fix(dataProcessPlotsPTM): Fix documentation around originalPlots parameter

[tonywu1999]

Motivation and Context

Documentation was confusing w.r.t what the originalPlots parameter does, leading to confusion with implementation in MSstatsShiny

Changes

Please provide a detailed bullet point list of your changes.

• Clarify that originalPlots is the profile plot without summarization, not normalization.

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

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 48b97048-1989-4077-bab4-cd8326a44a3d

📥 Commits

Reviewing files that changed from the base of the PR and between c753b85 and b75343e.

📒 Files selected for processing (3)

• R/dataProcessPlotsPTM.R
• man/DIANNtoMSstatsPTMFormat.Rd
• man/dataProcessPlotsPTM.Rd

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix-docs

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