Peptide Sequence Plotting. Solves issue #53

[Ayushmaan06]

Hey @jcharkow ! This PR addresses issue #53 by integrating the feature to plot peptide sequences with matched fragments into the Matplotlib backend interface. I have followed your instructions from the issue description. Also followed your instructions on the pr #62 .

Summary by CodeRabbit

• New Features

  • Introduced a method for peptide sequence annotation in spectrum plots, with customizable display options (font size, colors, highlight) based on user configurations.
  • Enhanced clarity by indicating unsupported plotting modes for peptide sequences in specific backends.

• Tests

  • Added tests to verify proper peptide sequence rendering on supported backends and ensure clear error handling for unsupported backends.

[coderabbitai[bot]]

Walkthrough

The changes introduce peptide sequence plotting functionality into the project. A new method, plot_peptide_sequence, has been added in various plotting classes to handle peptide sequence annotations. In the abstract SpectrumPlot class, the method is declared and conditionally invoked based on configuration settings from an enhanced SpectrumConfig. For the Matplotlib backend, an actual implementation renders text and annotations, while for the Bokeh and Plotly backends, the method raises a NotImplementedError. Additional tests have been added to ensure the correct behavior in both supported and unsupported backends.

Changes

File(s)	Change Summary
pyopenms_viz/_bokeh/core.py, pyopenms_viz/_plotly/core.py	Add plot_peptide_sequence method that raises a NotImplementedError for unsupported peptide sequence plotting in these backends.
pyopenms_viz/_config.py	Augment SpectrumConfig with new fields: display_peptide_sequence, peptide_sequence, matched_fragments to support peptide sequence plotting.
pyopenms_viz/_core.py	Introduce an abstract plot_peptide_sequence method in SpectrumPlot and update the plot method to call it conditionally based on configuration settings.
pyopenms_viz/_matplotlib/core.py	Implement plot_peptide_sequence to render peptide sequence annotations using Matplotlib for visualizing matched fragments.
test/test_chromatogram.py	Add configuration for Matplotlib backend to a non-interactive mode to avoid display issues.
test/test_spectrum.py	Add test_spectrum_peptide_sequence_matplotlib to validate plotting of peptide sequences using Matplotlib, including configuration for the Matplotlib backend, and test_spectrum_peptide_sequence_unsupported to check for NotImplementedError in unsupported backends.

Sequence Diagram(s)

sequenceDiagram
    participant S as SpectrumPlot
    participant C as SpectrumConfig
    participant M as MATPLOTLIBSpectrumPlot
    participant U as UnsupportedBackend

    S->>C: Check if display_peptide_sequence is enabled
    alt Enabled (Matplotlib)
        S->>M: Call plot_peptide_sequence(peptide_sequence, matched_fragments)
        M->>M: Render text and annotations via ax.text/annotate
    else Unsupported
        S->>U: Call plot_peptide_sequence
        U-->>S: Raise NotImplementedError
    end

Possibly related issues

• OpenMS/pyopenms_viz#53: The changes in the main issue are directly related to the modifications proposed in the retrieved issue, as both involve the addition of a plot_peptide_sequence method in the SpectrumPlot class and its integration into the plotting framework, along with updates to the SpectrumConfig class for peptide sequence handling.

Poem

I'm a bunny coding through the night,
Hopping to changes, feeling just right.
Peptide sequences now waltz on the screen,
With Matplotlib magic, a joyful scene.
Bokeh and Plotly say, "Not yet, it seems!"
🐇✨

[!TIP]

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