docs/notebooks/widget_brain_h5ad.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "nbsphinx": "hidden"
   },
   "source": [
    "# Vitessce Widget Tutorial"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Visualization of single-cell RNA seq data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "from os.path import join, isfile, isdir\n",
    "from urllib.request import urlretrieve\n",
    "from anndata import read_h5ad\n",
    "import scanpy as sc\n",
    "import json\n",
    "\n",
    "from vitessce import (\n",
    "    VitessceConfig,\n",
    "    Component as cm,\n",
    "    CoordinationType as ct,\n",
    "    AnnDataWrapper,\n",
    ")\n",
    "from vitessce.data_utils import (\n",
    "    generate_h5ad_ref_spec\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 0. Download data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "h5_url = \"https://datasets.cellxgene.cziscience.com/84df8fa1-ab53-43c9-a439-95dcb9148265.h5ad\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata_filepath = join(\"data\", \"84df8fa1-ab53-43c9-a439-95dcb9148265.h5ad\")\n",
    "if not isfile(adata_filepath):\n",
    "    os.makedirs(\"data\", exist_ok=True)\n",
    "    urlretrieve(h5_url, adata_filepath)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Create a Reference Spec JSON file for the H5AD file\n",
    "\n",
    "In order for Vitessce to load H5AD files, we also need to provide a corresponding [Reference Spec](https://fsspec.github.io/kerchunk/spec.html) JSON file which contains mappings between AnnData object keys and the byte offsets at which those AnnData object values begin within the H5AD file binary contents."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "json_filepath = join(\"data\", \"84df8fa1-ab53-43c9-a439-95dcb9148265.h5ad.reference.json\")\n",
    "if not isfile(json_filepath):\n",
    "    ref_dict = generate_h5ad_ref_spec(h5_url)\n",
    "    with open(json_filepath, \"w\") as f:\n",
    "        json.dump(ref_dict, f)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "## 2. Create the Vitessce widget configuration\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "vc = VitessceConfig(schema_version=\"1.0.17\", name='Nakshatri et al', description='snRNA-seq analyses of breast tissues of healthy women of diverse genetic ancestry')\n",
    "\n",
    "dataset = vc.add_dataset(name='84df8fa1').add_object(AnnDataWrapper(\n",
    "        adata_path=adata_filepath,\n",
    "        ref_path=json_filepath, # We specify paths to both the H5AD and JSON files\n",
    "        obs_embedding_paths=[\"obsm/X_wnn.umap\"],\n",
    "        obs_embedding_names=[\"UMAP\"],\n",
    "        obs_set_paths=[\"obs/cell_type\"],\n",
    "        obs_set_names=[\"Cell Type\"],\n",
    "        obs_feature_matrix_path=\"X\",\n",
    "    )\n",
    ")\n",
    "\n",
    "scatterplot = vc.add_view(cm.SCATTERPLOT, dataset=dataset, mapping=\"UMAP\")\n",
    "cell_sets = vc.add_view(cm.OBS_SETS, dataset=dataset)\n",
    "cell_set_sizes = vc.add_view(cm.OBS_SET_SIZES, dataset=dataset)\n",
    "genes = vc.add_view(cm.FEATURE_LIST, dataset=dataset)\n",
    "\n",
    "vc.layout((scatterplot | cell_sets) / (cell_set_sizes | genes));"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "## 3. Create the widget"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "vw = vc.widget()\n",
    "vw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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