From b4340045a1c2701bfce6e31e6b95fb38ba252c9b Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Mon, 2 Mar 2026 09:23:10 +0000
Subject: [PATCH 1/3] docs: AI-generated doc upgrade for
 `cytoscapeNetworkOutput`

Auto-generated by weekly doc workflow.
Target: R/cytoscapeNetwork.R::cytoscapeNetworkOutput
Date: 2026-03-02T09:23:10Z
---
 R/cytoscapeNetwork.R | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/R/cytoscapeNetwork.R b/R/cytoscapeNetwork.R
index cc3a3e8..e2b57a6 100644
--- a/R/cytoscapeNetwork.R
+++ b/R/cytoscapeNetwork.R
@@ -1,3 +1,4 @@
+```r
 #' Render a Cytoscape network visualisation
 #'
 #' Creates an interactive network diagram powered by Cytoscape.js and the dagre
@@ -106,6 +107,44 @@ cytoscapeNetwork <- function(nodes,
 # ── Shiny helpers ───────────────────────────────────────────────────────────
 
 #' Shiny output binding for cytoscapeNetwork
+#'
+#' Creates a Shiny output binding for a Cytoscape network visualization, allowing
+#' the network to be rendered within Shiny applications.
+#'
+#' @param outputId \code{character}. The output variable to read from.
+#' @param width \code{character}. The width of the rendered widget. Default is \code{"100%"}.
+#' @param height \code{character}. The height of the rendered widget. Default is \code{"500px"}.
+#'
+#' @return A Shiny output binding for a Cytoscape network visualization.
+#'
+#' @examples
+#' \dontrun{
+#' library(shiny)
+#' 
+#' 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)
+#' }
+#'
 #' @importFrom htmlwidgets shinyWidgetOutput
 #' @inheritParams htmlwidgets::shinyWidgetOutput
 #' @export
@@ -134,3 +173,4 @@ renderCytoscapeNetwork <- function(expr, env = parent.frame(), quoted = FALSE) {
         quoted  = TRUE
     )
 }
+```
\ No newline at end of file

From f9f93c074d9494db281b6eaf235570be45074ed0 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Tue, 3 Mar 2026 19:22:02 -0500
Subject: [PATCH 2/3] Remove unnecessary code comments and formatting

---
 R/cytoscapeNetwork.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/cytoscapeNetwork.R b/R/cytoscapeNetwork.R
index e2b57a6..89c48b7 100644
--- a/R/cytoscapeNetwork.R
+++ b/R/cytoscapeNetwork.R
@@ -1,4 +1,3 @@
-```r
 #' Render a Cytoscape network visualisation
 #'
 #' Creates an interactive network diagram powered by Cytoscape.js and the dagre
@@ -173,4 +172,3 @@ renderCytoscapeNetwork <- function(expr, env = parent.frame(), quoted = FALSE) {
         quoted  = TRUE
     )
 }
-```
\ No newline at end of file

From 0e9ebde3eba14c74f75232d893c0563da063a39c Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Tue, 3 Mar 2026 19:29:14 -0500
Subject: [PATCH 3/3] fix documentation problems

---
 R/cytoscapeNetwork.R          |  4 ----
 man/cytoscapeNetworkOutput.Rd | 35 ++++++++++++++++++++++++++++++++++-
 2 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/R/cytoscapeNetwork.R b/R/cytoscapeNetwork.R
index 89c48b7..cfdf293 100644
--- a/R/cytoscapeNetwork.R
+++ b/R/cytoscapeNetwork.R
@@ -110,10 +110,6 @@ cytoscapeNetwork <- function(nodes,
 #' Creates a Shiny output binding for a Cytoscape network visualization, allowing
 #' the network to be rendered within Shiny applications.
 #'
-#' @param outputId \code{character}. The output variable to read from.
-#' @param width \code{character}. The width of the rendered widget. Default is \code{"100%"}.
-#' @param height \code{character}. The height of the rendered widget. Default is \code{"500px"}.
-#'
 #' @return A Shiny output binding for a Cytoscape network visualization.
 #'
 #' @examples
diff --git a/man/cytoscapeNetworkOutput.Rd b/man/cytoscapeNetworkOutput.Rd
index 39ec60f..be2fa1c 100644
--- a/man/cytoscapeNetworkOutput.Rd
+++ b/man/cytoscapeNetworkOutput.Rd
@@ -13,6 +13,39 @@ cytoscapeNetworkOutput(outputId, width = "100\%", height = "500px")
 \code{"400px"}, \code{"auto"}) or a number, which will be coerced to a
 string and have \code{"px"} appended.}
 }
+\value{
+A Shiny output binding for a Cytoscape network visualization.
+}
 \description{
-Shiny output binding for cytoscapeNetwork
+Creates a Shiny output binding for a Cytoscape network visualization, allowing
+the network to be rendered within Shiny applications.
+}
+\examples{
+\dontrun{
+library(shiny)
+
+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)
+}
+
 }