📝 Polish

laminlabs · Nov 7, 2023 · 51c2eda · 51c2eda
1 parent 6438202
commit 51c2eda
Showing 1 changed file with 31 additions and 23 deletions.
diff --git a/docs/scrna.ipynb b/docs/scrna.ipynb
@@ -25,7 +25,7 @@
     "\n",
     "Along the way, you'll see how to create reports, leverage data lineage, and query individual data batches stored as files.\n",
     "\n",
-    "If you're interested in directly using the type of large curated atlas of scRNA-seq datasets that arises from the present guide, see the [CELLxGENE Census guide](docs:cellxgene-census).\n",
+    "If you're only interested in _using_ a large curated scRNA-seq dataset, see the [CELLxGENE Census guide](docs:cellxgene-census).\n",
     "\n",
     "Here, you will:\n",
     "\n",
@@ -71,15 +71,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "import lamindb as ln\n",
     "import lnschema_bionty as lb\n",
     "\n",
-    "ln.track()\n",
     "ln.settings.verbosity = \"hint\"\n",
-    "lb.settings.organism = \"human\""
+    "lb.settings.organism = \"human\"\n",
+    "ln.track()"
    ]
   },
   {
@@ -108,27 +112,19 @@
    },
    "outputs": [],
    "source": [
-    "adata = ln.dev.datasets.anndata_human_immune_cells(populate_registries=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "adata = ln.dev.datasets.anndata_human_immune_cells(populate_registries=True)\n",
     "adata"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This `AnnData` is standardized using the [CZI single-cell-curation validator](https://github.com/chanzuckerberg/single-cell-curation) with the same public ontologies that underlie {mod}`lnschema_bionty`. Because registries are pre-populated, validation passes.\n",
+    "This `AnnData` object is standardized using the [CZI single-cell-curation validator](https://github.com/chanzuckerberg/single-cell-curation) with the same public ontologies that underlie {mod}`lnschema_bionty`. Because registries are pre-populated, validation passes.\n",
     "\n",
     "```{note}\n",
     "\n",
-    "In the [next guide](/scrna2), we'll curate a non-standardized dataset as you might get from an external partner.\n",
+    "In the [next guide](/scrna2), we'll curate a non-standardized dataset.\n",
     "\n",
     "```"
    ]
@@ -137,7 +133,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The gene registry provides metadata for each of the 36k gene measured in the `AnnData`:"
+    "The gene registry provides metadata for each of the 36k genes measured in the `AnnData`:"
    ]
   },
   {
@@ -150,14 +146,14 @@
    },
    "outputs": [],
    "source": [
-    "lb.Gene.filter().df().head()"
+    "lb.Gene.filter().df()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When we create a `File` object from an `AnnData`, we automatically link its features:"
+    "When we create a {class}`~lamindb.File` object from an `AnnData`, we automatically link its features:"
    ]
   },
   {
@@ -184,7 +180,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "file.save()"
@@ -200,7 +200,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "file.features"
@@ -210,7 +214,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let's now validate the corresponding label slots in the `AnnData` and annotate the file with labels:"
+    "Let's now annotate the file with labels:"
    ]
   },
   {
@@ -239,7 +243,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The file is now queryable by everything we linked:"
+    "The file is now validated & queryable by everything we linked:"
    ]
   },
   {
@@ -278,7 +282,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "dataset = ln.Dataset(file, name=\"My versioned scRNA-seq dataset\", version=\"1\")\n",