Visualize chemical space is important task for chemoinformatitian. And there are lots of way to represent chemical space. One of the common approach is PCA. And recently tSNE and UMAP are used.
I wrote template code for plotting these data in my task but didn’t write code as a package.
Today I found useful package for making chemical space plot with python named ChemPlot. You can get and read the article from following URL.
The article is open access! https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/cmtd.202200005
And fortunately the author shared the code on github. Pepople who have interest the pacakge, can install chemplot via conda or pip commmand.
I installed the package with conda.
$ mamba install -c conda-forge -c chemplot chemplot
After the installation, I tried to use chemplot and uploaded the code. It’s really easy to make chemical space plot with chemplot. I could make not only static plot but also interactive plot. Following code doesn’t render interactive plot but it worked on my PC. Interactive plot provides structure image when mouse over on the plot.
It’s worth to use for making your chemical space plot. In summary there are lots of useful packages are available in python. Thanks for sharing the code!