colorGraphNodes {rBiopaxParser} | R Documentation |
This function colors nodes of a graph, usually this is used to color subgraphs or add a color hue correlating with the expression level or fold change to the molecules.
colorGraphNodes(graph1, nodes, values, colors = c("greenred", "yellowred"))
graph1 |
graphNEL |
nodes |
vector of node names specifiying which nodes to color. must be same length as parameter foldChanges |
values |
vector of values indicating fold changes, gene expression values or similar. colors are mapped linearly over the range of these values |
colors |
string. either "greenred" or "yellowred", specifying which color gradient to use. |
Returns a graph with specified nodes colored according to the foldChanges
Frank Kramer
# 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)