Faerun (Python)
Faerun (Python) is based on the Lore.js 3D WebGL engine for interactive big data rendering and the FUn project. It facilitates the creation of interactive (2D and 3D) HTML plots of chemical data (or chemical spaces). Molecular structures are rendered using SmilesDrawer.
Associated Publication: https://academic.oup.com/bioinformatics/article/34/8/1433/4657075
Examples
The code of the examples shown above for creating interactive 2D and 3D maps from Drugbank can be found in the examples directory. Following, a simple example of plotting any data:
import numpy as np
from faerun import Faerun
faerun = Faerun(view='free', shader='circle')
t = np.linspace(0, 12.0, 326)
s = np.sin(np.pi * t)
c = np.cos(np.pi * t)
faerun.plot({ 'x': t, 'y': s, 'z': c, 'c': t / max(t) })
TODO
- Add the abilty to draw shapes as well as colours
- Make output templatable
Documentation
Faerun(title='python-faerun', point_size=5, tree_color='#aaaaaa', clear_color='#111111', fog_intensity=2.6, coords=True, coords_color='#888888', view='free', shader='circle')
| Parameter | Default | Description |
|---|---|---|
| title | 'python-faerun' |
The title of the HTML document. |
| point_size | 5 |
The size of the points. |
| tree_color | '#aaaaaa' |
Not yet implemented. |
| clear_color | '#111111' |
The clear colour, or background colour is used to clear the canvas after each rendering step. |
| fog_intensity | 2.6 |
Fog is used to darken / lighten far away points depending on the clear_color. This is a visual cue helpful for depth perception in orthogonal projections. |
| coords | True |
Whether or not to draw the coordinate axes. |
| coords_color | '#888888' |
The colour used to draw the coordinate axes. |
| view | 'free' |
The view mode. Available options: free, front, back, left, right, bottom, top |
| shader | circle |
The name of the shader used to draw the points. Available options: circle, legacyCircle, sphere |
Faerun.plot(path, data, x='x', y='y', z='z', c='c', colormap='plasma', smiles='smiles', tree=None)
| Parameter | Default | Description |
|---|---|---|
| data | A dict or a Pandas DataFrame containing the data. |
|
| x | x |
The name of the column containing the x-coordinates. |
| x | y |
The name of the column containing the y-coordinates. |
| x | z |
The name of the column containing the z-coordinates. |
| c | c |
The name of the column containing the values by which the points are coloured. Has to be normalized between 0.0 and 1.0 |
| smiles | smiles |
The name of the column containing the SMILES strings with which the points are annotated. |
| path | '' |
The path to which the HTML and data files will be written. |
| tree | None |
Not yet implemented. |
1 maintainer
Metadata
1 maintainer
Release files for faerun 0.1.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| faerun-0.1.7.tar.gz | 6.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| faerun-0.1.7-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 17.0 kB
Release files / faerun-0.1.7.tar.gz
| Download URL | faerun-0.1.7.tar.gz |
|---|---|
| Size | 6.3 kB |
| Tags | Source |
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Release files / faerun-0.1.7-py3-none-any.whl
| Download URL | faerun-0.1.7-py3-none-any.whl |
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| Size | 10.7 kB |
| Tags | Python 3 |
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