\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m spatial_query\n",
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"File \u001b[0;32m~/research/dbmi/vitessce/vitessce-python/.venv/lib/python3.10/site-packages/SpatialQuery/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspatial_query\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m spatial_query\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspatial_query_multiple_fov\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m spatial_query_multi\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m maximal_patterns, retrieve_niche_pattern_freq, plot_niche_pattern_freq\n",
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"File \u001b[0;32m~/research/dbmi/vitessce/vitessce-python/.venv/lib/python3.10/site-packages/SpatialQuery/spatial_query.py:20\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mstatsmodels\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mstats\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmultitest\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m multipletests\n\u001b[1;32m 18\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtime\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m time\n\u001b[0;32m---> 20\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mscfind4sp\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SCFind\n\u001b[1;32m 21\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mscanpy\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01msc\u001b[39;00m\n\u001b[1;32m 22\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m spatial_utils, spatial_gene_covarying, plotting\n",
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"File \u001b[0;32m~/research/dbmi/vitessce/vitessce-python/.venv/lib/python3.10/site-packages/SpatialQuery/scfind4sp/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcore_methods\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SCFind\n\u001b[1;32m 3\u001b[0m __all__ \u001b[38;5;241m=\u001b[39m [\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mSCFind\u001b[39m\u001b[38;5;124m'\u001b[39m]\n",
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"File \u001b[0;32m~/research/dbmi/vitessce/vitessce-python/.venv/lib/python3.10/site-packages/SpatialQuery/scfind4sp/core_methods.py:7\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpandas\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mpd\u001b[39;00m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mscipy\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msparse\u001b[39;00m\n\u001b[0;32m----> 7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mSpatialQueryEliasFanoDB\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m EliasFanoDB\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01manndata\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m AnnData\n\u001b[1;32m 9\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01manndata\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mad\u001b[39;00m\n",
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"\u001b[0;31mImportError\u001b[0m: dlopen(/Users/mkeller/research/dbmi/vitessce/vitessce-python/.venv/lib/python3.10/site-packages/SpatialQueryEliasFanoDB.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace '__ZNSt3__113__hash_memoryEPKvm'"
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]
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}
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],
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"source": [
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"from SpatialQuery import spatial_query"
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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": 3,
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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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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"ename": "ModuleNotFoundError",
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"evalue": "No module named 'SpatialQuery'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m plugin \u001b[38;5;241m=\u001b[39m \u001b[43mSpatialQueryPlugin\u001b[49m\u001b[43m(\u001b[49m\u001b[43madata\u001b[49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m~/research/dbmi/vitessce/vitessce-python/src/vitessce/widget_plugins/spatial_query.py:217\u001b[0m, in \u001b[0;36mSpatialQueryPlugin.__init__\u001b[0;34m(self, adata, spatial_key, label_key, feature_name, if_lognorm)\u001b[0m\n\u001b[1;32m 192\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__init__\u001b[39m(\u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 193\u001b[0m adata,\n\u001b[1;32m 194\u001b[0m spatial_key\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mX_spatial\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 197\u001b[0m if_lognorm\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 198\u001b[0m ):\n\u001b[1;32m 199\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 200\u001b[0m \u001b[38;5;124;03m Construct a new Vitessce widget.\u001b[39;00m\n\u001b[1;32m 201\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;124;03m vc.widget(plugins=[plugin], remount_on_uid_change=False)\u001b[39;00m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 217\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mSpatialQuery\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m spatial_query\n\u001b[1;32m 218\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpyplot\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mplt\u001b[39;00m \u001b[38;5;66;03m# Add as dependency / optional dependency?\u001b[39;00m\n\u001b[1;32m 220\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madata \u001b[38;5;241m=\u001b[39m adata\n",
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"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'SpatialQuery'"
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]
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}
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],
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"source": [
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"plugin = SpatialQueryPlugin(adata)"
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]

‎pyproject.toml‎

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"snakemake",
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"pyyaml",
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]
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sq = [
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# SpatialQuery
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# To install: uv sync --extra sq --no-build-isolation-package SpatialQuery
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# or: uv sync --extra all --extra notebook --extra sq --no-build-isolation-package SpatialQuery
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"pybind11",
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"SpatialQuery @ git+https://github.com/ShaokunAn/Spatial-Query@main"
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]
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[dependency-groups]
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dev = [
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[tool.hatch.build]
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exclude = [".github", "docs", "demos", "binder"]
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[tool.hatch.metadata]
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allow-direct-references = true
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[project.urls]
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repository = "https://github.com/vitessce/vitessce-python"
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