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velocyto-team / velocyto.R

RNA velocity estimation in R
http://velocyto.org
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Reversing velocities? #48

Open LineWulff opened 5 years ago

LineWulff commented 5 years ago

Hi,

Thanks for the awesome package!! I have been playing around with my dataset with velocyto for some time now and are wondering about a few things: 1) The velocities are reversed to what is expected and for some points which is already proven. I have mixed cell lineages and they are lying close to each other in the embedding. I guess I have a problem with neighborhoodbased projections probably with different attractors too. Is there any way to solve this? 2) What the "scale" parameter in the show.velocity.on.embedding.cor() function does? As far as I have understood, it is how arrows/velocities are scaled compared to single cells? Which is best recommended and why? In tutorials you have used sqrt but I can't find an explanation to why. 3) Is it possible to calculate the velocities (and show them on embedding) for a specific list of genes? E.g. for a specific lineage of cells. IF this is a possibility how many genes would I have to include? And can it be differentially expressed genes for one lineage?

Hope you can help me out so I can get even more use of your package.

tiagobrc commented 4 years ago

@LineWulff Did you manage to figure this out? I also have experienced the opposite direction to known trajectory experiments.

tiagobrc commented 4 years ago

Any thoughts regarding this? Or does it makes no sense? What are the assumption regarding the direction of the arrows?

vagabond12 commented 4 years ago

I have the same problem. Is it caused by the qualities of transcriptomes sequenced? If so, is there any method to estimate it?

I consider the authors of this software must reply this issue.

Thank anyone that could help us.

tiagobrc commented 3 years ago

I suggest reading all the supplementary note 2 (considerations for accurate determination and visualization of RNA velocity) of the RNA velocity publication. All of these questions are addressed there.