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🚸 Make use of new VitessceConfig interface (#24)
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falexwolf authored Oct 8, 2024
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8 changes: 5 additions & 3 deletions docs/vitessce.ipynb
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},
"outputs": [],
"source": [
"# !pip install vitessce\n",
"# !pip install vitessce>=0.3.4\n",
"# !pip install 'lamindb[jupyter,aws,bionty]'\n",
"!lamin load laminlabs/lamin-dev # <-- replace with your instance"
]
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")\n",
"dataset = vc.add_dataset(name=\"Habib 2017\").add_object(\n",
" vit.AnnDataWrapper(\n",
" adata_url=zarr_artifact.path.to_url(),\n",
" adata_artifact=zarr_artifact,\n",
" obs_feature_matrix_path=\"layers/X_uint8\",\n",
" obs_embedding_paths=[\"obsm/X_umap\"],\n",
" obs_embedding_names=[\"UMAP\"],\n",
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"\n",
"You can now see the Vitessce button show up on your dataset as in this [example dataset](https://lamin.ai/laminlabs/lamindata/artifact/HXJ4DDAw8012jVKwoxgd).\n",
"\n",
"If your `VitessceConfig` object contains multiple datasets, the Vitessce button will appear next to a `Collection` that groups these artifacts.\n",
"\n",
":::"
]
},
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"source": [
":::{dropdown} Upload speed\n",
"\n",
"Here is [a note](https://lamin.ai/laminlabs/lamindata/transform/WDjio16cQsdW5zKv) on folder upload speed and we why chose not to use the `.export(to=\"s3\")` functionality of Vitessce.\n",
"Here is [a note](https://lamin.ai/laminlabs/lamindata/transform/WDjio16cQsdW5zKv) on folder upload speed and why `lamindb` does not use the `.export(to=\"s3\")` functionality of Vitessce.\n",
"\n",
":::"
]
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