Tutorial 1 v2 extended notes

[josenimo]

ensured tutorial 1 changes, and jupyter notebook translation into docs work.

[Copilot]

Pull Request Overview

This PR updates the documentation for Tutorial 1, archives the old tutorial notebook, and ensures the Jupyter notebook is correctly translated into the docs.

• Removed the deprecated plotting.pca entry from the API docs.
• Archived the old Proteomics Integration notebook and cleaned up the main notebook.
• Updated the tutorial index headings and link labels for consistency.

Reviewed Changes

Copilot reviewed 4 out of 11 changed files in this pull request and generated no comments.

File	Description
docs/api/plotting.md	Removed the plotting.pca entry from the list
docs/Tutorials/index.md	Changed heading levels to ## and renamed the “Tutorials” section to “Tutorial links”
docs/Tutorials/T2_ProteomicsIntegration.ipynb	Removed the standalone title cell from the main tutorial
docs/Tutorials/old/T2_ProteomicsIntegration.ipynb	Added archived version of the Proteomics Integration notebook

Comments suppressed due to low confidence (3)

docs/api/plotting.md:27

• If plotting.pca is still supported in the code, please re-add it or note its deprecation and redirect users to the new plotting.pca_loadings function.

    plotting.pca_loadings

docs/Tutorials/index.md:19

• [nitpick] The link text uses lowercase “analysis” but the heading is “Image Analysis”; consider matching the casing for consistency.

- [Tutorial 1: Image analysis](T1_ImageAnalysis)

docs/Tutorials/T2_ProteomicsIntegration.ipynb:3

• [nitpick] The top markdown cell with the tutorial title was removed; consider restoring a header cell (e.g. # Integrating proteomics and imaging data) for clarity in standalone notebook views.

  {