Interpreting the output of Single Cell Velocity Analysis
Single Cell Velocity Analysis outputs:
- A Velocity Matrix (
) containing
- the imputed spliced and unspliced counts for all sufficiently expressed genes that, optionally, also are HVGs;
- the estimated velocities for the velocity genes;
- the cell-to-cell transition probabilities. Note that negative transition probabilities indicate that the "from" cell is transitioning away from the "to" cell.
- A Cell Annotations (
) containing the velocity coherence and length. If the dynamical model was run, the output also contains the estimated latent time.
See The velocity estimation algorithm for details.
When using the Velocity Matrix in a Dimensionality Reduction Plot (see Dimensionality reduction), the velocities are projected onto the embedding and visualized as arrows. The velocity coherence, length and, if available, the latent time can also be visualized in the Dimensionality Reduction Plot as any other Cell Annotations. See Manual Annotation for details.