Regression and scaling in scanpy

Question

[bioinfo]

Hello,

I was given a script using scanpy for analysis from a coworker that has left and I am trying to understand the analysis steps. He mainly seems to have followed the instructions from here https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering-2017.html.

However, I am trying to understand a few steps of the analysis.

I see that he regressed and scaled the data as shown below:

sc.pp.regress_out(adata, ["total_counts")]
sc.pp.scale(adata, max_value=10)

However, from what I understand that adata.raw (which contained the log normalized data) is being used for visualizations (eg. UMAP, matrixplots) and for DE analysis. Are the regressed and scaled data used in any part of the analysis?

Thank you