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‎docs/notebooks/__ipynb__/cellbrowser_to_vitessce_config_conversion.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "Hbol",
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"metadata": {},
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"outputs": [],
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"source": [
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"import marimo as mo"
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]
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},
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{
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"cell_type": "markdown",
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"id": "MJUe",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"# Load UCSC Cell Browser project in Vitessce"
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]
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},
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{
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"cell_type": "markdown",
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"id": "vblA",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"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",
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"1. Convert it into the AnnData format that is supported by Vitessce\n",
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"2. Save the AnnData object as a Zarr store\n",
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"3. Configure Vitessce with the AnnData-Zarr store\n",
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"4. Render a Vitessce widget based on the config (step 3) directly in the notebook.\n",
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"\n",
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"The dataset that you choose to convert needs to be a valid UCSC Cell Browser \"project\", accessible from https://cells.ucsc.edu/, with a configuration available in https://github.com/ucscGenomeBrowser/cellbrowser-confs\n",
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"\n",
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"The `convert_cell_browser_project_to_anndata` function takes the name of that project as an input. For example, to convert this project, https://cells.ucsc.edu/?ds=adultPancreas, you will neeed to pass `\"adultPancreas\"` as the project name."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "bkHC",
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"import json\n",
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"from os.path import join\n",
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"from vitessce import (\n",
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" convert_cell_browser_project_to_anndata,\n",
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" AnnDataWrapper,\n",
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" VitessceConfig,\n",
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")\n",
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"from vitessce.data_utils import VAR_CHUNK_SIZE"
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]
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},
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{
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"cell_type": "markdown",
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"id": "lEQa",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"## 1. Convert UCSC Cell Browser project to a format that is supported by Vitessce\n",
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"#### Output:\n",
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"An AnnData object"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "PKri",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Example run, coverting \"adultPancreas\" project:\n",
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"adata = convert_cell_browser_project_to_anndata(project_name=\"adultPancreas\", keep_only_marker_genes=True)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "Xref",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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"cells": [
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{
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"cell_type": "markdown",
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"id": "MJUe",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"# Load UCSC Cell Browser project in Vitessce"
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]
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},
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{
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"cell_type": "markdown",
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"id": "vblA",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"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",
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"1. Convert it into the AnnData format that is supported by Vitessce\n",
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"2. Save the AnnData object as a Zarr store\n",
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"3. Configure Vitessce with the AnnData-Zarr store\n",
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"4. Render a Vitessce widget based on the config (step 3) directly in the notebook.\n",
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"\n",
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"The dataset that you choose to convert needs to be a valid UCSC Cell Browser \"project\", accessible from https://cells.ucsc.edu/, with a configuration available in https://github.com/ucscGenomeBrowser/cellbrowser-confs\n",
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"\n",
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"The `convert_cell_browser_project_to_anndata` function takes the name of that project as an input. For example, to convert this project, https://cells.ucsc.edu/?ds=adultPancreas, you will neeed to pass `\"adultPancreas\"` as the project name."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "bkHC",
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"import json\n",
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"from os.path import join\n",
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"from vitessce import (\n",
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" convert_cell_browser_project_to_anndata,\n",
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" AnnDataWrapper,\n",
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" VitessceConfig,\n",
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")\n",
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"from vitessce.data_utils import VAR_CHUNK_SIZE"
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]
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},
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{
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"cell_type": "markdown",
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"id": "lEQa",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"## 1. Convert UCSC Cell Browser project to a format that is supported by Vitessce\n",
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"#### Output:\n",
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"An AnnData object"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "PKri",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Example run, coverting \"adultPancreas\" project:\n",
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"adata = convert_cell_browser_project_to_anndata(project_name=\"adultPancreas\", keep_only_marker_genes=True)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "Xref",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"## 2. Save the AnnData object as a Zarr store"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "SFPL",
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"metadata": {},
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"outputs": [],
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"source": [
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"zarr_filepath = join(\"data\", \"out.adata.zarr\")\n",
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"os.makedirs(os.path.dirname(zarr_filepath), exist_ok=True)\n",
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"adata.write_zarr(zarr_filepath, chunks=[adata.shape[0], VAR_CHUNK_SIZE])"
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]
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},
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{
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"cell_type": "markdown",
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"id": "BYtC",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"## 3. Configure Vitessce with the AnnData-Zarr store"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "RGSE",
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"metadata": {},
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"outputs": [],
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"source": [
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"anndata_wrapper_inst = AnnDataWrapper(\n",
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" adata_path=zarr_filepath,\n",
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" obs_feature_matrix_path=\"X\",\n",
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" obs_embedding_paths=[\"obsm/X_tsne\"],\n",
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" obs_embedding_names=[\"t-SNE\"],\n",
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" obs_set_paths=[\"obs/cluster\", \"obs/age\"],\n",
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" obs_set_names=[\"cluster\", \"age\"],\n",
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")\n",
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"vc = VitessceConfig(schema_version=\"1.0.15\", name=\"Vitessce configuration for CellBrowser project adultPancreas\")\n",
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"anndata_wrapper_inst.auto_view_config(vc)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "Kclp",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"## 4. Render the Vitessce widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "emfo",
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"metadata": {},
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"outputs": [],
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"source": [
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"vw = vc.widget()\n",
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"vw"
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]
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}
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},
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"source": [
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"## 2. Save the AnnData object as a Zarr store"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "SFPL",
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"metadata": {},
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"outputs": [],
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"source": [
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"zarr_filepath = join(\"data\", \"out.adata.zarr\")\n",
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"os.makedirs(os.path.dirname(zarr_filepath), exist_ok=True)\n",
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"adata.write_zarr(zarr_filepath, chunks=[adata.shape[0], VAR_CHUNK_SIZE])"
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]
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},
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{
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"cell_type": "markdown",
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"id": "BYtC",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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}
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},
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"source": [
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"## 3. Configure Vitessce with the AnnData-Zarr store"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "RGSE",
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"metadata": {},
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"outputs": [],
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"source": [
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"anndata_wrapper_inst = AnnDataWrapper(\n",
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" adata_path=zarr_filepath,\n",
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" obs_feature_matrix_path=\"X\",\n",
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" obs_embedding_paths=[\"obsm/X_tsne\"],\n",
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" obs_embedding_names=[\"t-SNE\"],\n",
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" obs_set_paths=[\"obs/cluster\", \"obs/age\"],\n",
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" obs_set_names=[\"cluster\", \"age\"],\n",
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")\n",
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"vc = VitessceConfig(schema_version=\"1.0.15\", name=\"Vitessce configuration for CellBrowser project adultPancreas\")\n",
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"anndata_wrapper_inst.auto_view_config(vc)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "Kclp",
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"metadata": {
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"marimo": {
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"config": {
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"hide_code": true
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.14"
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}
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},
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"source": [
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"## 4. Render the Vitessce widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "emfo",
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"metadata": {},
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"outputs": [],
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"source": [
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"vw = vc.widget()\n",
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"vw"
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]
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}
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],
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"metadata": {},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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"nbformat": 4,
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"nbformat_minor": 5
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}

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