colorGraphNodes: This function colors the nodes of a graph.

In rBiopaxParser: Parses BioPax files and represents them in R

Description

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.

Usage

colorGraphNodes(graph1, nodes, values, colors = c("greenred", "yellowred"))

Arguments

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.

Value

Returns a graph with specified nodes colored according to the foldChanges

Author(s)

Frank Kramer

Examples

 # 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)

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.