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morris-lab / CellOracle

This is the alpha version of the CellOracle package
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Vector Plots #185

Open sarah-chapin opened 4 months ago

sarah-chapin commented 4 months ago

Hello,

I am analyzing the results of a in silico perturbation experiment, and I would like to make sure my interpretation of the vector plot is correct.

To clarify, is it correct to say that a vector that begins inside of a given cell cluster and ends outside of the cluster indicates a decrease in the number of cells in that cluster post perturbation, while a vector that begins and ends inside the same cluster indicates an increase in the number of cells in that cluster post perturbation?

Additionally, is there a way to visualize the in silico perturbation results more quantitatively, such as generating post-perturbation cell cluster numbers?

KenjiKamimoto-wustl122 commented 4 months ago

CellOracle simulates the shift of cell identity rather than absolute cell number prediction. This is why we are focusing on the vector flow visualization. I'm sorry but the generating post perturbation cell cluster number is out of scope.