Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways
Fig 2
LPCA (a), t-SNE (b) and Jaccard coefficients (c) derived from a binary reaction matrix from differential reactions in 222 Escherichia GSMMs.
In panels (a) and (b), points represent individual GSMMs, with different genera indicated by distinct symbols and colors. The top row in panel (c) uses these same colors to indicate the corresponding genera. Circles in panel (a) highlight clusters of E. albertii strains (blue), E. fergusonii strains (red), and a mixed cluster of E. coli, S. dysenteriae, S. flexneri, and Clades II to VIII (orange). Labeled arrows in panel (a) denote subsystem-centric loading vectors from LPCA (refer to the results and methods section for definitions).