In ChemPlot, three different dimensionality reduction methods (PCA, t-SNE, and UMAP) can be applied to map the molecules onto 2D. Figure shows the representative visualizations of the Blood-brain barrier penetration (BBBP) and AqSolDB datasets that have been generated by applying these three methods. While PCA provides a linear projection of given dimensions, both t-SNE and UMAP apply non-linear 2D mappings by clustering and locating molecules depending on their local neighborhoods. For the t-SNE and UMAP parameters, users can choose between the two available options of: i) resorting to the optimized values that are calculated and assigned automatically by ChemPlot, or ii) assigning the values themselves.