refactor(getSubnetworkFromIndra): Switch column from pvalue to adj.pvalue for nodes table

[tonywu1999]

Summary by CodeRabbit

• Bug Fixes
  • Corrected the column name for adjusted p-values in the output data to ensure consistency with the input data.

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PR Type

Bug fix

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Description

• Rename nodes column to adj.pvalue

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File Walkthrough

	Relevant files
Bug fix	utils_getSubnetworkFromIndra.R Rename nodes column to adj.pvalue                                                R/utils_getSubnetworkFromIndra.R Renamed data.frame column from pvalue to adj.pvalue Updated .constructNodesDataFrame to use adjusted p-value field +1/-1

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[coderabbitai]

Walkthrough

The change updates the .constructNodesDataFrame function in R/utils_getSubnetworkFromIndra.R to correct the column name for adjusted p-values in the nodes data frame from pvalue to adj.pvalue, ensuring consistency with the input data. No other logic or exported entity signatures are affected.

Changes

Cohort / File(s)	Change Summary
Adjusted p-value Column Name Correction R/utils_getSubnetworkFromIndra.R	Corrects the nodes data frame column name from pvalue to adj.pvalue for naming consistency.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Poem

A hop and a skip, a column renamed,
From pvalue to adj.pvalue, now properly framed.
Consistency blooms in the data’s neat row,
As rabbits rejoice in the code’s tidy flow.
🐇✨

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[github-actions]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Column Naming Change Verify that downstream code and documentation reference the renamed column adj.pvalue instead of the old pvalue, including tests, plotting functions, and export routines. adj.pvalue = input$adj.pvalue, Data Completeness Confirm that removal of the original pvalue column (which held raw p-values) is intentional and that no subsequent analysis steps depend on it. adj.pvalue = input$adj.pvalue, Input Validation Ensure input$adj.pvalue always exists and is numeric, or implement a fallback or error if it's missing to avoid creating a completely NA column. adj.pvalue = input$adj.pvalue,

[coderabbitai]

Actionable comments posted: 0

🔭 Outside diff range comments (1)

R/utils_getSubnetworkFromIndra.R (1)

260-266: Update downstream references to the renamed adj.pvalue column

We only found one consumer still expecting nodes$pvalue, so you’ll need to adjust that before merging:

• R/visualizeNetworks.R
– Line 8 & 12 (roxygen tags): change mentions of “pvalue (number)” and @param pvalueCutoff description if they imply the old column name
– Line 47: replace nodes$pvalue with nodes$adj.pvalue in the color‐assignment expression

With these updates in place, all code reading the nodes table will correctly use adj.pvalue.

🧹 Nitpick comments (1)

R/utils_getSubnetworkFromIndra.R (1)

260-266: Roxygen docs & examples need update.

The roxygen block above .constructNodesDataFrame() still refers generically to "p-value"; update it (and any examples) to mention adj.pvalue so that generated docs stay accurate.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 0fde597 and c7b5edb.

📒 Files selected for processing (1)

• R/utils_getSubnetworkFromIndra.R (1 hunks)

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	Add legacy pvalue alias Preserve the original pvalue column for backward compatibility by adding it alongside the new adj.pvalue assignment. This prevents downstream code that expects pvalue from breaking. R/utils_getSubnetworkFromIndra.R [264] adj.pvalue = input$adj.pvalue, +pvalue = input$adj.pvalue, Suggestion importance[1-10]: 5 __ Why: Preserving the original pvalue alongside adj.pvalue ensures backward compatibility and prevents breaking downstream code that expects pvalue.	Low
Possible issue	Coerce adj.pvalue to numeric Ensure that adj.pvalue is treated as numeric to avoid unexpected type issues in downstream filtering or plotting. Wrap the assignment in as.numeric() to coerce factors or character vectors into numbers. R/utils_getSubnetworkFromIndra.R [264] -adj.pvalue = input$adj.pvalue, +adj.pvalue = as.numeric(input$adj.pvalue), Suggestion importance[1-10]: 4 __ Why: Coercing adj.pvalue to numeric guards against potential type issues, but is a minor precaution since input likely already provides numeric values.	Low

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.71%. Comparing base (0fde597) to head (c7b5edb).

Additional details and impacted files

@@           Coverage Diff           @@
##            devel      #52   +/-   ##
=======================================
  Coverage   64.71%   64.71%           
=======================================
  Files           7        7           
  Lines         598      598           
=======================================
  Hits          387      387           
  Misses        211      211           

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