From CSBLwiki
- E-book: Methods in bioengineering : systems analysis of biological networks
- Graph Visualization
- Bioconductor Install
- BioC packages
- Rgraphviz
- rsbml
- BiGGR
- Drawing network graphs (nodes and edges) with R/BioConductor [1]
- AdjMat to Graph - Simbiology in Matlab
source("http://bioconductor.org/biocLite.R")
## requirement: libsbml, graphviz library
biocLite("rsbml","Rgraphviz","BiGGR",type="source") # compiling from source code
###
### visualization of stoichiometric matrix
###
library("BiGGR") # <- related packages automatically ON (graph, igraph,...)
load("shewanella.rdata")
#sm # stoichiometric matrix
metabo = rownames(sm) # metabolites
fluxname = colnames(sm) # reactions
dim(sm)
am = matrix(0,729,729) # null adj. matrix
dimnames(am) = list(metabo,metabo); am[1:5,1:5]
## converting sm to am
for(i in 1:ncol(sm)) {
# i = 1
ind = names(sm[which(sm[,i]!=0),i])
am[ind,ind] = 1
# print(i)
}
diag(am) = 0 # set digonal '0'
## Too many edges such as ATP, H2O, PPi....
cofact = sort(rowSums(am),decreasing=T)[1:100]
cofact # top 100; mostly cofactors, tRNA...
cof.ind = which(metabo %in% names(cof))
am.m = am[-cof.ind,-cof.ind]
dim(am.m) # 629 629
## adjacency matrix to graph obj.
gl = new("graphAM",adjMat=am.m)
#> gl
#A graphAM graph with undirected edges
#Number of Nodes = 629
#Number of Edges = 1091
### draw network
pdf(file="net.pdf")
plot(gl)
dev.off()
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