Enhance Van Krevelen and DBE plots with all-class view

[robertyoung3]

Summary

• Make classe parameter optional in plot_van_krevelen() and plot_dbe_vs_carbon_number() — when omitted, plots all assigned classes using existing atoms_ratio_all/carbon_number_all/dbe_all helper methods
• Add log_abundance parameter for log10 color scaling (useful for high dynamic range mass spec data)
• Add alpha parameter for configurable point transparency
• Add abundance-based z-ordering so higher values render on top
• Add colorbars and grid lines for readability
• Fully backward-compatible: existing plot_van_krevelen("O2") calls work unchanged

Test plan

• Verify plot_van_krevelen("O2") still works (single class, backward compat)
• Verify plot_van_krevelen() plots all assigned classes
• Verify plot_van_krevelen(log_abundance=True) applies log10 scaling
• Verify plot_dbe_vs_carbon_number() works with same parameter options
• Verify colorbar appears and labels correctly for both regular and log modes

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[kheal]

@robertyoung3; this seems pretty interesting - can you add some before/after examples (with code and figures) to the PR for easier review? Ideally using some of the test data shipped. This functionality would also be good to be integrated into one of the tests for CI/CD (see tests/ folder).

[robertyoung3]

DirectInfusion_FTICR_Tutorial.ipynb

Thanks for the guidance.

I have attached a Jupyter notebook based on the DirectInfusion_FTICR_Tutorial. I just changed the hard-coded datafile locations to something Path-based, and used ESI_NEG_SRFA_Auto.d in place of ESI_NEG_SRFA.d. The different plots are at the end of the notebook.

I also added tests as you requested using the classified_mass_spectrum fixture, and ran the full test suite. All tests passed. The added tests would run a little faster if the fixture was shared between the functions, but I didn't want to touch anything outside the test file.

I'll follow the same pattern with future enhancements.

Thank you!