Update

Author: keller-mark

docs/notebooks/__ipynb__/cellbrowser_to_vitessce_config_conversion.ipynb

@@ -3,74 +3,37 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "vblA",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "import json\n",
-    "from os.path import join\n",
-    "from vitessce import (\n",
-    "    convert_cell_browser_project_to_anndata,\n",
-    "    AnnDataWrapper,\n",
-    "    VitessceConfig,\n",
-    ")\n",
-    "from vitessce.data_utils import VAR_CHUNK_SIZE"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "lEQa",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "## 3. Convert UCSC Cell Browser project to a Vitessce view config"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "Hstk",
+   "id": "Hbol",
    "metadata": {},
    "outputs": [],
    "source": [
     "import marimo as mo"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "PKri",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Example run, coverting \"adultPancreas\" project:\n",
-    "adata = convert_cell_browser_project_to_anndata(project_name=\"adultPancreas\", keep_only_marker_genes=True)"
-   ]
-  },
   {
    "cell_type": "markdown",
-   "id": "BYtC",
-   "metadata": {},
-   "source": [
-    "## 3. Configure Vitessce with the AnnData-Zarr store"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "bkHC",
-   "metadata": {},
+   "id": "MJUe",
+   "metadata": {
+    "marimo": {
+     "config": {
+      "hide_code": true
+     }
+    }
+   },
    "source": [
-    "## 1. Convert UCSC Cell Browser project to a format that is supported by Vitessce\n",
-    "#### Output:\n",
-    "An AnnData object"
+    "# Load UCSC Cell Browser project in Vitessce"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "MJUe",
-   "metadata": {},
+   "id": "vblA",
+   "metadata": {
+    "marimo": {
+     "config": {
+      "hide_code": true
+     }
+    }
+   },
    "source": [
     "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:\n",
     "1. Convert it into the AnnData format that is supported by Vitessce\n",
@@ -84,27 +47,62 @@
    ]
   },
   {
-   "cell_type": "markdown",
-   "id": "Kclp",
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bkHC",
    "metadata": {},
+   "outputs": [],
    "source": [
-    "## 4. Render the Vitessce widget"
+    "import os\n",
+    "import json\n",
+    "from os.path import join\n",
+    "from vitessce import (\n",
+    "    convert_cell_browser_project_to_anndata,\n",
+    "    AnnDataWrapper,\n",
+    "    VitessceConfig,\n",
+    ")\n",
+    "from vitessce.data_utils import VAR_CHUNK_SIZE"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "Xref",
+   "id": "lEQa",
+   "metadata": {
+    "marimo": {
+     "config": {
+      "hide_code": true
+     }
+    }
+   },
+   "source": [
+    "## 1. Convert UCSC Cell Browser project to a format that is supported by Vitessce\n",
+    "#### Output:\n",
+    "An AnnData object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "PKri",
    "metadata": {},
+   "outputs": [],
    "source": [
-    "## 2. Save the AnnData object as a Zarr store"
+    "# Example run, coverting \"adultPancreas\" project:\n",
+    "adata = convert_cell_browser_project_to_anndata(project_name=\"adultPancreas\", keep_only_marker_genes=True)"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "Hbol",
-   "metadata": {},
+   "id": "Xref",
+   "metadata": {
+    "marimo": {
+     "config": {
+      "hide_code": true
+     }
+    }
+   },
    "source": [
-    "# Load UCSC Cell Browser project in Vitessce"
+    "## 2. Save the AnnData object as a Zarr store"
    ]
   },
   {
@@ -119,6 +117,20 @@
     "adata.write_zarr(zarr_filepath, chunks=[adata.shape[0], VAR_CHUNK_SIZE])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "BYtC",
+   "metadata": {
+    "marimo": {
+     "config": {
+      "hide_code": true
+     }
+    }
+   },
+   "source": [
+    "## 3. Configure Vitessce with the AnnData-Zarr store"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -138,6 +150,20 @@
     "anndata_wrapper_inst.auto_view_config(vc)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "Kclp",
+   "metadata": {
+    "marimo": {
+     "config": {
+      "hide_code": true
+     }
+    }
+   },
+   "source": [
+    "## 4. Render the Vitessce widget"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,