https://github.com/dvdkouril/chromospyce
chromospace but as a notebook widget
https://github.com/dvdkouril/chromospyce
hidivelab
Last synced: 11 months ago
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chromospace but as a notebook widget
- Host: GitHub
- URL: https://github.com/dvdkouril/chromospyce
- Owner: dvdkouril
- Created: 2024-03-05T23:52:42.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-12-18T20:06:30.000Z (over 1 year ago)
- Last Synced: 2025-07-01T02:04:56.180Z (11 months ago)
- Topics: hidivelab
- Language: Jupyter Notebook
- Homepage:
- Size: 1.97 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# chromospyce
This is an [anywidget](https://github.com/manzt/anywidget)-powered version of
the [chromospace](https://github.com/dvdkouril/chromospace) library intended
for use in computational notebooks, such as Jupyter Notebook.
## Basic usage
The available functionality is pretty limited at this moment. We will stabilize the API as we go. At this point, you can display 3D chromatin models.
```python
import chromospyce
import numpy as np
BINS_NUM = 1000
# Step 1: Generate random structure, returns a 2D numpy array:
def make_random_3D_chromatin_structure(n):
position = np.array([0.0, 0.0, 0.0])
positions = [position.copy()]
for _ in range(n):
step = np.random.choice([-1.0, 0.0, 1.0], size=3) # Randomly choose to move left, right, up, down, forward, or backward
position += step
positions.append(position.copy())
return np.array(positions)
random_structure = make_random_3D_chromatin_structure(BINS_NUM)
# Step 2: Display the structure in a chromospyce widget
numbers = list(range(0, BINS_NUM+1))
vc = {
"color": {
"values": numbers,
"min": 0,
"max": BINS_NUM,
"colorScale": "Spectral"
},
"scale": 0.01,
"links": True,
"mark": "sphere"
}
chromospyce.Widget(random_structure, vc)
```
The underlying JS library, **chromospace**, [only supports data in the Apache
Arrow
format](https://github.com/dvdkouril/chromospace/tree/main/docs#data-loading).
In **chromospyce**, on the other hand, you can also visualize structures
defined as 2D numpy arrays, or pandas dataframe (with columns named `'x'`,
`'y'`, `'z'`.
Quickly test out **chromospyce** with [uv](https://docs.astral.sh/uv/):
1. `uv run --with chromospyce --with numpy --with pyarrow --with jupyterlab
jupyter lab`
2. make a new notebook
3. copy and paste the code above into an empty cell
Or: [run the example in Google
Colab](https://colab.research.google.com/drive/1EZh9HcGS3cgPF4C6eFyMm5iHGVGS4Cj_?usp=sharing).
## Contributing
Running tests:
`uv run pytest`