chromospyce 0.1.0

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chromospyce

This is an anywidget-powered version of the 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.

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.

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:

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.