This function gracefully removes nodes from a regulatory graph. If the node to be removed has both parent and child nodes, these are connected directly. The weight of the new direct edge is the product of multiplying the incomming and outgoing edge weights of the original node.
vector of node names specifiying which nodes to remove.
Returns a graph with specified nodes removed.
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# load data and retrieve wnt pathway data(biopaxexample) pwid1 = "pid_p_100002_wntpathway" mygraph1 = pathway2RegulatoryGraph(biopax, pwid1) mygraph1 = layoutRegulatoryGraph(mygraph1) # retrieve all nodes nodes = nodes(mygraph1) # random expression data for your nodes values = rnorm(length(nodes), mean=6, sd=2) # color nodes of the graph mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred") # plot the now colored graph plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)
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