Added intercept to regress_out()

[ggit12]

Added the boolean argument "add_intercept" to regress_out, and implemented code to optionally add the intercept back to the residuals in the result of regress_out().

• Closes Best practices for using regress_out? theislab/single-cell-tutorial#35
• Tests included or not required because:

• Release notes not necessary because:

[ggit12]

@LuckyMD

[codecov]

Codecov Report

Attention: Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 75.44%. Comparing base (a28fe88) to head (5063fe9).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/scanpy/preprocessing/_simple.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2731      +/-   ##
==========================================
- Coverage   75.44%   75.44%   -0.01%     
==========================================
  Files         113      113              
  Lines       13250    13254       +4     
==========================================
+ Hits         9997     9999       +2     
- Misses       3253     3255       +2     

Files with missing lines	Coverage Δ
src/scanpy/preprocessing/_simple.py	89.75% <50.00%> (-0.41%)	⬇️

[flying-sheep]

Hi! Can you explain a bit what use cases this helps people with? When would one want to set this to True?

Once we have a good example, you can use that to write a small test that checks if it works as intended.

[ggit12]

Hi,

I believe @LuckyMD detailed one use case here theislab/single-cell-tutorial#35.

Is this enough to get started?

[danielee0707]

Thanks for implementing this! I used it to regress out total counts and cell cycle scores before highly variable gene selection, and it worked well. The clusters are better separated without artifacts, unlike running regressing function after HVG.

[flying-sheep]

Is this enough to get started?

For sure, thank you for the context!

Is it possible to add a unit test that checks that with this set to True, clusters are better separated?