Event handler

[tonywu1999]

Motivation and Context

This PR adds a programmatic function to delete edges from network edge data frames. It provides the programmatic counterpart to the interactive edge deletion (Ctrl+click / right-click) available in the cytoscapeNetwork function, enabling developers to manipulate network structures outside of the interactive visualization context.

Changes

• New exported function deleteEdgeFromNetwork() in R/deleteEdgeFromNetwork.R:

  • Accepts an edges data frame and three matching criteria: source, target, and interaction
  • Validates that the input is a data frame and contains required columns (source, target, interaction)
  • Filters and removes row(s) from the edges data frame matching all three criteria
  • Returns the modified edges data frame with matching rows removed
  • Throws informative errors for invalid inputs

• Documentation file man/deleteEdgeFromNetwork.Rd generated by roxygen2:

  • Includes function title, parameter descriptions, return value description
  • Contains executable example demonstrating the function's usage

• NAMESPACE update:

  • Added export directive for deleteEdgeFromNetwork function

Unit Tests

No unit tests were added for the new deleteEdgeFromNetwork function. The repository has an established testing framework using testthat and mockery (as evidenced by existing test files in tests/testthat/), but no corresponding test file was created for this new functionality.

Coding Guidelines

No violations of coding guidelines were identified. The function implementation:

• Follows the roxygen2 documentation format consistent with other exported functions in the package
• Includes appropriate input validation with clear error messages
• Uses standard R data frame manipulation
• Provides clear, executable examples in the documentation

[coderabbitai]

📝 Walkthrough

Walkthrough

A new function deleteEdgeFromNetwork() was added to remove edges from a network data frame based on specified source, target, and interaction criteria. The function includes input validation, filtering logic, roxygen documentation, and an example.

Changes

Cohort / File(s)	Summary
Function Implementation NAMESPACE, R/deleteEdgeFromNetwork.R	New exported function deleteEdgeFromNetwork() that validates input data frame structure, filters edges matching provided source/target/interaction values, and returns the filtered data frame with matching rows removed.
Documentation man/deleteEdgeFromNetwork.Rd	Roxygen-generated documentation file defining function signature, parameter descriptions, return value, and executable usage example.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 With a hop and a snip, we delete with care,
Edges vanish when source and target pair!
From networks so tangled, connections take flight,
deleteEdgeFromNetwork makes interactions right! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Event handler' is vague and does not clearly describe the main change. The PR primarily adds a deleteEdgeFromNetwork function for programmatic edge deletion, but the title suggests event handling functionality.	Provide a more specific title that reflects the actual changes, such as 'Add deleteEdgeFromNetwork function for removing edges' or 'Add programmatic edge deletion functionality'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The pull request description comprehensively addresses all required template sections with detailed information about motivation, changes, and testing considerations.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch event-handler

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[codecov-commenter]

Codecov Report

❌ Patch coverage is 0% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.31%. Comparing base (8991901) to head (9d2832e).

Files with missing lines	Patch %	Lines
R/deleteEdgeFromNetwork.R	0.00%	19 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel      #98      +/-   ##
==========================================
- Coverage   76.70%   75.31%   -1.40%     
==========================================
  Files           8        9       +1     
  Lines        1026     1045      +19     
==========================================
  Hits          787      787              
- Misses        239      258      +19     

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@R/deleteEdgeFromNetwork.R`:
- Around line 28-39: The deleteEdgeFromNetwork function currently risks NA
propagation and vector recycling; add input validation to ensure that source,
target, and interaction are scalar (length 1) and not NA (use explicit checks
and stop with a clear message if violated), and change the matching predicate to
guard against NA in edges columns by only comparing when the column value is not
NA (e.g., require !is.na(edges$source) && !is.na(edges$target) &&
!is.na(edges$interaction) in the comparison) so that NA comparisons evaluate to
FALSE instead of NA; update the symbol deleteEdgeFromNetwork and parameter names
source, target, interaction accordingly and keep returning edges[keep, , drop =
FALSE].

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: fd6a7d3a-a264-49f5-995f-fc0340c50bea

📥 Commits

Reviewing files that changed from the base of the PR and between 8991901 and 398b2dc.

📒 Files selected for processing (3)

• NAMESPACE
• R/deleteEdgeFromNetwork.R
• man/deleteEdgeFromNetwork.Rd