Render a Cytoscape network visualisation

Creates an interactive network diagram powered by Cytoscape.js and the dagre layout algorithm. Nodes can carry log fold-change (logFC) values which are mapped to a blue-grey-red colour gradient. PTM (post-translational modification) site information is shown as small satellite nodes and edge overlaps are surfaced as hover tooltips.

Usage

cytoscapeNetwork(
  nodes,
  edges = data.frame(),
  displayLabelType = "id",
  nodeFontSize = 12,
  layoutOptions = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

nodes

Data frame with at minimum an id column. Optional columns: logFC (numeric), hgncName (character), Site (character, underscore-separated PTM site list).

edges

Data frame with columns source, target, interaction. Optional: site, evidenceLink.

displayLabelType

"id" (default) or "hgncName" – controls which column is used as the visible node label.

nodeFontSize

Font size (px) for node labels. Default 12.

layoutOptions

Named list of dagre layout options to override the defaults (e.g. list(rankDir = "LR")).

width, height

Widget dimensions passed to createWidget.

elementId

Optional explicit HTML element id.

Value

An htmlwidget object that renders in R Markdown, Shiny, or the RStudio Viewer pane.

Examples

if (FALSE) { # \dontrun{
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)
} # }