Projecting the simulated flows on a specific cluster

[jyang635]

Hi,

Thanks for developing this wonderful tool! The projection of simulated flow is very intuitive. I am wondering if there is a way to only project the flows (arrows) for a specific cluster on UMAP like what the paper did in figure 1d while assigning colors to different clusters?

All the best,
Junkai

[KenjiKamimoto-ac]

@jyang635

You can make plots for a specific cell population using Oracle_development_module.
Here is an example notebook. https://github.com/morris-lab/CellOracle/blob/master/docs/notebooks/05_simulation/misc/scale_up_simulation/01_Systematic_KO_simulations_Calculate_and_save_results.ipynb

In this notebook, we can specify a cell group of interest first, and then calculate and save the results.
I hope it helps.