Fig. 7

The RNA velocity application on FUCCI dataset. a RNA velocity vector field is visualized using the transition probability method on the UMAP embeddings of the FUCCI data. Each point represents a cell and is colored by the tricycle cell cycle position. b Phase portrait of gene MELK, of which the likelihood is the highest among all velocity genes inferred by the dynamical model. The purple lines represent the dynamics inferred by the dynamical model. c Scatter plot shows smoothed expression of MELK over cell cycle position. The dashed line is the fitted line by periodic loess (Methods). The expected direction of change is inferred on the fitted loess line and visualized by colors. d Scatter plot shows the estimated RNA velocity of MELK over cell cycle position. The signs of velocity estimations are compared to those inferred in c, with inconsistent directions colored purple/orange. The variance explained by cell cycle position (\(R^2\) in the figure) is comparable for velocity values compared to Ms in c. e The velocity latent time for MELK generally agrees with cell cycle position, except for cells around G1 or G0 phases (abbreviation: incons., inconsistent)