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velocyto-team / velocyto.R

RNA velocity estimation in R
http://velocyto.org
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Problem with precalculated tsne coordinates #12

Open abhaduri opened 6 years ago

abhaduri commented 6 years ago

When I run the program with tSNE.velocity.plot, it works fine with my rvel, but when I run show.velocity.on.embedding.cor I get the dots colored by cluster and in the tSNE space I am aiming for, but there are no velocity arrows. The rvel is clearly fine though, because the tSNE.velocity.plot on the exact same data shows them.

Any help would be appreciated!

pkharchenko commented 6 years ago

Can you show the command you’re using to do .cor projection? No arrows (only dots) would indicate that the velocity vectors projected into this embedding space were too small. There can be a few reasons for that … such as too small of a neighborhood which is being used for projection (the recommendation for n is somewhere within 1/5 to 2/3 of the number of cells in the embedding). You can also increase arrow.scale parameter to simply increase the length of the arrows being drawn … but if you’re not seeing any arrows at the default scale that probably means the estimated projections are too small.

The tSNE.velocity.plot() can be tricky, as extrapolated positions may end up clustering together. Best, -peter.

On Jan 26, 2018, at 2:05 PM, abhaduri notifications@github.com wrote:

When I run the program with tSNE.velocity.plot, it works fine with my rvel, but when I run show.velocity.on.embedding.cor I get the dots colored by cluster and in the tSNE space I am aiming for, but there are no velocity arrows. The rvel is clearly fine though, because the tSNE.velocity.plot on the exact same data shows them.

Any help would be appreciated!

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abhaduri commented 6 years ago

Hi there-

There are no dots even, just blank circles. Could there be an error in the arrow drawing part of the command?

Here is the command I am using.

show.velocity.on.embedding.cor(emb,vel,n=2000,scale='sqrt',cell.colors=ac(cell.colors,alpha=cell.alpha),cex=cell.cex,arrow.scale=arrow.scale,arrow.lwd=1)

Thanks!

Aparna