fix(dataProcessPlots): Remove duplicate log-transformation of intensity

[tonywu1999]

Motivation and Context

In this google group post, the user pointed out that medians were not equalized in the QC plot. After investigating, it looks to be a bug in the dataProcessPlots function.

Changes

• Remove code that log transforms the intensity into the abundance column in dataProcessPlots. This code essentially log transforms the data and removes all normalization applied earlier.

Testing

• Generated new plots with summary.data object and medians are equalized now.
• Added unit test that verified abundance data was not manipulated - i.e. medians are all equal

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules