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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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subset for velocity estimates and mapping #93

Open DRLaks opened 6 years ago

DRLaks commented 6 years ago

Is there a way to make the gene.relative.velocity.estimates and resultant map only for a subset of the data based on clusters?

gioelelm commented 6 years ago

From the way you refer to it, it seems that you are referring to the R implementation of velocyto. This Issues page is for python implementation.

Anyways, if instead, you were interested in the python implementation the answer follows.

You need to use the filter_cells methods and then proceed normally with the analysis. If clusters are derived somehow after feature selection or other analysis steps I recommend saving the cluster labels and restarting a new analysis from scratch and call filter_cells as one of the first lines.

DRLaks commented 6 years ago

Thanks for the quick response. I didn't realize this was for python and indeed I'd like input for R if possible.