https://github.com/gosling-lang/gos
A declarative interactive genomics visualization library for Python.
https://github.com/gosling-lang/gos
biovis colab data-visualization dataviz gosling grammar hidivelab higlass jupyter python visualization
Last synced: about 1 month ago
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A declarative interactive genomics visualization library for Python.
- Host: GitHub
- URL: https://github.com/gosling-lang/gos
- Owner: gosling-lang
- License: mit
- Created: 2021-07-20T18:00:50.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-08-26T06:29:35.000Z (2 months ago)
- Last Synced: 2025-09-06T22:51:14.674Z (about 2 months ago)
- Topics: biovis, colab, data-visualization, dataviz, gosling, grammar, hidivelab, higlass, jupyter, python, visualization
- Language: Python
- Homepage: https://gosling-lang.github.io/gos
- Size: 13 MB
- Stars: 230
- Watchers: 3
- Forks: 16
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# gos 🦆
[](https://github.com/gosling-lang/gos/raw/main/LICENSE)
[](https://pypi.org/project/gosling)
[](https://github.com/gosling-lang/gos/actions)
**gos** is a declarative genomics visualization library for Python. It is built
on top of the [Gosling] JSON specification, providing a simplified interface for
authoring interactive genomic visualizations.
## Installation
> The **gos** API is under active development. Feedback is appreciated and
> welcomed.
```bash
pip install gosling[all]
```
## Documentation
See the [Documentation Site](https://gosling-lang.github.io/gos) for more
information.
## Example
```python
import gosling as gos
data = gos.multivec(
url="https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec",
row="sample",
column="position",
value="peak",
categories=["sample 1", "sample 2", "sample 3", "sample 4"],
binSize=5,
)
base_track = gos.Track(data, width=800, height=100)
heatmap = base_track.mark_rect().encode(
x=gos.X("start:G", axis="top"),
xe="end:G",
row=gos.Row("sample:N", legend=True),
color=gos.Color("peak:Q", legend=True),
)
bars = base_track.mark_bar().encode(
x=gos.X("position:G", axis="top"),
y="peak:Q",
row="sample:N",
color=gos.Color("sample:N", legend=True),
)
lines = base_track.mark_line().encode(
x=gos.X("position:G", axis="top"),
y="peak:Q",
row="sample:N",
color=gos.Color("sample:N", legend=True),
)
gos.vertical(heatmap, bars, lines).properties(
title="Visual Encoding",
subtitle="Gosling provides diverse visual encoding methods",
layout="linear",
centerRadius=0.8,
xDomain=gos.GenomicDomain(chromosome="1", interval=[1, 3000500]),
)
```
## Example Gallery
We have started a
[gallery](https://gosling-lang.github.io/gos/gallery/index.html) of community
examples in `gosling/examples/`. If you are interested in contributing, please
feel free to submit a PR! Checkout the
[existing JSON examples](http://gosling-lang.org/examples/) if you are looking
for inspiration.
## Changelog
Check the [GitHub Releases](https://github.com/gosling-lang/gos/releases) for a
detailed changelog.
## **Development**
The source code for **gos** is a hybrid of Python and TypeScript (used for the
[anywidget](https://github.com/manzt/anywidget) component). It requires both:
- [uv](https://github.com/astral-sh/uv) (for Python development)
- [Deno](https://deno.land) (for building the widget)
Please ensure both are installed before proceeding.
**Tests**
Run the test suite with:
```sh
uv run pytest
```
**Notebooks**
To try out the library in the example `notebooks/`, launch Jupyter Lab with:
```sh
uv run jupyter lab
```
**Widget**
The widgets implementation is split between `./gosling/_widget.py` (the Python
component) and `./frontend/widget.ts` (the TypeScript component).
To modify the widget's behavior in the front end, edit `./frontend/widget.ts`
and compile with:
```sh
deno task build
```
Use `deno task dev` to watch for changes and recompile automatically.
**Docs**
To build and preview the documentation locally:
```sh
uv run docs/build.py
uv run python -m http.server -d docs/dist
```
Open your browser to http://localhost:8000 to view the generated docs.
**Auto-generate Schema Bindings**
Much of the Python code in this repository is automatically generated from the
Gosling schema to keep the bindings in sync. This includes both the bindings in
`gosling/schema/` and the corresponding API documentation in
`doc/user_guide/API.rst`.
Do not edit these files manually. Instead, regenerate them using:
```sh
# Update gosling/schema/*
uv run tools/generate_schema_wrapper.py
# Update API docs
uv run tools/generate_api_docs.py
```
Use a `tag_name` that corresponds to a valid
[Gosling.js Release](https://github.com/gosling-lang/gosling.js/releases) (e.g.,
`v0.12.3`).
You must commit the changes and create a new release. Schema updates usually
require at least a minor version bump, but the exact versioning is up to the
maintainer.
## Release
Releases are managed via the GitHub UI. The release **tag determines the package
version** published to PyPI.
[Draft a new release](https://github.com/gosling-lang/gos/releases/new):
1. **Create a tag**
- Click _"Choose a tag"_, then **type a new tag** in the format
`v[major].[minor].[patch]` to create it.
- _Note_: The UI is not obvious about this. You can create a tag here, not
just select one.
2. **Generate release notes**
- Click _"Generate Release Notes"_ to auto-summarize changes from merged PRs.
- Edit to exclude irrelevant changes for end users (e.g., docs or CI).
3. **Document significant changes**
- Add migration steps or noteworthy updates.
- Ensure PR titles are clear and consistent.
4. **Publish the release**
- Click _Publish release_ to make it public.
- This triggers a [workflow](.github/workflows/release.yml) that builds the
package and publishes it to PyPI using the new tag.
## Design & Implementation
gos is inspired by and borrows heavily from [Altair] both in project philosophy
and implementation. The internal Python API is auto-generated from the [Gosling]
specification using code adapted directly from Altair to generate [Vega-Lite]
bindings. This design choice guarantees that visualizations are type-checked in
complete concordance with the [Gosling] specification, and that the Python API
remains consistent with the evolving schema over time. Special thanks to
[Jake Vanderplas](https://github.com/jakevdp) and others on
[`schemapi`](https://github.com/altair-viz/altair/tree/master/tools/schemapi).
[Gosling]: https://github.com/gosling-lang/gosling.js
[Altair]: https://github.com/altair-viz/altair
[Vega-Lite]: https://github.com/vega/vega-lite