support for multigraph

[Robert M. Flight]

Hi Paul,

I was wondering if multiGraph class support ever got added to RCy, as I don't see anything in the NEWS file. I have a case where it would be especially useful for this. I know I can do it directly by addCyEdge after passing in the graph, but thought I would check if there is planned support for multiGraph.

Cheers,

-Robert

[Mark Grimes]

Robert

You can use addGraphToGraph.

Below are two functions that you may find useful; "loadedges" illustrates how addGraphToGraph may be used.

Mark

plot.cy.2 <- function (cytoscape.file, edge.file) {

mydata <- new("graphNEL", edgemode='directed', nodes=as.character(cytoscape.file[, 1]))

# Set up and load all the node attributes

for (i in 2:ncol(cytoscape.file)) {

if (class(cytoscape.file[1,i]) != "numeric") {

mydata <- initNodeAttribute (graph=mydata,  attribute.name=names(cytoscape.file[i]), attribute.type='char', default.value=0.0)

nodeData (mydata, n=as.character(cytoscape.file[, 1]), attr=names(cytoscape.file[i])) <- as.character(cytoscape.file[,i]) }

if (class(cytoscape.file[1,i])=="numeric") {

mydata <- initNodeAttribute (graph=mydata,  attribute.name=names(cytoscape.file[i]), attribute.type='numeric', default.value=0.0) 

nodeData (mydata, n=as.character(cytoscape.file[, 1]), attr=names(cytoscape.file[i])) <- as.numeric(cytoscape.file[,i]) } 

}

# load standard edge attributes

mydata <- initEdgeAttribute (graph= mydata, attribute.name='edgeType', attribute.type='char', default.value='undefined')

  mydata <- initEdgeAttribute(mydata, attribute.name = "Weight", attribute.type = "numeric", default.value = 0.0)

  mydata = addEdge (as.vector(edge.file$Gene.1, mode="character"), as.vector(edge.file$Gene.2, mode="character"), mydata) 

  edgeData (mydata, as.vector(edge.file$Gene.1, mode="character"), as.vector(edge.file$Gene.2, mode="character"), attr='edgeType') <- as.character(edge.file$edgeType)

edgeData (mydata, as.vector(edge.file$Gene.1, mode="character"), as.vector(edge.file$Gene.2, mode="character"), attr='Weight') <- edge.file$Weight

return(mydata) }

#

loadedges <- function (Cy_Wind, Network.File) {

filename=NULL

a = as.character(Network.File$Gene.1)

b = as.character(Network.File $Gene.2)

nodenames <- unique(c(a,b))

edgeTypes <- levels(as.factor(Network.File$edgeType))

sepedges <- dlply(Network.File, .(edgeType)) 

subgraph2 <- new("graphNEL", nodes= nodenames, edgemode='undirected')

subgraph2 <- initEdgeAttribute (graph= subgraph2, attribute.name='edgeType', attribute.type='char', default.value='undefined')

  subgraph2 <- initEdgeAttribute(subgraph2, attribute.name = "Weight", attribute.type = "numeric", default.value = 0.0)

#

for(i in 1:length(sepedges)) {

filename[i] <- paste(edgeTypes[i], noquote("edges"), sep=" ", collapse=NULL)

edgefile <- data.frame(sepedges[i])

names(edgefile) <- names(Network.File)

subgraph2 = addEdge (as.vector(edgefile$Gene.1, mode="character"), as.vector(edgefile$Gene.2, mode="character"), subgraph2) 

edgeData (subgraph2, as.vector(edgefile$Gene.1, mode="character"), as.vector(edgefile$Gene.2, mode="character"), attr='edgeType') <- as.character(edgefile$edgeType)

edgeData (subgraph2, as.vector(edgefile$Gene.1, mode="character"), as.vector(edgefile$Gene.2, mode="character"), attr='Weight') <-edgefile$Weight

addGraphToGraph (Cy_Wind, subgraph2)

redraw(Cy_Wind) 

cat("\n", filename[i], "\n") 

}

cat("\n", filename) 

showGraphicsDetails(Cy_Wind, TRUE)

}

#

--
You received this message because you are subscribed to the Google Groups "RCytoscape" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rcytoscape+...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.