chore(visualizeNetworks, getSubnetworkFromIndra): Adjust font size, reorder table columns

[tonywu1999]

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• Ran styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
• Ran devtools::document()

Summary by CodeRabbit

• Style

  • Increased edge label font size in network visualizations from 9px to 12px for improved readability.

• Refactor

  • Reordered and renamed node attributes (id, hgncName, Site, logFC, adj.pvalue) for more consistent outputs.
  • Reordered site column for edge table

[coderabbitai]

Walkthrough

Updates adjust node column ordering/renaming in R/utils_getSubnetworkFromIndra.R and briefly add then remove an edges “site” field, leaving no site column. R/visualizeNetworksWithHTML.R increases Cytoscape edge label font size from 9px to 12px. No exported interfaces or control flow are changed.

Changes

Cohort / File(s)	Summary of Changes
Subnetwork construction R/utils_getSubnetworkFromIndra.R	Temporarily introduced a site field in edges creation then removed it, resulting in no site column on edges. Reordered node columns to select Protein, HgncName, Site, log2FC, adj.pvalue and renamed to id, hgncName, Site, logFC, adj.pvalue.
HTML visualization config R/visualizeNetworksWithHTML.R	In generateCytoscapeConfig, increased edge label font size from 9px to 12px; no logic or control-flow changes.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• tests(visualizeNetworksWithHTML): Add unit tests for generateCytoscapeConfig #55 — Also modifies generateCytoscapeConfig, changing function signature and construction of node/edge elements.
• refactor(getSubnetworkFromIndra): Switch column from pvalue to adj.pvalue for nodes table #52 — Adjusts nodes data frame construction in utils_getSubnetworkFromIndra.R, including handling of adj.pvalue.

Poem

A bunny tweaks the nets with care,
Nodes in neat new rows to wear;
Edge labels puff, a bigger grin,
At twelve small px, the lines begin.
No sites for edges, hop along—
The graph now hums a tidy song. 🐇✨

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description Check	⚠️ Warning	The pull request description only includes the checklist section and omits all required template sections such as Motivation and Context, Changes, and Testing, so it does not conform to the repository’s description template.	Please update the PR description to include the “Motivation and Context” section with problem background, a “Changes” section listing all modifications, and a “Testing” section describing any added or updated tests, following the repository’s template.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title Check	✅ Passed	Title accurately and concisely summarizes the key changes—adjusting the edge font size in visualizeNetworks and reordering the subnetwork table columns in getSubnetworkFromIndra—matching the diff.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

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• Commit unit tests in branch font-size

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[github-actions]

Failed to generate code suggestions for PR

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.30%. Comparing base (fbfbcaa) to head (2657daf).

Additional details and impacted files

@@           Coverage Diff           @@
##            devel      #59   +/-   ##
=======================================
  Coverage   64.30%   64.30%           
=======================================
  Files           7        7           
  Lines        1216     1216           
=======================================
  Hits          782      782           
  Misses        434      434           

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