3. Visualization

import pyrfume
import seaborn as sns
sns.set(font_scale=1.5)
sns.set_style('whitegrid')

molecules = pyrfume.load_data('my_data/molecules.csv')  # Load the data from the last chapter

Now that our molecules have standard representations (from Part 1), we can easily visualize them:

from pyrfume.odorants import display_molecules
display_molecules(molecules)
_images/visualization_3_0.png

Or we can ask where they live in low-dimensional spaces built from features, compared with other odorous molecules.

from pyrfume.odorants import embed_molecules
acetophenone = molecules.loc[[7410]]
embed_molecules(acetophenone)
_images/visualization_5_0.png

The above shows thousands of molecules from the Pyrfume database (black) and acetophenone in red, using a 2-dimensional UMAP embedding built from those thousands of molecules.