Here is an example of RNA velocity from [Manno .et .al 2018](https://www.nature.com/articles/s41586-018-0414-6).

![enter image description here][1]

Colour of cells denote cell type. Layout denotes how cells cluster by some measure of similarity. The direction of the arrows denote the future state of the current cells. Or I guess one can say the differentiation trajectory.

What do length of the arrows denote? Can we say something about the propensity of that cell to differentiate in that direction? Can we say if there are more or less spliced or unspliced transcripts?

My understanding is that an arrow is based on the number of spliced and unspliced transcripts for each gene, summarised over all genes and further summarised over all cells in a small neighbourhood.

Other comments on understanding RNA velocity plots are welcome. I am trying to understand this better.

  [1]: https://i.ibb.co/YDmQJFN/41586-2018-414-Fig4-HTML.png
This paragraph in Svensson and Pachter, *Molecular Cell* 2018 (https://www.sciencedirect.com/science/article/pii/S1097276518307974) might help understand the concept of these arrows:

> "Long arrows, corresponding to large changes in gene expression, will
> in the low-dimensional representation imply that cells are undergoing
> rapid differentiation, while short arrows can be intuitively
> associated with terminally differentiated cells maintaining
> homeostasis. While some care needs to be taken when interpreting the
> lengths of arrows in low-dimensional representations, RNA velocity
> representations can be biologically informative. In principal
> component analysis, the vector lengths are meaningful, scaling
> linearly with RNA velocity estimates in high dimensions. We note that
> this will not be the case in t-SNE representations (Van der Maaten and
> Hinton, 2008), though directions remain meaningful and can be
> interpreted as “RNA arguments” in vector nomenclature."

