feat(visualizeNetworks): Enable use of other columns for node labels

[tonywu1999]

PR Type

Enhancement, Documentation

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Description

• Added support for custom node label columns in network visualization.

• Updated .constructNodesDataFrame to include hgncName column if available.

• Modified visualizeNetworks function to accept node_label_column parameter.

• Enhanced documentation to reflect new parameter and functionality.

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Changes walkthrough 📝

	Relevant files
Enhancement	utils_getSubnetworkFromIndra.R Include `hgncName` column in nodes dataframe                          R/utils_getSubnetworkFromIndra.R Added hgncName column to nodes dataframe if available. Ensured compatibility with existing edge filtering logic. +1/-0      visualizeNetworks.R Add `node_label_column` parameter to `visualizeNetworks`  R/visualizeNetworks.R Introduced node_label_column parameter for custom node labels. Updated visual style mapping to use the specified column. Adjusted function signature and internal logic accordingly. +5/-2
Documentation	visualizeNetworks.Rd Update documentation for `visualizeNetworks` function        man/visualizeNetworks.Rd Documented node_label_column parameter in function usage. Updated examples and descriptions to reflect new functionality. +10/-1

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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 Possible Issue The addition of the hgncName column in .constructNodesDataFrame assumes that the column HgncName exists in the input dataframe. If it does not, it defaults to NA. This behavior should be validated to ensure it does not cause unintended issues downstream. hgncName = if ("HgncName" %in% colnames(input)) input$HgncName else NA, stringsAsFactors = FALSE Parameter Validation The new node_label_column parameter in visualizeNetworks is not validated to ensure it corresponds to an existing column in the nodes dataframe. This could lead to runtime errors if an invalid column name is provided. logfcCutoff = 0.5, node_label_column = "id") {

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Possible issue	Validate existence of user-specified column Add validation to ensure that the node_label_column parameter corresponds to a valid column in the nodes dataframe to prevent runtime errors. R/visualizeNetworks.R [35-38] visualizeNetworks <- function(nodes, edges, pvalueCutoff = 0.05, logfcCutoff = 0.5, node_label_column = "id") { + if (!node_label_column %in% colnames(nodes)) { + stop("The specified node_label_column does not exist in the nodes dataframe.") + } Suggestion importance[1-10]: 9 Why: Adding validation to ensure the node_label_column exists in the nodes dataframe is crucial for preventing runtime errors. This suggestion directly addresses a potential issue introduced by the new parameter and improves the robustness of the function.	9
	Validate column data type before usage Ensure that the HgncName column is properly validated before accessing it to avoid potential runtime errors if the column exists but contains unexpected or malformed data. R/utils_getSubnetworkFromIndra.R [192] -hgncName = if ("HgncName" %in% colnames(input)) input$HgncName else NA, +hgncName = if ("HgncName" %in% colnames(input) && is.character(input$HgncName)) input$HgncName else NA, Suggestion importance[1-10]: 8 Why: This suggestion adds a validation step to ensure that the HgncName column is of the expected data type before accessing it. This is a significant improvement as it prevents potential runtime errors caused by unexpected or malformed data in the column.	8
General	Handle missing values in label column Provide a fallback mechanism or warning if the node_label_column contains missing or NA values to ensure robust visualization. R/visualizeNetworks.R [61] -mapVisualProperty("Node Label", node_label_column, "p"), +mapVisualProperty("Node Label", ifelse(is.na(nodes[[node_label_column]]), "id", node_label_column), "p"), Suggestion importance[1-10]: 7 Why: This suggestion introduces a fallback mechanism for missing or NA values in the node_label_column, which enhances the robustness of the visualization process. While not critical, it is a valuable improvement for handling edge cases.	7

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 71.42857% with 2 lines in your changes missing coverage. Please review.

Project coverage is 87.09%. Comparing base (c33b317) to head (8fead2f).

Files with missing lines	Patch %	Lines
R/utils_getSubnetworkFromIndra.R	66.66%	1 Missing ⚠️
R/utils_visualizeNetworks.R	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel      #31      +/-   ##
==========================================
- Coverage   87.41%   87.09%   -0.32%     
==========================================
  Files           7        7              
  Lines         429      434       +5     
==========================================
+ Hits          375      378       +3     
- Misses         54       56       +2     

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