layoutRegulatoryGraph: This function generates a (more or less) beautiful layout for...
In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

Description Usage Arguments Value Author(s) Examples

This function generates a (more or less) beautiful layout for a regulatory graph. Call this after you generated a graph with pathway2RegulatoryGraph. Since beauty is always in the eye of the beholder consider this a starting point for making your graphs even nicer. Rgraphviz with dot layout is used. Edges are green/red with normal/tee arrowheads for activations/inhibitions. If you want to specifically paint subgraphs in different colors use lists of vectors with node names for parameter subgraphs and vector of color names for subgraphs.color for your choice of color. The output can be further tweaked by setting layout options using nodeRenderInfo(mygraph) <- list() ... See the Rgraphviz and Graphviz documentations.

layoutRegulatoryGraph(
  mygraph,
  label = "",
  node.fixedsize = FALSE,
  edge.weights = c("green", "black", "red"),
  edge.arrowheads = c("normal", "tee"),
  subgraphs = list(),
  subgraphs.colors = c("#B3E2CD", "#FDCDAC", "#F4CAE4", "#E6F5C9", "#FFF2AE")
)

`mygraph`	graphNEL
`label`	Label of the graph
`node.fixedsize`	logical. If font size is fixed or variable in regards to the nodes.
`edge.weights`	vector. which colors to use for weighted edges
`edge.arrowheads`	vector. which arrowheads to use for weighted edges
`subgraphs`	A list of character vectors with node names defining the sub graphs.
`subgraphs.colors`	vector. which colors to use for subgraphs

Returns the supplied graph in a layouted form with several parameters set for regulatory graph plotting.

Frank Kramer

 # load data
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 pwid2 = "pid_p_100146_hespathway"
 mygraph = pathway2RegulatoryGraph(biopax, pwid1)
 mygraph = layoutRegulatoryGraph(mygraph)
 plotRegulatoryGraph(mygraph)