Adding the rate_diff_transformation function.

[ptajvar]

rate_diff_transformation is an alternative transformation that has been shown to improve the raw pearson values for colocalization analysis especially in terms of removing the correlation between colocalization values and marker abundance. It is now being added as an option but will not be set as the default transformation yet for colocalization analysis (the default is currently log1p).

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Added a unit-test for colocalization calculation with rate-diff transformation to verify run without errors. The colocalization values with rate-diff transformation are also checked for different datasets and are shown to result in high agreement between raw pearson values and pearson_z scores and expected biological signals such as HLA-ABC with B2M and CD11a and CD18 appear consistently in top marker pairs.
There will be further inspection and comparison before setting this transformation as default.

PR checklist:

• This comment contains a description of changes (with reason).
• I have performed a self-review of my own code
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• I have checked my code and documentation and corrected any misspellings
• I have documented any significant changes to the code in CHANGELOG.md

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 81.81%. Comparing base (12c9bbc) to head (00be3d6).

Additional details and impacted files

@@           Coverage Diff            @@
##           dev     #138       +/-   ##
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+ Coverage     0   81.81%   +81.81%     
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  Files        0      118      +118     
  Lines        0     6560     +6560     
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+ Hits         0     5367     +5367     
- Misses       0     1193     +1193     

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[johandahlberg]

This looks really nice and clean! I had a small comment on the formatting of the doc sting. The other thing I think would be good to do is to add a simple test for rate_diff_tranformation. Lets fix that and then I think we are good to go.

[johandahlberg]

Super!