ipygosling

Here be dragons 🐉

This is an experimental project that is planned to merge with gosling.py. Feedback is much appreciated and most welcomed. Please use with caution.

pip install gosling

Usage

import gosling as gos

data = gos.Data(
    url="https://resgen.io/api/v1/tileset_info/?d=UvVPeLHuRDiYA3qwFlm7xQ",
    type="multivec",
    row="sample",
    column="position",
    value="peak",
    categories=["sample 1"],
    binSize=5,
)

track = gos.Track(data=data, layout="linear").mark_bar().encode(
    y="peak:Q",
    x="start:G",
    xe="end:G",
    stroke=gos.Channel(value=0.5),
    strokeWidth=gos.Channel(value=0.5),
).properties(width=180)

spec = track.view(title="Basic Marks: Bar", subtitle="Tutorial Examples")

print(spec.to_json())

# {
#   "subtitle": "Tutorial Examples",
#   "title": "Basic Marks: Bar",
#   "tracks": [
#     {
#       "data": {
#         "binSize": 5,
#         "categories": [
#           "sample 1"
#         ],
#         "column": "position",
#         "row": "sample",
#         "type": "multivec",
#         "url": "https://resgen.io/api/v1/tileset_info/?d=UvVPeLHuRDiYA3qwFlm7xQ",
#         "value": "peak"
#       },
#       "height": 180,
#       "layout": "linear",
#       "mark": "bar",
#       "stroke": {
#         "value": 0.5
#       },
#       "strokeWidth": {
#         "value": 0.5
#       },
#       "width": 180,
#       "x": {
#         "field": "start",
#         "type": "genomic"
#       },
#       "xe": {
#         "field": "end",
#         "type": "genomic"
#       },
#       "y": {
#         "field": "peak",
#         "type": "quantitative"
#       }
#     }
#   ]
# }

Jupyter notebook

spec # render spec in jupyter cell!

widget = gos.GoslingWidget(spec) # create widget
widget.spec = new_spec # update view

Development

pip install -e .

Generate source code (you should not need to run these steps)

The schema bindings (gosling/schema) and JS static assets (gosling/static/) are automatically generated using the following scripts. Please do not edit these files directly.

Python schema bindings

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

JavScript Jupyter extension/widget

yarn install && yarn build:js # generates gosling/static/{widget.js, index.js}

# Only run this if using gos.GoslingWidget
jupyter nbextension install --py --symlink --overwrite --sys-prefix gosling
jupyter nbextension enable gosling --py --sys-prefix

Add an example

We have started a gallery of community examples in example/. If you are intereseted in contributing, please feel free to submit a PR! Checkout the existing examples for gosling.js if you are looking for inspiration. To add an example, create a .py file in example, and add the new "route" for the website in example/routes.json.