An example of programmatically coloring nodes/edges of an existing Cytoscape network with R

RunColorExistingCytoscapeNetworkExample.R

# An example of programmatically coloring nodes/edges of an existing Cytoscape network with R

library(RCytoscape)
library(RColorBrewer)

# Generate demo Cytoscape network
cy <- CytoscapeConnection()
cw <- new.CytoscapeWindow("demo", graph=makeSimpleGraph(), overwriteWindow=TRUE)
displayGraph(cw)
layoutNetwork(cw)
redraw(cw)

# Get existing Cytoscape network
cw <- existing.CytoscapeWindow("demo", copy.graph.from.cytoscape.to.R=TRUE)

# Get nodes/edges and their attributes
edges <- getAllEdgeAttributes(cw, onlySelectedEdges=FALSE)
nodes <- getAllNodeAttributes (cw, onlySelectedNodes=FALSE)

# Color Edges
edgeValues = unique(edges$edgeType)

# Generate color palette
colors <- brewer.pal(length(edgeValues), "Set3")

# NOTE: This function exists for nodes and edges
setEdgeColorRule(cw, "edgeType",  edgeValues, colors, mode="lookup")

# Color Nodes 
nodeValues = unique(nodes$lfc)
colors <- brewer.pal(length(nodeValues), "YlOrRd")

for(i in seq_along(nodeValues)) {
  # NOTE: This function exists for nodes and edges
  setNodeColorDirect (cw, rownames(nodes)[i], colors[i])  
}

redraw(cw)