Towards reliable quantification of cell state velocities
Fig 2
Visualisation of simulated velocities with linear and nonlinear projection methods.
A. Velocities projected on PCA embedding. The blue outline highlights a region of high velocity variation and the red outline shows a low-variance, high-velocity region. The arrows in the PCA linear projection capture both the plasticity in direction and magnitude of the velocities. B. Velocities projected on PCA embedding by scVelo. scVelo smoothes the velocities as artefact of the projection method, thereby losing the information on cell state velocities variation as illustrated in the cells outlined in blue. scVelo also loses the information of vector length as shown in the cells outlined in red. C. Summary of velocity projection using the Nyström method D-E. Velocities projected by Nyström-projection method shown on PCA in (D) and t-SNE in (E).