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‎.github/workflows/test_widget.yml‎

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@@ -29,11 +29,11 @@ jobs:
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- name: Install vitessce
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run: uv sync --extra dev --extra all --extra notebook
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- name: Export Jupyter notebook to HTML
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run: uv run jupyter nbconvert --to=html --execute docs/notebooks/widget_from_dict.ipynb
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run: uv run jupyter nbconvert --to=html --execute docs/notebooks/__ipynb__/widget_from_dict.ipynb
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- name: Export Marimo notebook to HTML
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run: uv run marimo export html docs/notebooks/marimo.py -o docs/notebooks/marimo.html
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run: uv run marimo export html docs/notebooks/marimo.mo.py -o docs/notebooks/marimo.mo.html
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- name: Export Marimo notebook to HTML-WASM
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run: uv run marimo export html-wasm docs/notebooks/marimo-wasm.py -o docs/notebooks/marimo-wasm.html --mode edit
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run: uv run marimo export html-wasm docs/notebooks/marimo-wasm.mo.py -o docs/notebooks/marimo-wasm.mo.html --mode edit
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- name: Check that widget renders in HTML output using Playwright
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run: pnpm exec playwright test
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working-directory: ./tests-widget

‎.gitignore‎

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!tests/data/test.ome.tif
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./notebooks/
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docs/notebooks/data/
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docs/notebooks/data-cropped/
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docs/notebooks/*.html
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docs/notebooks/*.ipynb
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docs/notebooks/*.zarr/
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__pycache__/
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.snakemake/
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.coverage
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demos/*/data/
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demos/*/vitessce.local.json
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demos/*/vitessce.remote.json
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.pytest_cache/
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__marimo__/
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# Compiled javascript
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vitessce/static/

‎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": "vblA",
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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": "code",
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"execution_count": null,
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"id": "lEQa",
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"metadata": {},
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"outputs": [],
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"source": [
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"## 3. Convert UCSC Cell Browser project to a Vitessce view config"
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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": "Hstk",
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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": "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": "BYtC",
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"metadata": {},
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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": "markdown",
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"id": "bkHC",
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"metadata": {},
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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": "markdown",
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"id": "MJUe",
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"metadata": {},
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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": "markdown",
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"id": "Kclp",
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"metadata": {},
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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": "markdown",
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"id": "Xref",
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"metadata": {},
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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": "markdown",
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"id": "Hbol",
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"metadata": {},
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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": "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": "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": "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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}

‎docs/notebooks/__ipynb__/config_to_python.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": "MJUe",
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"metadata": {},
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"outputs": [],
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"source": [
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"from vitessce import VitessceConfig, VitessceChainableConfig, VitessceConfigDatasetFile"
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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": "vblA",
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"metadata": {},
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"outputs": [],
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"source": [
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"from example_configs import dries as dries_config"
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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": "ROlb",
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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": "code",
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"execution_count": null,
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"id": "lEQa",
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"metadata": {},
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"outputs": [],
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"source": [
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"vc = VitessceConfig.from_dict(dries_config)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "nWHF",
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"metadata": {},
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"source": [
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"## Evaluate the code and render a Vitessce widget"
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]
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},
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{
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"cell_type": "markdown",
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"id": "Hstk",
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"metadata": {},
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"source": [
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"The second value is the code snippet. When evaluated, the result will be a new `VitessceConfig` instance."
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]
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},
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{
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"cell_type": "markdown",
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"id": "PKri",
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"metadata": {},
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"source": [
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"## Print to JSON"
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]
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},
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{
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"cell_type": "markdown",
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"id": "SFPL",
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"metadata": {},
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"source": [
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"## Print to Python\n",
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"\n",
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"The `vc.to_python` function generates formatted Python code which can be used to re-generate the `vc` instance."
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]
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},
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{
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"cell_type": "markdown",
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"id": "RGSE",
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"metadata": {},
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"source": [
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"The first value returned is a list of classes used by the code snippet."
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]
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},
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{
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"cell_type": "markdown",
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"id": "bkHC",
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"metadata": {},
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"source": [
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"## Load a view config from a dict representation"
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]
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},
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{
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"cell_type": "markdown",
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"id": "Hbol",
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"metadata": {},
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"source": [
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"# Generate Python code to reconstruct a VitessceConfig instance"
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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": "BYtC",
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"metadata": {},
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"outputs": [],
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"source": [
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"imports, code = vc.to_python()"
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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": "Xref",
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"metadata": {},
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"outputs": [],
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"source": [
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"import json\n",
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"print(json.dumps(vc.to_dict(), indent=2))"
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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": "iLit",
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"metadata": {},
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"outputs": [],
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"source": [
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"reconstructed_vc = eval(code)"
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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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"print(code)"
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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": "Kclp",
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"metadata": {},
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"outputs": [],
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"source": [
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"imports"
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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": "ZHCJ",
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"metadata": {},
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"outputs": [],
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"source": [
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"reconstructed_vc.widget()"
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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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