samuell / gos-fork

A declarative library for Python designed to create interactive multi-scale visualizations of genomics and epigenomics data.

gos 🦆

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.

pip install gosling[all]

Documentation

See the Documentation Site for more information.

Example

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 of community examples in gosling/examples/. If you are interested in contributing, please feel free to submit a PR! Checkout the existing JSON examples if you are looking for inspiration.

Development

pip install -e '.[dev]'

The schema bindings (gosling/schema/) and docs (doc/user_guide/API.rst) are automatically generated using the following. Please do not edit these files directly.

# generate gosling/schema/*
python tools/generate_schema_wrapper.py

Release

git checkout main && git pull
git commit -m "v0.[minor].[patch]"
git tag -a v0.[minor].[patch] -m "v0.[minor].[patch]"
git push --follow-tags

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 and others on schemapi.