feat(network-interpretation): Add button to download network analysis code#111
feat(network-interpretation): Add button to download network analysis code#111tonywu1999 merged 7 commits intodevelfrom
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WalkthroughRemoves in-file Cytoscape helper/rendering functions and shifts to using package-level Cytoscape config generation; adds a display_label_type parameter for label selection; implements reproducible R script generation and download UI; updates related UI text and NAMESPACE imports; deletes some Rd docs and simplifies tests. Changes
Sequence Diagram(s)sequenceDiagram
participant U as User
participant UI as Network Settings UI
participant S as visualizeNetworkServer
participant MS as MSstatsBioNet (pkg)
participant DL as downloadHandler
U->>UI: Click "Show Network" (input$showNetwork)
UI->>S: provide current inputs (filters, cutoffs, displayLabelType)
S->>MS: getSubnetworkFromIndra(...) / annotate (uses inputs)
MS-->>S: nodes_table, edges_table
S->>S: generate_network_code() builds parameterized R script
S->>UI: render download button (output$network.code.button)
U->>UI: Click "Download analysis code"
UI->>DL: request file
DL->>S: fetch script string
S-->>DL: return script
DL-->>U: save network-analysis-code-YYYY-MM-DD.R
sequenceDiagram
participant S as visualizeNetworkServer
participant MS as MSstatsBioNet (pkg)
participant JS as generateCytoscapeJSForShiny
S->>MS: produce nodes_table, edges_table
S->>JS: generateCytoscapeJSForShiny(nodes_table, edges_table, display_label_type)
JS-->>S: js_code (Cytoscape init + Shiny handlers)
S->>UI: inject js_code into UI container (session$ns("cy"))
Estimated code review effort🎯 4 (Complex) | ⏱️ ~45 minutes Possibly related PRs
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Actionable comments posted: 3
🧹 Nitpick comments (2)
R/module-visualize-network-ui.R (1)
491-496: Consider adding error handling for missing UI output.The function creates a download button container, but there's no guarantee that
network.code.buttonwill be populated if the network generation fails or is never triggered.Consider adding a placeholder or conditional rendering to handle cases where the button is not yet available:
createCodeDownloadBox <- function(ns) { div( style = "text-align: right; padding: 10px;", - uiOutput(ns("network.code.button")) + conditionalPanel( + condition = paste0("output['", ns("network.code.button"), "'] != null"), + uiOutput(ns("network.code.button")) + ) ) }R/module-visualize-network-server.R (1)
889-892: Simplify vector construction for statement types.The current approach creates the R vector literal correctly but could be more maintainable.
Consider using
deparse()for safer R code generation:# Handle statement types if (is.null(params$statementTypes)) { codes <- paste(codes, " statement_types = NULL,\n", sep = "") } else { - statement_types_str <- paste0("c(\"", paste(params$statementTypes, collapse = "\", \""), "\")") + statement_types_str <- deparse(params$statementTypes) codes <- paste(codes, " statement_types = ", statement_types_str, ",\n", sep = "") }This approach would automatically handle special characters and ensure valid R syntax.
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R/module-visualize-network-server.R(2 hunks)R/module-visualize-network-ui.R(2 hunks)
🔇 Additional comments (2)
R/module-visualize-network-ui.R (1)
455-455: LGTM! Clean integration of the code download feature.The placement of the code download box at the top of the right column provides good visibility and accessibility for users.
R/module-visualize-network-server.R (1)
959-963: LGTM! Well-styled download button with clear labeling.The download button is properly namespaced and styled consistently with the application's theme.
| generate_network_code <- eventReactive(input$showNetwork, { | ||
| params <- getInputParameters(input) | ||
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| codes <- "" | ||
| codes <- paste(codes, "\n# Load Required Packages\n", sep = "") | ||
| codes <- paste(codes, "library(MSstatsBioNet)\nlibrary(dplyr)\n\n", sep = "") | ||
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| codes <- paste(codes, "# Read data\n", sep = "") | ||
| codes <- paste(codes, "df <- read.csv(\"path/to/your/data.csv\")\n\n", sep = "") | ||
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| # Add label filtering if not default | ||
| if (params$selectedLabel != "" && !is.null(params$selectedLabel)) { | ||
| codes <- paste(codes, "# Filter by selected comparison\n", sep = "") | ||
| codes <- paste(codes, "filtered_df <- df[df$Label == \"", params$selectedLabel, "\" & !is.na(df$Label), ]\n\n", sep = "") | ||
| } else { | ||
| codes <- paste(codes, "filtered_df <- df\n\n", sep = "") | ||
| } | ||
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| codes <- paste(codes, "# Annotate protein information\n", sep = "") | ||
| codes <- paste(codes, "annotated_df <- annotateProteinInfoFromIndra(filtered_df, \"", params$proteinIdType, "\")\n\n", sep = "") | ||
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| codes <- paste(codes, "# Extract subnetwork with filtering parameters\n", sep = "") | ||
| codes <- paste(codes, "subnetwork <- getSubnetworkFromIndra(\n", sep = "") | ||
| codes <- paste(codes, " annotated_df,\n", sep = "") | ||
| codes <- paste(codes, " pvalueCutoff = ", params$pValue, ",\n", sep = "") | ||
| codes <- paste(codes, " evidence_count_cutoff = ", params$evidence, ",\n", sep = "") | ||
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| # Handle statement types | ||
| if (is.null(params$statementTypes)) { | ||
| codes <- paste(codes, " statement_types = NULL,\n", sep = "") | ||
| } else { | ||
| statement_types_str <- paste0("c(\"", paste(params$statementTypes, collapse = "\", \""), "\")") | ||
| codes <- paste(codes, " statement_types = ", statement_types_str, ",\n", sep = "") | ||
| } | ||
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| # Handle sources | ||
| if (is.null(params$sources)) { | ||
| codes <- paste(codes, " sources_filter = NULL,\n", sep = "") | ||
| } else { | ||
| sources_str <- paste0("c(\"", paste(params$sources, collapse = "\", \""), "\")") | ||
| codes <- paste(codes, " sources_filter = ", sources_str, ",\n", sep = "") | ||
| } | ||
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| codes <- paste(codes, " logfc_cutoff = ", params$absLogFC, sep = "") | ||
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| # Handle selected proteins | ||
| if (!is.null(params$selectedProteins) && length(params$selectedProteins) > 0) { | ||
| selected_proteins_str <- paste0("c(\"", paste(params$selectedProteins, collapse = "\", \""), "\")") | ||
| codes <- paste(codes, ",\n force_include_proteins = ", selected_proteins_str, "\n", sep = "") | ||
| } else { | ||
| codes <- paste(codes, ",\n force_include_proteins = NULL\n", sep = "") | ||
| } | ||
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| codes <- paste(codes, ")\n\n", sep = "") | ||
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| codes <- paste(codes, "# View network components\n", sep = "") | ||
| codes <- paste(codes, "print(\"Nodes in network:\")\n", sep = "") | ||
| codes <- paste(codes, "print(subnetwork$nodes)\n\n", sep = "") | ||
| codes <- paste(codes, "print(\"Edges in network:\")\n", sep = "") | ||
| codes <- paste(codes, "print(subnetwork$edges)\n\n", sep = "") | ||
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| codes <- paste(codes, "# Save results\n", sep = "") | ||
| codes <- paste(codes, "write.csv(subnetwork$nodes, \"network_nodes.csv\", row.names = FALSE)\n", sep = "") | ||
| codes <- paste(codes, "write.csv(subnetwork$edges, \"network_edges.csv\", row.names = FALSE)\n", sep = "") | ||
| codes <- paste(codes, "# Visualize network on web browser and export as an HTML file\n", sep = "") | ||
| displayLabelTypeStr <- paste0("\"", paste(input$displayLabelType, collapse = "\", \""), "\"") | ||
| codes <- paste(codes, "previewNetworkInBrowser(subnetwork$nodes, subnetwork$edges, displayLabelType=", displayLabelTypeStr, ")\n", sep = "") | ||
| codes <- paste(codes, "exportNetworkToHTML(subnetwork$nodes, subnetwork$edges, displayLabelType=", displayLabelTypeStr, ")\n", sep = "") | ||
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| return(codes) | ||
| }) |
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Add input validation and error handling for code generation.
The generate_network_code function concatenates strings without validating inputs that could contain special characters or quotes, which might break the generated R code.
Apply input sanitization for string parameters that will be embedded in the generated code:
generate_network_code <- eventReactive(input$showNetwork, {
params <- getInputParameters(input)
+ # Helper function to escape quotes in strings
+ escape_quotes <- function(x) {
+ if (is.null(x) || length(x) == 0) return(NULL)
+ gsub("\"", "\\\"", x, fixed = TRUE)
+ }
+
codes <- ""
codes <- paste(codes, "\n# Load Required Packages\n", sep = "")
codes <- paste(codes, "library(MSstatsBioNet)\nlibrary(dplyr)\n\n", sep = "")
codes <- paste(codes, "# Read data\n", sep = "")
codes <- paste(codes, "df <- read.csv(\"path/to/your/data.csv\")\n\n", sep = "")
# Add label filtering if not default
if (params$selectedLabel != "" && !is.null(params$selectedLabel)) {
codes <- paste(codes, "# Filter by selected comparison\n", sep = "")
- codes <- paste(codes, "filtered_df <- df[df$Label == \"", params$selectedLabel, "\" & !is.na(df$Label), ]\n\n", sep = "")
+ codes <- paste(codes, "filtered_df <- df[df$Label == \"", escape_quotes(params$selectedLabel), "\" & !is.na(df$Label), ]\n\n", sep = "")
} else {
codes <- paste(codes, "filtered_df <- df\n\n", sep = "")
}Also, escape quotes in other string parameters:
- Line 878:
params$proteinIdType - Line 890:
params$statementTypeselements - Line 898:
params$sourceselements - Line 906:
params$selectedProteinselements
🤖 Prompt for AI Agents
In R/module-visualize-network-server.R around lines 859-929, the generated code
embeds raw string inputs which can contain quotes or backslashes and break the
produced R code; sanitize all string inputs before embedding by replacing
backslashes and double quotes (e.g., sanitized <- gsub('(["\\\\])', '\\\\\\1',
as.character(x))) and handle NULL/NA by converting to NULL or "" as appropriate;
then use these sanitized values when building the code strings for
params$proteinIdType (line ~878), each element of params$statementTypes (~890),
params$sources (~898), and params$selectedProteins (~906) so the paste calls
insert the escaped strings (wrap in quotes after escaping) and avoid injecting
unescaped values into the generated R code.
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Actionable comments posted: 0
🧹 Nitpick comments (4)
R/module-visualize-network-ui.R (4)
140-149: Evidence should be an integer count; add step = 1 to the sliderPrevents fractional evidence values from entering the pipeline and exported code.
Apply this diff:
- sliderInput(ns("evidence"), - label = NULL, # Remove since we're handling it above - min = 0, max = 50, value = 5) + sliderInput(ns("evidence"), + label = NULL, # Remove since we're handling it above + min = 0, max = 50, value = 5, step = 1)
157-197: Ensure values match INDRA statement types and handle 'all' sentinel consistentlyUI labels look fine. Please verify the server maps these choice values as-is (case-sensitive) and that selecting "all" is handled unambiguously (e.g., ignored if any specific type is chosen, or treated as a true “select all”).
To reduce duplication and drift between UI/server/exported code, consider centralizing these choices:
- selectInput(ns("statementTypes"), - label = NULL, # Remove since we're handling it above - choices = list("All Types" = "all", - "Complex" = "Complex", - "Inhibition" = "Inhibition", - "Activation" = "Activation", - "Increase Amount" = "IncreaseAmount", - "Decrease Amount" = "DecreaseAmount", - "Phosphorylation" = "Phosphorylation", - "Dephosphorylation" = "Dephosphorylation", - "Ubiquitination" = "Ubiquitination", - "Deubiquitination" = "Deubiquitination", - "Sumoylation" = "Sumoylation", - "Desumoylation" = "Desumoylation", - "Hydroxylation" = "Hydroxylation", - "Dehydroxylation" = "Dehydroxylation", - "Acetylation" = "Acetylation", - "Deacetylation" = "Deacetylation", - "Glycosylation" = "Glycosylation", - "Deglycosylation" = "Deglycosylation", - "Farnesylation" = "Farnesylation", - "Defarnesylation" = "Defarnesylation", - "Geranylgeranylation" = "Geranylgeranylation", - "Degeranylgeranylation" = "Degeranylgeranylation", - "Palmitoylation" = "Palmitoylation", - "Depalmitoylation" = "Depalmitoylation", - "Myristoylation" = "Myristoylation", - "Demyristoylation" = "Demyristoylation", - "Ribosylation" = "Ribosylation", - "Deribosylation" = "Deribosylation", - "Methylation" = "Methylation", - "Demethylation" = "Demethylation"), - selected = "all", - multiple = TRUE) + selectInput(ns("statementTypes"), + label = NULL, # Remove since we're handling it above + choices = listIndraStatementTypes(), + selected = "all", + multiple = TRUE)Place this helper alongside other UI helpers:
listIndraStatementTypes <- function() { list( "All Types" = "all", "Complex" = "Complex", "Inhibition" = "Inhibition", "Activation" = "Activation", "Increase Amount" = "IncreaseAmount", "Decrease Amount" = "DecreaseAmount", "Phosphorylation" = "Phosphorylation", "Dephosphorylation" = "Dephosphorylation", "Ubiquitination" = "Ubiquitination", "Deubiquitination" = "Deubiquitination", "Sumoylation" = "Sumoylation", "Desumoylation" = "Desumoylation", "Hydroxylation" = "Hydroxylation", "Dehydroxylation" = "Dehydroxylation", "Acetylation" = "Acetylation", "Deacetylation" = "Deacetylation", "Glycosylation" = "Glycosylation", "Deglycosylation" = "Deglycosylation", "Farnesylation" = "Farnesylation", "Defarnesylation" = "Defarnesylation", "Geranylgeranylation" = "Geranylgeranylation", "Degeranylgeranylation" = "Degeranylgeranylation", "Palmitoylation" = "Palmitoylation", "Depalmitoylation" = "Depalmitoylation", "Myristoylation" = "Myristoylation", "Demyristoylation" = "Demyristoylation", "Ribosylation" = "Ribosylation", "Deribosylation" = "Deribosylation", "Methylation" = "Methylation", "Demethylation" = "Demethylation" ) }
200-243: Source values look comprehensive; de-duplicate via a shared helper and confirm 'all' handlingGood coverage of text-mined and curated sources. To keep UI, server filters, and exported code in sync, centralize the choices. Also verify the server treats "all" as a sentinel consistently with statement types.
Replace the inline choices with a helper:
- selectInput(ns("sources"), - label = NULL, # Remove since we're handling it above - choices = list("All Sources" = "all", - "Text Mining Systems" = list( - "REACH" = "reach", - "TRIPS/DRUM" = "trips", - "Sparser" = "sparser", - "Eidos" = "eidos", - "TEES" = "tees", - "MedScan" = "medscan", - "RLIMS-P" = "rlimsp", - "ISI/AMR" = "isi", - "Geneways" = "geneways", - "GNBR" = "gnbr", - "SemRep" = "semrep" - ), - "Curated Databases" = list( - "BEL" = "bel", - "BioPAX" = "biopax", - "SIGNOR" = "signor", - "BioGRID" = "biogrid", - "HPRD" = "hprd", - "TRRUST" = "trrust", - "PhosphoELM" = "phosphoelm", - "VirHostNet" = "virhostnet", - "OmniPath" = "omnipath", - "UbiBrowser" = "ubibrowser", - "ACSN" = "acsn", - "WormBase" = "wormbase", - "CTD" = "ctd", - "DrugBank" = "drugbank", - "DGI" = "dgi", - "TAS" = "tas", - "CROG" = "crog", - "CREEDS" = "creeds" - )), - selected = "all", - multiple = TRUE) + selectInput(ns("sources"), + label = NULL, # Remove since we're handling it above + choices = listIndraSources(), + selected = "all", + multiple = TRUE)Add this helper near the other UI helpers:
listIndraSources <- function() { list( "All Sources" = "all", "Text Mining Systems" = list( "REACH" = "reach", "TRIPS/DRUM" = "trips", "Sparser" = "sparser", "Eidos" = "eidos", "TEES" = "tees", "MedScan" = "medscan", "RLIMS-P" = "rlimsp", "ISI/AMR" = "isi", "Geneways" = "geneways", "GNBR" = "gnbr", "SemRep" = "semrep" ), "Curated Databases" = list( "BEL" = "bel", "BioPAX" = "biopax", "SIGNOR" = "signor", "BioGRID" = "biogrid", "HPRD" = "hprd", "TRRUST" = "trrust", "PhosphoELM" = "phosphoelm", "VirHostNet" = "virhostnet", "OmniPath" = "omnipath", "UbiBrowser" = "ubibrowser", "ACSN" = "acsn", "WormBase" = "wormbase", "CTD" = "ctd", "DrugBank" = "drugbank", "DGI" = "dgi", "TAS" = "tas", "CROG" = "crog", "CREEDS" = "creeds" ) ) }
498-503: Minor accessibility and layout polish for the download boxAdd an explicit min-height to prevent layout shift when the button is first rendered, and ARIA attributes so screen readers announce the newly available control.
Apply this diff:
-createCodeDownloadBox <- function(ns) { - div( - style = "text-align: right; padding: 10px;", - uiOutput(ns("network.code.button")) - ) -} +createCodeDownloadBox <- function(ns) { + div( + style = "text-align: right; padding: 10px; min-height: 42px;", # reserve space for the button + role = "region", + `aria-live` = "polite", + uiOutput(ns("network.code.button")) + ) +}
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R/module-visualize-network-ui.R(6 hunks)
🔇 Additional comments (2)
R/module-visualize-network-ui.R (2)
455-463: Nice UX touch with the contextual paragraph and button placementCentering the explainer text and placing the code download UI above the visualization reads well and matches the PR goals to expose reproducible code prominently.
33-37: CSV Column Names VerifiedConfirmed that the server-side and plotting code consistently expect the columns named exactly
Protein,log2FC, andadj.pvalue. No further changes needed.• In R/module-visualize-network-server.R (lines 645–650),
loadCsvData()checks for"Protein"innames(df)and usesdf$Protein.
• In plotting_functions.R, various calls tocolnames(data)[3] == "log2FC"and references todata$adj.pvalueenforce those exact names.
• Existing tests in tests/testthat/test_network_visualization.R construct mock data frames withProtein,log2FC, andadj.pvalue.
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⚠️ Outside diff range comments (1)
R/module-visualize-network-server.R (1)
22-44: Fix Shiny input namespacing: avoid double dashes and mismatched observersPassing
module_id = session$ns(NULL)likely yields a trailing “-” (e.g., "ns-"), so concatenating-edgeClickedproduces "ns--edgeClicked". Observers listen oninput$edgeClicked(module-scoped), so this mismatch breaks click events.Normalize the prefix once and always append the id without an extra dash.
Apply this diff:
generateCytoscapeJSForShiny <- function(node_elements, edge_elements, display_label_type = "id", container_id = "network-cy", module_id = "network") { - # Define Shiny-specific event handlers for both edges and nodes + # Normalize module prefix: ensure it ends with exactly one '-' + ns_prefix <- if (grepl("-$", module_id)) module_id else paste0(module_id, "-") + + # Define Shiny-specific event handlers for both edges and nodes shiny_event_handlers <- list( edge_click = paste0("function(evt) { var edge = evt.target; const edgeId = edge.id(); - Shiny.setInputValue('", module_id, "-edgeClicked', { + Shiny.setInputValue('", ns_prefix, "edgeClicked', { source: edge.data('source'), target: edge.data('target'), interaction: edge.data('interaction'), edge_type: edge.data('edge_type'), category: edge.data('category') }); }"), node_click = paste0("function(evt) { var node = evt.target; const nodeId = node.id(); - Shiny.setInputValue('", module_id, "-nodeClicked', { + Shiny.setInputValue('", ns_prefix, "nodeClicked', { id: node.data('id'), label: node.data('label'), color: node.data('color') }); }") )
♻️ Duplicate comments (2)
R/module-visualize-network-server.R (2)
469-476: Add error handling to downloadHandler contentFile writes can fail and
generate_network_code()may be NULL before the button is used. Wrap in tryCatch and notify the user on error.Apply this diff:
output$network_download_code <- downloadHandler( filename = function() { paste("network-analysis-code-", Sys.Date(), ".R", sep="") }, content = function(file) { - writeLines(generate_network_code(), file) + tryCatch({ + code_content <- generate_network_code() + if (is.null(code_content) || length(code_content) == 0) { + stop("No code generated. Please click 'Show Network' first.") + } + writeLines(code_content, file) + }, error = function(e) { + showNotification(paste("Error downloading code:", e$message), type = "error") + }) } )
362-432: Escape user-supplied strings in generated code + fix displayLabelType constructionRaw embedding of strings (labels, id types, vectors) can break the generated R script or lead to injection of malformed code. Also,
displayLabelTypeStrtreats a radio input as a vector.Apply this diff:
generate_network_code <- eventReactive(input$showNetwork, { params <- getInputParameters(input) - + # Helper to safely embed strings into generated R code + escape_r_string <- function(x) { + if (is.null(x)) return(NULL) + x <- as.character(x) + x <- gsub("\\\\", "\\\\\\\\", x) # escape backslashes + x <- gsub("\"", "\\\\\"", x, fixed = TRUE) # escape double quotes + x + } + codes <- "" codes <- paste(codes, "\n# Load Required Packages\n", sep = "") codes <- paste(codes, "library(MSstatsBioNet)\nlibrary(dplyr)\n\n", sep = "") codes <- paste(codes, "# Read data\n", sep = "") codes <- paste(codes, "df <- read.csv(\"path/to/your/data.csv\")\n\n", sep = "") # Add label filtering if not default if (params$selectedLabel != "" && !is.null(params$selectedLabel)) { codes <- paste(codes, "# Filter by selected comparison\n", sep = "") - codes <- paste(codes, "filtered_df <- df[df$Label == \"", params$selectedLabel, "\" & !is.na(df$Label), ]\n\n", sep = "") + codes <- paste(codes, "filtered_df <- df[df$Label == \"", escape_r_string(params$selectedLabel), "\" & !is.na(df$Label), ]\n\n", sep = "") } else { codes <- paste(codes, "filtered_df <- df\n\n", sep = "") } codes <- paste(codes, "# Annotate protein information\n", sep = "") - codes <- paste(codes, "annotated_df <- annotateProteinInfoFromIndra(filtered_df, \"", params$proteinIdType, "\")\n\n", sep = "") + codes <- paste(codes, "annotated_df <- annotateProteinInfoFromIndra(filtered_df, \"", escape_r_string(params$proteinIdType), "\")\n\n", sep = "") codes <- paste(codes, "# Extract subnetwork with filtering parameters\n", sep = "") codes <- paste(codes, "subnetwork <- getSubnetworkFromIndra(\n", sep = "") codes <- paste(codes, " annotated_df,\n", sep = "") codes <- paste(codes, " pvalueCutoff = ", params$pValue, ",\n", sep = "") codes <- paste(codes, " evidence_count_cutoff = ", params$evidence, ",\n", sep = "") # Handle statement types if (is.null(params$statementTypes)) { codes <- paste(codes, " statement_types = NULL,\n", sep = "") } else { - statement_types_str <- paste0("c(\"", paste(params$statementTypes, collapse = "\", \""), "\")") + sanitized_st <- vapply(params$statementTypes, escape_r_string, character(1)) + statement_types_str <- paste0("c(\"", paste(sanitized_st, collapse = "\", \""), "\")") codes <- paste(codes, " statement_types = ", statement_types_str, ",\n", sep = "") } # Handle sources if (is.null(params$sources)) { codes <- paste(codes, " sources_filter = NULL,\n", sep = "") } else { - sources_str <- paste0("c(\"", paste(params$sources, collapse = "\", \""), "\")") + sanitized_src <- vapply(params$sources, escape_r_string, character(1)) + sources_str <- paste0("c(\"", paste(sanitized_src, collapse = "\", \""), "\")") codes <- paste(codes, " sources_filter = ", sources_str, ",\n", sep = "") } codes <- paste(codes, " logfc_cutoff = ", params$absLogFC, sep = "") # Handle selected proteins if (!is.null(params$selectedProteins) && length(params$selectedProteins) > 0) { - selected_proteins_str <- paste0("c(\"", paste(params$selectedProteins, collapse = "\", \""), "\")") + sanitized_prots <- vapply(params$selectedProteins, escape_r_string, character(1)) + selected_proteins_str <- paste0("c(\"", paste(sanitized_prots, collapse = "\", \""), "\")") codes <- paste(codes, ",\n force_include_proteins = ", selected_proteins_str, "\n", sep = "") } else { codes <- paste(codes, ",\n force_include_proteins = NULL\n", sep = "") } codes <- paste(codes, ")\n\n", sep = "") @@ codes <- paste(codes, "# Save results\n", sep = "") codes <- paste(codes, "write.csv(subnetwork$nodes, \"network_nodes.csv\", row.names = FALSE)\n", sep = "") codes <- paste(codes, "write.csv(subnetwork$edges, \"network_edges.csv\", row.names = FALSE)\n", sep = "") codes <- paste(codes, "# Visualize network on web browser and export as an HTML file\n", sep = "") - displayLabelTypeStr <- paste0("\"", paste(input$displayLabelType, collapse = "\", \""), "\"") + displayLabelTypeStr <- paste0("\"", escape_r_string(input$displayLabelType), "\"") codes <- paste(codes, "previewNetworkInBrowser(subnetwork$nodes, subnetwork$edges, displayLabelType=", displayLabelTypeStr, ")\n", sep = "") codes <- paste(codes, "exportNetworkToHTML(subnetwork$nodes, subnetwork$edges, displayLabelType=", displayLabelTypeStr, ")\n", sep = "") return(codes) })
🧹 Nitpick comments (3)
man/generateCytoscapeJSForShiny.Rd (1)
10-21: Docs reflect new display_label_type parameterThe usage and arguments now include
display_label_type = "id", which aligns with the server code. Consider clarifying accepted values (e.g., "id", "hgncName") in the roxygen source so Rd is regenerated with that detail.tests/testthat/test_network_visualization.R (2)
62-66: Good coverage for JS handler wiring; consider adding label-type coverageThis validates Shiny event handler emission. Consider a follow-up test passing
display_label_type = "hgncName"to ensure it propagates into the generated JS/config as expected.
240-244: Minimal end-to-end check looks good; add assertions on JS contentAsserting non-empty JS is useful. You could also assert that the emitted JS includes the container id ("network-cy" default) or input ids ("network-edgeClicked"/"network-nodeClicked") for stronger guarantees.
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📒 Files selected for processing (6)
NAMESPACE(1 hunks)R/module-visualize-network-server.R(5 hunks)man/generateCytoscapeConfig.Rd(0 hunks)man/generateCytoscapeJSForShiny.Rd(2 hunks)man/generateJavaScriptCode.Rd(0 hunks)tests/testthat/test_network_visualization.R(2 hunks)
💤 Files with no reviewable changes (2)
- man/generateJavaScriptCode.Rd
- man/generateCytoscapeConfig.Rd
🔇 Additional comments (4)
NAMESPACE (1)
41-41: Import addition aligns with new dependency usageAdding
importFrom(MSstatsBioNet,generateCytoscapeConfig)matches the updated server usage and prevents namespace issues at runtime.R/module-visualize-network-server.R (3)
13-17: Roxygen updates and import look correctThe added
@param display_label_typeand@importFrom MSstatsBioNet generateCytoscapeConfigmatch the NAMESPACE change and the function’s new signature.
48-53: Config generation call is consistent with new API
nodes,edges, anddisplay_label_typeare passed through to the package function; looks good.
462-466: Rendering the download button post-network render is a nice UX touchShowing the button only after the network is displayed keeps the UI clean and avoids confusion. Style choice is consistent with app patterns.
1 participant
PR Type
Enhancement
Description
Add code generation for network analysis
Provide downloadable R script via button
Include UI box for download control
Integrate display label options in exports
Diagram Walkthrough
File Walkthrough
module-visualize-network-server.R
Server-side code generation and download hookR/module-visualize-network-server.R
module-visualize-network-ui.R
UI container for code download buttonR/module-visualize-network-ui.R
Summary by CodeRabbit
New Features
UI
UX
Refactor
Tests / Documentation