Simplifying MultiPlot Interface #83

[Nishantrde]

feat(ChromatogramPlot): Add tile_by parameter for automated subplot creation

• Introduced the tile_by parameter in ChromatogramPlot to split data into subplots automatically.
• Eliminated the need for manual canvas specification by handling subplot creation internally.
• Added validation to ensure the tile_by column exists in both the chromatogram and annotation data.
• Refactored code with a helper function to reduce duplication.
• Updated documentation and tests for the new functionality.

Summary by CodeRabbit

• New Features
  • Enhanced plotting capabilities now automatically group and tile visualizations, offering improved clarity and a more organized layout.
  • Expanded configuration options empower users to customize plot arrangements, including multi-run spectrum analysis with refined grid layouts.
• Refactor
  • Simplified error handling and streamlined plotting logic enhance stability and performance.

[coderabbitai[bot]]

Walkthrough

This pull request enhances plotting capabilities across multiple modules. Gallery scripts now automate subplot creation using a new facet_column parameter to group data, while the spectrum binning script supports multiple runs and a revised subplot layout. In internal modules, new configuration attributes (facet_column, facet_col_wrap) and validation logic have been added to support tiled layouts. Additionally, new methods in the Matplotlib plotting class manage subplot grid creation and axis cleanup. Minor updates include refined error handling, adjusted import statements, and small test file formatting changes.

Changes

File(s)	Change Summary
docs/gallery_scripts_template/plot_spyogenes_subplots_ms_matplotlib.py docs/gallery_scripts_template/plot_investigate_spectrum_binning_ms_matplotlib.py	Enhanced plotting logic to automate subplot creation using a facet_column, update subplot layouts (including a 4x2 grid for spectrum binning), and modify error and display handling.
pyopenms_viz/_config.py pyopenms_viz/_core.py	Added new attributes (facet_column, facet_col_wrap) to plotting configuration; restructured ChromatogramPlot.plot() with configuration validation and subplot grouping.
pyopenms_viz/__init__.py	Inserted a commented-out placeholder argument (tile_by) within the PlotAccessor class.
pyopenms_viz/_matplotlib/core.py	Introduced three new utility methods (_compute_y_range_and_padding, _create_subplots, _delete_extra_axes) for subplot management and set the Matplotlib backend to "Agg".
test/conftest.py test/test_spectrum.py	Added extra imports and a commented-out dynamic path resolution line; adjusted formatting (e.g. insertion of a blank line).

Sequence Diagram(s)

sequenceDiagram
    participant U as User/Application
    participant CP as ChromatogramPlot
    participant DF as DataFrame

    U->>CP: Call plot()
    CP->>CP: _validate_plot_config()
    alt Valid facet_column
        CP->>DF: Group data by facet_column
        DF-->>CP: Return grouped data
        CP->>CP: Create subplots and prepare tooltips
    else Invalid facet_column
        CP->>CP: Fallback to single plot logic
    end
    CP-->>U: Display plot with subplots

Possibly related PRs

• OpenMS/pyopenms_viz#82: Modifies subplot management and plot display methods, aligning closely with these plotting enhancements.
• OpenMS/pyopenms_viz#57: Involves similar enhancements in plotting functionality by introducing grouping parameters.
• OpenMS/pyopenms_viz#39: Introduces the facet_column parameter, directly relating to the new subplot configuration methods.

Suggested reviewers

• jcharkow

Poem

I'm a rabbit, hopping through code with glee,
Plotting data in subplots as neat as can be.
Facets and grids now dance in a row,
Each run and axis in a neat, tiled show.
I nibble through changes, swift and bright,
Celebrating each line from morning till night.
Carrots and code—what a delightful sight!

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[Nishantrde]

Hi @jcharkow I have solved most of the conflicts if you want you can review it.

[jcharkow]

Hi @jcharkow I have solved most of the conflicts if you want you can review it.

I'll wait untill all the conflicts are solved and then I'll review