Make interactive chemical space plot in jupyter notebook #cheminformatics #Altair

I often use seaborn for data visualization. With the library, user can make beautiful visualization.
BTW, today I tried to use another library that can make interactive plot in jupyter notebook.
Name of the library is ‘altair’.
https://altair-viz.github.io/index.html
The library can be installed from pip or conda and this package based vega and vega-lite. Vega is a python package for data visualization.

Regarding the tutorial, Altair can make beautiful plow with very simple code. I wrote an example that plot chemical space of cdk2.sdf which is provided by RDKit.

Following code is conducted in Google colab.
At first install rdkit in my environment. Fortunately Altair can call directly without installation to colab.

!wget https://repo.anaconda.com/miniconda/Miniconda3-4.5.1-Linux-x86_64.sh
!chmod +x Miniconda3-4.5.1-Linux-x86_64.sh
!time bash ./Miniconda3-4.5.1-Linux-x86_64.sh -b -f -p /usr/local
!time conda install -q -y -c conda-forge rdkit

After installation of RDKit, append rdkit path to sys path,

import sys
import os
sys.path.append('/usr/local/lib/python3.6/site-packages/')

Now ready. Let’s import some libraries.

import pandas as pd
import numpy as np
import altair as alt

from rdkit import Chem
from rdkit import rdBase
from rdkit.Chem import AllChem
from rdkit.Chem import DataStructs
from rdkit.Chem import PandasTools
from rdkit.Chem import RDConfig
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

from sklearn.decomposition import PCA

Then load dataset

moldf = PandasTools.LoadSDF(os.path.join(RDConfig.RDDocsDir, 'Book/data/cdk2.sdf'))
moldf['SMILES'] = moldf.ROMol.apply(Chem.MolToSmiles)
def mol2fparr(mol):
    arr = np.zeros((0,))
    fp = AllChem.GetMorganFingerprintAsBitVect(mol,2)
    DataStructs.ConvertToNumpyArray(fp, arr)
    return arr

The conduct PCA with molecular fingerprint for plot chemical space.
And make new dataset. cdk2.sdf has Cluster number, so I used the annotation for coloring.

pca = PCA(n_components=2)
X = np.asarray([mol2fparr(mol) for mol in moldf.ROMol])
print(X.shape)
res = pca.fit_transform(X)
print(res.shape)
moldf['PCA1'] = res[:,0]
moldf['PCA2'] = res[:,1]
moldf2 = moldf[['ID', 'PCA1', 'PCA2', 'SMILES' ]]
moldf2['Cluster'] = ["{:0=2}".format(int(cls)) for cls in moldf.loc[:,'Cluster']]

To make scatter plot in Altair, it is easy just call ‘alt.Cahrt.mark_point(pandas data frame)’
mark_* is the method which can access many kids of plots.
From the document, following plots are provided.

Mark Name Method Description Example
area mark_area() A filled area plot. Simple Stacked Area Chart
bar mark_bar() A bar plot. Simple Bar Chart
circle mark_circle() A scatter plot with filled circles. One Dot Per Zipcode
geoshape mark_geoshape() A geographic shape Choropleth Map
line mark_line() A line plot. Simple Line Chart
point mark_point() A scatter plot with configurable point shapes. Multi-panel Scatter Plot with Linked Brushing
rect mark_rect() A filled rectangle, used for heatmaps Simple Heatmap
rule mark_rule() A vertical or horizontal line spanning the axis. Candlestick Chart
square mark_square() A scatter plot with filled squares. N/A
text mark_text() A scatter plot with points represented by text. Bar Chart with Labels
tick mark_tick() A vertical or horizontal tick mark. Simple Strip Plot

Now I would like to make scatter plot, so I call mark_point.
“interactive()” method returns interactive plot in jupyter.
So After run the code, I can see interactive plot in notebook the plot returns tooltip when mouse over the point.

alt.Chart(moldf2).mark_point().encode(
           x = 'PCA1',
           y = 'PCA2',
           color = 'Cluster',
           tooltip = ['ID', 'SMILES']).interactive()

This library is interesting for me because it is easy to implement tooltip. I tried to embed SVG image to tooltip but it did not work. I would like to know how to embed image to the tooltip if it possible.

How to visualize your data is important because it receives different impression from different visualization even if data is same.

Reader who is interested in the post can found whole code from google colab or github. ;-)
https://colab.research.google.com/drive/1hKcWRBcQG51eGsbpDBF2gl6CoZsmVvTs
https://github.com/iwatobipen/playground/blob/master/plot_chemicalspace.ipynb

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