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wgzgithub / VeTra

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How to get the delta_embedding from velocyto? #1

Open danshu opened 4 years ago

danshu commented 4 years ago

Hi,

"delta_embedding - a txt file with N cells in rows and 2D velocity vectors in columns. Users can run "velocyto"(http://velocyto.org/) or "scVelo" (https://github.com/theislab/scvelo) to get delta_embedding." I have checked the velocyto output but can not find the 2D velocity vectors. I can only find "current" and "projected" gene-cell matrix, which may need further projection into the current embedding for the velocity vectors.

Best, danshu

wgzgithub commented 3 years ago

Hi, for example, you created a objective in velocyto like"vlm = vcy.VelocytoLoom("data/DentateGyrus.loom")" . After running velocity analysis, you will get delta_embedding by vlm.delta_embedding