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# file dna/R/network.modules.R
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 or 3 of the License
# (at your option).
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
network.modules=function(s,m,epsilon,plot=FALSE,interactive=FALSE,...){
p=as.integer(nrow(s))
if (is.null(colnames(s))){
colnames(s)=paste("Gene",1:p)
rownames(s)=paste("Gene",1:p)
}
out=.C("rgmd",as.double(s),module=integer(p),as.integer(m),as.double(epsilon),p)
out$module=as.factor(out$module)
names(out$module)=rownames(s)
if (plot==TRUE){
if (requireNamespace("igraph",quietly=TRUE)){
if (sum(out$module!=0)>0){
graph.genenames=names(out$module)[out$module!=0]
graph.s=s[out$module!=0,out$module!=0]
Is=abs(graph.s)>=epsilon
rs=row(graph.s)
cs=col(graph.s)
vIs=c(Is)
vrs=c(rs)
vcs=c(cs)
orc=rs<cs
ex=vrs[vIs&orc]
ey=vcs[vIs&orc]
edges=rbind(ex,ey)
g=igraph::graph.empty(directed=FALSE)
g=igraph::add.vertices(g,length(graph.genenames),names=graph.genenames)
g=igraph::add.edges(g,edges)
if (interactive==TRUE)
igraph::tkplot(g,vertex.label=igraph::V(g)$names,...)
else
plot(g,vertex.label=igraph::V(g)$names,...)
}
}
else{
cat("No plot created since there are no modules in this network.\n")
}
}
new("modules",module=out$module)
}
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