Drawing network graphs (nodes and edges) with R/BioConductor Skip to main content Skip to navigation Sign in Study Research Business Alumni News Engagement Search Warwick Search Molecular Organisation and Assembly in Cells About MOAC Find MOAC MOAC Research Protein Structure Cellular Structure Biological Fibres Intercellular Communication Molecular Interactions Analytical Science Student Publications MOAC Degrees Chemistry with Scientific Writing (MSc)(Restricted permissions) Scientific Research and Communication (MSc)(Restricted permissions) MOAC News MOAC Events Calendar News Graduations Joint DTC Conferences Annual Conferences MOAC Seminars MOAC People MOAC Students Staff How to find and contact MOAC Student Destinations MOAC People MOAC Students Peter Cock R Programming Network Graphs Drawing network graphs (nodes and edges) with R/BioConductor How do you draw network graphs in R? - the mathematical type of graph made up of nodes and edges that is. Several people recommended an R/BioConductor package called Rgraphviz, which is an interface to Graphviz - Graph Visualization Software. You'll need to install R, BioConductor and Graphviz first, and then install the Rgraphviz package and its dependancies from within R as follows: source("http://www.bioconductor.org/biocLite.R")
biocLite("Ruuid")
biocLite("graph")Replace broken link
biocLite("Rgraphviz")
So, documentation: How To use the graph package , HowTo Render A Graph Using Rgraphviz , very general. HowTo layout a pathway , focuses on drawing genetic networks using a KEGG pathway as an example. If you are more interested in the Graphviz and its DOT file format you could try: An Introduction to GraphViz and dot, includes a little bit on using Python with Graphviz. Here is a simple example converting an adjacency matrix into a graphAM object and plotting it. The matrix elements are taken to be the edge weights (zero being the absence of an edge), with the row and column names asssumed to be the nodes. > library(Rgraphviz)
...
> test.matrix<-matrix(rep(c(0,1,0,0), 9), ncol=6, nrow=6)
> rownames(test.matrix)<-c("a", "b", "c", "d", "e", "f")
> colnames(test.matrix)<-c("a", "b", "c", "d", "e", "f")
> test.matrix
a b c d e f
a 0 0 0 0 0 0
b 1 0 1 0 1 0
c 0 0 0 0 0 0
d 0 1 0 1 0 1
e 0 0 0 0 0 0
f 1 0 1 0 1 0
> am.graph<-new("graphAM", adjMat=test.matrix, edgemode="directed")
> am.graph
A graphAM graph with directed edges
Number of Nodes = 6
Number of Edges = 9
> plot(am.graph, attrs = list(node = list(fillcolor = "lightblue"),
edge = list(arrowsize=0.5)))
BioConductor also has a graphNEL object that uses Nodes and Edge-List internally. You can also use the as command to convert matrices into graphs, but using new is recommended as it gives you more control. For this simple example it makes no difference: > am.graph <- as(test.matrix, Class="graphAM")
> am.graph
A graphAM graph with directed edges
Number of Nodes = 6
Number of Edges = 9
> nel.graph <-as(test.matrix, Class="graphNEL")
> nel.graph
A graphNEL graph with directed edges
Number of Nodes = 6
Number of Edges = 9 The as command can also convert between the NEL and AM graph objects: > as(am.graph, Class="graphNEL")
A graphNEL graph with directed edges
Number of Nodes = 6
Number of Edges = 9
> as(nel.graph, Class="graphAM")
A graphAM graph with directed edges
Number of Nodes = 6
Number of Edges = 9 The R Project Graphviz : Graph Visualization Software BioConductor for Rgraphviz MOAC DTC, Senate House, University of Warwick, Coventry CV4 7AL Tel: 024 765 75808 Email: moac@warwick.ac.uk MOAC Intranet Page contact: MAS Resource Last revised: Mon 11 Apr 2011 Powered by Sitebuilder © MMXXII Terms Privacy Cookies Accessibility Coronavirus (Covid-19): Latest updates and information Let us know you agree to cookies We use cookies to give you the best online experience. Please let us know if you agree to functional, advertising and performance cookies. You can update your cookie preferences at any time. Cookie policy Essential cookies Functional cookies Advertising cookies Performance cookies Accept all Remember my preference More information
