Marimo conversion

Author: keller-mark

docs/notebooks/cellbrowser_to_vitessce_config_conversion.ipynb

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+import marimo
+
+__generated_with = "0.13.15"
+app = marimo.App()
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        # Load UCSC Cell Browser project in Vitessce
+        """
+    )
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        This notebook shows you how to use the `convert_cell_browser_project_to_anndata` function, which allows you to take an existing project, published in https://cells.ucsc.edu/ and:
+        1. Convert it into the AnnData format that is supported by Vitessce
+        2. Save the AnnData object as a Zarr store
+        3. Configure Vitessce with the AnnData-Zarr store
+        4. Render a Vitessce widget based on the config (step 3) directly in the notebook.
+
+        The dataset that you choose to convert needs to be a valid UCSC Cell Browser "project", accessible from https://cells.ucsc.edu/, with a configuration available in https://github.com/ucscGenomeBrowser/cellbrowser-confs
+
+        The `convert_cell_browser_project_to_anndata` function takes the name of that project as an input. For example, to convert this project, https://cells.ucsc.edu/?ds=adultPancreas, you will neeed to pass `"adultPancreas"` as the project name.
+        """
+    )
+    return
+
+
+@app.cell
+def _():
+    import os
+    import json
+    from os.path import join
+    from vitessce import (
+        convert_cell_browser_project_to_anndata,
+        AnnDataWrapper,
+        VitessceConfig,
+    )
+    from vitessce.data_utils import VAR_CHUNK_SIZE
+    return (
+        AnnDataWrapper,
+        VAR_CHUNK_SIZE,
+        VitessceConfig,
+        convert_cell_browser_project_to_anndata,
+        join,
+        os,
+    )
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        ## 1. Convert UCSC Cell Browser project to a format that is supported by Vitessce
+        #### Output:
+        An AnnData object
+
+        """
+    )
+    return
+
+
+@app.cell
+def _():
+    ## 3. Convert UCSC Cell Browser project to a Vitessce view config
+    return
+
+
+@app.cell
+def _(convert_cell_browser_project_to_anndata):
+    # Example run, coverting "adultPancreas" project:
+    adata = convert_cell_browser_project_to_anndata(project_name="adultPancreas", keep_only_marker_genes=True)
+    return (adata,)
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        ## 2. Save the AnnData object as a Zarr store
+        """
+    )
+    return
+
+
+@app.cell
+def _(VAR_CHUNK_SIZE, adata, join, os):
+    zarr_filepath = join("data", "out.adata.zarr")
+    os.makedirs(os.path.dirname(zarr_filepath), exist_ok=True)
+    adata.write_zarr(zarr_filepath, chunks=[adata.shape[0], VAR_CHUNK_SIZE])
+    return (zarr_filepath,)
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        ## 3. Configure Vitessce with the AnnData-Zarr store
+        """
+    )
+    return
+
+
+@app.cell
+def _(AnnDataWrapper, VitessceConfig, zarr_filepath):
+    anndata_wrapper_inst = AnnDataWrapper(
+        adata_path=zarr_filepath,
+        obs_feature_matrix_path="X",
+        obs_embedding_paths=["obsm/X_tsne"],
+        obs_embedding_names=["t-SNE"],
+        obs_set_paths=["obs/cluster", "obs/age"],
+        obs_set_names=["cluster", "age"],
+    )
+    vc = VitessceConfig(schema_version="1.0.15", name="Vitessce configuration for CellBrowser project adultPancreas")
+    anndata_wrapper_inst.auto_view_config(vc)
+    return (vc,)
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        ## 4. Render the Vitessce widget
+        """
+    )
+    return
+
+
+@app.cell
+def _(vc):
+    vw = vc.widget()
+    vw
+    return
+
+
+@app.cell
+def _():
+    import marimo as mo
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()