A minimal example: 3 nodes, no edges

Here we create a 3-node graphNEL in R, send it to Cytoscape for display and layout. For the sake of simplicity, no node attributes, no edges, and no vizmapping is included; those topics are covered in subsequent examples.

> library(RCytoscape)
> g <- new("graphNEL", edgemode = "directed")
> g <- graph::addNode("A", g)
> g <- graph::addNode("B", g)
> g <- graph::addNode("C", g)
> cw <- CytoscapeWindow("vignette", graph = g)
> ping(cw)

[1] "It works!"

> displayGraph(cw)

You should see a single red dot in the middle of a small Cytoscape window titled 'vignette' in the Cytoscape Desktop:

This graph needs layout.

> layoutNetwork(cw, 'grid')

After layout, you will see the structure of this graph: simply 3 unconnected nodes. These nodes will be unlabeled, small and colored red -- not very informative.

Fortunately, Cytoscape has some built-in rendering rules in which (and unless instructed otherwise) nodes are rendered round in shape, pale red in color, and labeled with the names supplied when they were added to the graph; edges (if any) are simple blue lines. To get this default rendering, simply type.

> redraw(cw)