multimodal review

docs/multimodal.ipynb

@@ -14,6 +14,30 @@
     "# Validate & register multi-modal data"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Background"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "scRNA data has moved beyond just RNA and can also include the measurements of other modalities such as chromatin accessibility, surface proteins or adaptive immune receptors.\n",
+    "ECCITE-seq is designed to enable interrogation of single-cell transcriptomes together with surface protein markers in the context of CRISPR screens.\n",
+    "\n",
+    "Here, we'll showcase how to curate and register ECCITE-seq data from [Papalexi21](https://www.nature.com/articles/s41592-019-0392-0) in the form of [MuData](https://github.com/scverse/mudata) objects."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Setup"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -55,7 +79,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## MuData object"
+    "## Papalexi21"
    ]
   },
   {
@@ -65,6 +89,13 @@
     "Let's use a MuData object:"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Transform ![](https://img.shields.io/badge/Transform-10b981)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -75,16 +106,16 @@
    },
    "outputs": [],
    "source": [
-    "mdata = ln.dev.datasets.mudata_papalexi21_subset()"
+    "mdata = ln.dev.datasets.mudata_papalexi21_subset()\n",
+    "mdata"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "mdata"
+    "MuData objects build on top of AnnData objects to store and serialize multimodal data.\n",
+    "More information can be found on the [MuData documentation](https://mudata.readthedocs.io/en/latest/)."
    ]
   },
   {
@@ -110,31 +141,24 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Register features"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Now let's register the 3 feature sets this data contains:\n",
-    "1. rna\n",
-    "2. adt\n",
+    "Now let's validate and register the 3 feature sets this data contains:\n",
+    "1. RNA (gene expression)\n",
+    "2. ADT (antibody derived tags reflecting surface proteins)\n",
     "3. obs (metadata)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### modalities"
+    "For the two modalities rna and adt, we use bionty tables as the reference:"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For the two modalities rna and adt, we use bionty tables as the reference:"
+    "### Validate ![](https://img.shields.io/badge/Validate-10b981)"
    ]
   },
   {
@@ -253,6 +277,13 @@
     "lb.CellMarker.validate(mdata[\"adt\"].var_names, field=lb.CellMarker.name);"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Register ![](https://img.shields.io/badge/Register-10b981) "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -281,13 +312,6 @@
     "file.features.add_feature_set(feature_set_adt, slot=\"adt\")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### metadata"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -440,7 +464,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py39",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -454,7 +478,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.12"
   },
   "nbproject": {
    "id": "yMWSFirS6qv2",
@@ -468,5 +492,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }