[ENH] Add interaction map visualization utility using heatmap

[xPREMy]

Reference Issues/PRs

issue #283

What does this implement/fix? Explain your changes.

This PR introduces visualization utilities for AptaTrans interaction maps and restructures related tests.
Specifically, it:

• Adds _plot.py to utils, which implements robust functionality to visualize single-nucleotide and single-amino-acid resolution interaction maps.
• Restructures the tests by moving test_plot.py into the utils/tests/ directory to keep plotting tests clean and collocated with the utilities.
• Updates pipeline.py to integrate the new plotting utility into the core analytical pipeline, enabling proper tensor mapping and visualization outputs.

What should a reviewer concentrate their feedback on?

• The visual styling and accuracy of the heatmap plots generated by utils/_plot.py.
• The integration points in pipeline.py to ensure it passes data structures appropriately to the plotting function.
• The test coverage and assertions in utils/tests/test_plot.py.

Did you add any tests for the change?

• Yes, test_plot.py has been added/updated and run across the pipeline changes.

Any other comments?

PR checklist

• The PR title starts with either [ENH], [MNT], [DOC], or [BUG]. [BUG] - bugfix, [MNT] - CI, test framework, [ENH] - adding or improving code, [DOC] - writing or improving documentation or docstrings.
• Added/modified tests
• Used pre-commit hooks when committing to ensure that code is compliant with hooks. Install hooks with pre-commit install.
  To run hooks independent of commit, execute pre-commit run --all-files

[siddharth7113]

Hi, Please ensure pre-commit in installed and only if you have ran the check, please mark it in the PR.

Used pre-commit hooks when committing to ensure that code is compliant with hooks. Install hooks with pre-commit install.
To run hooks independent of commit, execute pre-commit run --all-files

[xPREMy]

Apologies, I’ve now rerun pre-commit, and the issues should be resolved. Would you mind reviewing it again?

[siddharth7113]

Please ensure your tests are passing before requesting a re-review.

[xPREMy]

I now have ran all the tests. would you please check again.

[NennoMP]

@xPREMy Couple of issues:

• (i) The TODO comment explicitly mentioned that an idea was to leave the untouched interaction map as is, rather than plot it. Before starting a PR, it would have made sense to at least have a discussion with maintainers within the corresponding issue.
• (ii) In my opinion, if we really want to add a plotting functionality, it should be within pyaptamer.aptatrans. The interaction map is unique so AptaTrans, so I would not put a method used by just one algorithm in utils.
• (iii) Most importantly, plotting should be implemented as a refactored version of the original authors' code (see method get_interaction_map at link).

Related to point (ii), I also don't see the plotting method being called and/or made available within the AptaTrans pipeline. Basically, the user is not able to use it via the pipeline right now, am I missing something?