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), entity_name (character; may be semicolon-joined for multi-grounded rows), entity_id (character), site (character, underscore-separated PTM site list), and the node status columns of validate_network(): entity_type sets the node shape (e.g. a hexagon for "metabolite"); measured = FALSE draws a node with no fill and a dashed grey border ("not in input data"); included_in_query = FALSE fades it. A node with an NA logFC has no fill. A protein with site rows takes its colour from its row with no site; without one, only its sites are coloured. Missing status columns count as TRUE.

edges

Data frame with columns source, target, interaction. Optional: directed (an edge with FALSE has no arrow and is drawn once for both directions; without the column, Complex and Association edges are undirected), site, evidence_url, opened when an edge is clicked.

displayLabelType

"id" (default) or "entity_name": which column is used as the visible node label. "entityName" is deprecated and is treated as "entity_name" with a warning.

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)
} # }