From cde26045d933ecf64460d2ffb7a54324b156f930 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 04:07:40 +0000
Subject: [PATCH] docs: AI-generated doc upgrade for `renderCytoscapeNetwork`

Auto-generated by weekly doc workflow.
Target: R/cytoscapeNetwork.R::renderCytoscapeNetwork
Date: 2026-02-27T04:07:40Z
---
 R/cytoscapeNetwork.R | 42 ++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 40 insertions(+), 2 deletions(-)

diff --git a/R/cytoscapeNetwork.R b/R/cytoscapeNetwork.R
index 149ca72..095f957 100644
--- a/R/cytoscapeNetwork.R
+++ b/R/cytoscapeNetwork.R
@@ -1,3 +1,4 @@
+```r
 # R/cytoscapeNetwork.R
 #
 # htmlwidgets binding for the Cytoscape network visualisation.
@@ -490,8 +491,44 @@ cytoscapeNetworkOutput <- function(outputId,
   )
 }
 
-#' Shiny render binding for cytoscapeNetwork
-#' @inheritParams htmlwidgets::shinyRenderWidget
+#' Render a Cytoscape network in a Shiny application
+#'
+#' This function is used to render a Cytoscape network visualization within a Shiny application.
+#'
+#' @param expr \code{expression} that generates a Cytoscape network widget.
+#' @param env \code{environment} in which to evaluate \code{expr}. Defaults to \code{parent.frame()}.
+#' @param quoted \code{logical}, is \code{expr} a quoted expression (with \code{quote()})? Default is \code{FALSE}.
+#'
+#' @return A rendered Cytoscape network widget for use in Shiny applications.
+#'
+#' @examples
+#' \dontrun{
+#' library(shiny)
+#' library(MSstatsBioNet)
+#'
+#' ui <- fluidPage(
+#'   cytoscapeNetworkOutput("cytoNetwork")
+#' )
+#'
+#' server <- function(input, output, session) {
+#'   output$cytoNetwork <- renderCytoscapeNetwork({
+#'     nodes <- data.frame(
+#'       id    = c("TP53", "MDM2", "CDKN1A"),
+#'       logFC = c(1.5, -0.8, 2.1),
+#'       stringsAsFactors = FALSE
+#'     )
+#'     edges <- data.frame(
+#'       source      = c("TP53",  "MDM2"),
+#'       target      = c("MDM2",  "TP53"),
+#'       interaction = c("Activation", "Inhibition"),
+#'       stringsAsFactors = FALSE
+#'     )
+#'     cytoscapeNetwork(nodes, edges)
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
 #' @export
 renderCytoscapeNetwork <- function(expr, env = parent.frame(), quoted = FALSE) {
   if (!quoted) expr <- substitute(expr)
@@ -502,3 +539,4 @@ renderCytoscapeNetwork <- function(expr, env = parent.frame(), quoted = FALSE) {
     quoted  = TRUE
   )
 }
+```
\ No newline at end of file