Easy Vitessce

🪄 Configure Vitessce with a single line of code!

Turn your static Scanpy and SpatialData plots into interactive Vitessce visualizations simply by importing the easy_vitessce package!

Supported Functions

• sc.pl.umap
• sc.pl.tsne
• sc.pl.pca
• sc.pl.embedding
• sc.pl.spatial
• sc.pl.violin
• sc.pl.dotplot
• sc.pl.heatmap
• sdata.pl (.render_images, .render_labels, and .render_shapes)

See the documentation for further details.

Installation

Install package using pip:

pip install easy_vitessce

How to Use

Importing Easy Vitessce

import easy_vitessce as ev

🪄 By default, interactive plots are enabled via this import statement.

Deactivating Interactive Plots:

ev.configure_plots(disable_plots = ["embedding", "violin", "spatialdata-plot"])

Reactivating Interactive Plots:

ev.configure_plots(enable_plots = ["spatialdata-plot"])

Development

Set up environment

uv sync --extra dev --extra docs

This command should also be run after updating dependencies in pyproject.toml.

Run tests

# uv sync --extra dev
uv run pytest

Make documentation

uv run make html # on mac/linux
# uv run make.bat html # on windows
open _build/html/index.html

Launch Jupyter notebook or lab

# uv sync --extra dev
uv run jupyter notebook --notebook-dir .
# or
uv run jupyter lab --notebook-dir .