faerun 0.1.25

A python package for generating interactive views of chemical spaces.

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

Installation

pip install faerun

Examples

• Drugbank 3D
• Drugbank 2D

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')

t = np.linspace(0, 12.0, 326)
s = np.sin(np.pi * t)
c = np.cos(np.pi * t)

faerun.add_scatter('my_scatter',  { 'x': t, 'y': s, 'z': c, 'c': t / max(t) })
faerun.plot()

The code above writes two files to the current directory: index.html and data.js. These files can be used locally or be moved to a (even minimalistic) web server.

TODO

• Add the abilty to draw shapes as well as colours
• Make output templatable

Documentation

Faerun(title='python-faerun', clear_color='#111111', coords=True, coords_color='#888888', view='free', shader='circle')

Parameter	Default	Description
title	'python-faerun'	The title of the HTML document.
clear_color	'#111111'	The clear colour, or background colour is used to clear the canvas after each rendering step.
coords	True	Whether or not to draw the coordinate axes.
coords_color	'#888888'	The colour used to draw the coordinate axes.
coords_box	False	Whether or not to show an encosing box as part of the coordinates.
view	'free'	The view mode. Available options: free, front, back, left, right, bottom, top

Faerun.add_scatter(self, name, data, mapping={'x': 'x', 'y': 'y', 'z': 'z', 'c': 'c', 's': 's', 'labels': 'labels'},
                   colormap='plasma', shader='sphere', point_scale=1.0, max_point_size=100, fog_intensity=0.0, interactive=True)

Parameter	Default	Description
name		The name of the plot (has to be unique, if another plot with the same name is added, the existing one will be overwritten).
data		A dict or a Pandas DataFrame containing the data.
mapping	{'x': 'x', 'y': 'y', 'z': 'z', 'c': 'c', 's': 's', 'labels': 'labels'}	The mapping from the dict or DataFrame to the plot attributes.
colormap	'plasma'	The colour map to be used. Valid values are matplotlib colormap names.
shader	circle	The name of the shader used to draw the points. Available options: circle, smoothCircle, sphere
point_scale	1.0	The scale of the points, which is also the radius for raycaster intersections.
max_point_size	100	The maximum size of a point when zooming in.
fog_intensity	0.0	The intensity of the fog (points further away fade to the background colour).
interactive	True	Whether the points are interactive (can be hovered).
, shader='circle'

Faerun.add_tree(self, name, data, mapping={'form': 'form', 'to': 'to', 'x': 'x', 'y': 'y', 'z': 'z', 'c': 'c'},
                color='#666666', colormap='plasma', fog_intensity=0.0, point_helper=None)

Parameter	Default	Description
name		The name of the plot (has to be unique, if another plot with the same name is added, the existing one will be overwritten).
data		A dict or a Pandas DataFrame containing the data.
mapping	{'form': 'form', 'to': 'to', 'x': 'x', 'y': 'y', 'z': 'z', 'c': 'c', 's': 's', 'labels': 'labels'}	The mapping from the dict or DataFrame to the plot attributes.
color	'#666666'	The default colour used when no colour values are supplied.
colormap	'plasma'	The colour map to be used. Valid values are matplotlib colormap names.
fog_intensity	0.0	The intensity of the fog (points further away fade to the background colour).
point_helper	None	Using coordinates from a point helper (specified by name) via indices.

Faerun.plot(file_name='index', path='./', template='default')

Parameter	Default	Description
file_name	'index'	The file name that is given to both the html and js file.
path	'./'	The path to which the HTML and data files will be written.
template	'default'	The HTML template to use. Currently the following templates are available: 'default', 'url_image', and 'smiles'