Options for UMAP generation

[sophie-harrington]

Hello!

I have been working with the raw counts data, from the facs-official-raw-obj.h5ad file, and wanted to regenerate the facs-specific clustering and UMAP projection from Extended Data Fig. 1A-C as an internal check. I'm not clear what code within the provided ipynb files was used to generate these plots in particular-- would you be able to point me towards it? In particular, which options were used to run the PCA and generate the neighborhood graph?

Thank you very much!