feat(visualizeNetworks): Add legend to cytoscape network

[tonywu1999]

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Motivation and Context

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Changes

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Testing

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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()

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PR Type

Enhancement, Tests

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Description

• Added a legend to Cytoscape network visualizations.

• Adjusted node size and font size based on logFC.

• Enhanced visual style mappings for edge labels and node properties.

• Added unit tests for legend functionality and updated existing tests.

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Changes walkthrough 📝

	Relevant files
Dependencies	NAMESPACE Update namespace with new RCy3 imports                                      NAMESPACE Added imports for new RCy3 functions used in legend creation. Updated namespace to include additional dependencies. +5/-0
Enhancement	utils_visualizeNetworks.R Add `.addLegendInCytoscape` function for legend creation  R/utils_visualizeNetworks.R Introduced .addLegendInCytoscape function to add a legend. Utilized RCy3 functions for annotations and grouping. Configured legend layout and appearance dynamically. +63/-0    visualizeNetworks.R Enhance `visualizeNetworks` with legend and visual updates R/visualizeNetworks.R Integrated legend creation into visualizeNetworks. Adjusted node size and font size based on logFC. Enhanced visual style mappings for edge labels and node properties. +21/-5
Tests	test-utils_visualizeNetworks.R Add unit tests for `.addLegendInCytoscape`                              tests/testthat/test-utils_visualizeNetworks.R Added unit tests for .addLegendInCytoscape. Mocked RCy3 functions for testing legend creation. +44/-0    test-visualizeNetworks.R Update tests for `visualizeNetworks` with legend validation tests/testthat/test-visualizeNetworks.R Updated tests to validate legend integration in visualizeNetworks. Added mocks for .addLegendInCytoscape and related functions. +13/-1

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[github-actions]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪

🧪 PR contains tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Possible Issue The x_start calculation in .addLegendInCytoscape assumes that node_coordinates$x_location is always numeric after conversion. This could fail if non-numeric values exist in the input data. Consider adding validation or error handling for this scenario. node_coordinates <- getNodePosition() node_coordinates$x_location <- as.numeric(node_coordinates$x_location) x_start <- max(node_coordinates$x_location) + 50 # Place the legend 50 units to the right of the rightmost node Visual Style Mapping The mapVisualProperty for Node Fill Color uses a hardcoded color scale. Ensure this scale is appropriate for all potential datasets or consider making it configurable. "Node Fill Color", "logFC_color", "c", c(-logfcCutoff, 0.0, logfcCutoff), c("#ADD8E6", "#ADD8E6", "#D3D3D3", "#FFA590", "#FFA590")

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Possible issue	Add validation to ensure legend_items contains the required fields before processing Validate the structure and content of legend_items to ensure it contains the required fields (color and label) before processing, to prevent runtime errors. R/utils_visualizeNetworks.R [32-34] +if (!all(sapply(legend_items, function(item) all(c("color", "label") %in% names(item))))) { + stop("Each legend item must contain 'color' and 'label' fields.") +} for (i in seq_along(legend_items)) { item <- legend_items[[i]] y_pos <- y_start + (i - 1) * (box_size + spacing) # Adjust position for each item Suggestion importance[1-10]: 9 Why: This suggestion adds a crucial validation step to ensure that legend_items contains the required fields (color and label), preventing potential runtime errors. It is highly relevant and improves the robustness of the function.	9
	Add error handling for addAnnotationShape and addAnnotationText to ensure robustness Check the return values of addAnnotationShape and addAnnotationText to ensure they are valid and handle any errors or unexpected results. R/utils_visualizeNetworks.R [37-54] -shape_name <- addAnnotationShape( - type = "rectangle", - x.pos = x_start, - y.pos = y_pos, - width = box_size, - height = box_size, - fillColor = item$color, - borderColor = "black", - borderThickness = 1 -) -text_name <- addAnnotationText( - text = item$label, - x.pos = x_start + box_size + spacing, - y.pos = y_pos + box_size / 4, # Center text vertically with the rectangle - fontSize = 12, - color = "black" -) +shape_name <- tryCatch({ + addAnnotationShape( + type = "rectangle", + x.pos = x_start, + y.pos = y_pos, + width = box_size, + height = box_size, + fillColor = item$color, + borderColor = "black", + borderThickness = 1 + ) +}, error = function(e) stop("Error adding annotation shape: ", e$message)) +text_name <- tryCatch({ + addAnnotationText( + text = item$label, + x.pos = x_start + box_size + spacing, + y.pos = y_pos + box_size / 4, # Center text vertically with the rectangle + fontSize = 12, + color = "black" + ) +}, error = function(e) stop("Error adding annotation text: ", e$message)) Suggestion importance[1-10]: 8 Why: Adding error handling for addAnnotationShape and addAnnotationText ensures that unexpected errors during annotation creation are caught and handled gracefully, improving the function's reliability.	8
	Add a check to ensure the logFC column exists before computing logFC_abs Ensure that the logFC_abs column is computed only after confirming the presence of the logFC column in the nodes dataframe to avoid potential errors. R/visualizeNetworks.R [40] +if (!"logFC" %in% colnames(nodes)) { + stop("The 'logFC' column is missing from the nodes dataframe.") +} nodes$logFC_abs <- abs(nodes$logFC) Suggestion importance[1-10]: 7 Why: This suggestion adds a validation step to ensure the presence of the logFC column before computation, which prevents potential errors and enhances code safety. However, the likelihood of the column being absent in this context is low, slightly reducing its impact.	7
General	Ensure visualization functions are executed only in interactive environments Validate that the interactive() function returns TRUE before proceeding with visualization steps to avoid unexpected behavior in non-interactive environments. R/visualizeNetworks.R [43-44] -if (interactive()) { - createNetworkFromDataFrames(nodes, edges) +if (!interactive()) { + stop("Visualization is only supported in interactive mode.") +} +createNetworkFromDataFrames(nodes, edges) Suggestion importance[1-10]: 6 Why: While the PR already includes a warning for non-interactive environments, this suggestion enforces a stricter validation by stopping execution, which could be useful in some cases. However, it may limit flexibility unnecessarily, slightly reducing its impact.	6

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