feat: render mutated residues as spheres in ChimeraX plots for better…

[St3451]

Summary

Mutated residues are colored by attribute in chimerax-plot output, but the color is washed out by the cartoon ribbon, making it hard to read. Mirror the visualization used in the Oncodrive3D paper: hide the cartoon for the mutated residues and render them as spheres in their attribute color.

Mutated residues = colored residues = positions written to the .defattr file (result_gene.dropna()), so they're computed once per gene from the existing data — no new inputs.

Changes

• get_chimerax_command gets a new optional colored_positions=None parameter. When provided, appends to the ChimeraX --cmd script: sel :<positions>; style sel sphere; hide sel cartoons; show sel atoms; ~sel;
• generate_chimerax_plot computes colored_positions once per gene and passes it to both the regular and cluster-variant chimerax calls.

[Copilot]

Pull request overview

This PR improves ChimeraX snapshot readability by rendering the residues that receive attribute-based coloring as spheres, making the mutation-associated colors stand out more clearly against the cartoon ribbon.

Changes:

• Extend get_chimerax_command(...) to optionally render “colored/mutated” residue positions as spheres (and hide their cartoons) before saving the image.
• Compute and pass colored_positions from the per-gene result table so the highlighted residues match those present in the generated .defattr files.
• Minor formatting/whitespace cleanup around the updated call sites.

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated no new comments.