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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| { | ||
| "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": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.9.0" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } |
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