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# Bios2cor 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 of the License, or
# any later version.
#
# 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.
#
# See the GNU General Public License at:
# http://www.gnu.org/licenses/
#
network.plot <- function(top_pairs, filepathroot){
pairs_i <- top_pairs$pairs_i
pairs_j <- top_pairs$pairs_j
if (is.null(filepathroot)) {
filename <- paste(tempdir(), "/NETWORK.pdf", sep="")
} else {
filename <- paste(filepathroot, "_NETWORK.pdf", sep="")
}
pdf(filename)
# create data:
links <- data.frame(source= pairs_i, target= pairs_j)
# Turn it into igraph object
network <- graph_from_data_frame(d= links, directed= F)
# Count the number of degree for each node:
deg <- degree(network, mode= "all")
# Plot
plot(network, vertex.size= deg*6, vertex.color= rgb(0.1,0.7,0.8,0.5))
dev.off()
}
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