I have nodes and edges information, and trying to make a network plot with that. The nodes information has 1552 rows with information like below:
The nodes file is here  nodes information file
And the edges information is with four columns with 1203576 entries:
The edges file is here  edges information file
Using the above nodes and edges data I used below code to make a network plot.
library(igraph)
net < graph_from_data_frame(d=edges, vertices=nodes, directed=F)
plot(net, edge.arrow.size=.4,vertex.label=NA,
vertex.color=as.numeric(factor(nodes$type)))
Grouped.net = net
E(Grouped.net)$weight = 1
colnames(nodes)[4] < "Clusters"
## Add edges with high weight between all nodes in the same group
for(Clus in unique(nodes$Clusters)) {
GroupV = which(nodes$Clusters == Clus)
Grouped.net = add_edges(Grouped.net, combn(GroupV, 2), attr=list(weight=80))
}
## Now create a layout based on G_Grouped
set.seed(567)
LO = layout_with_fr(Grouped.net)
# Generate colors based on media type:
colrs < c("gray50", "yellow", "tomato")
V(net)$color < colrs[V(net)$type_num]
plot(net, layout=LO, edge.arrow.size=.1,vertex.label=NA, verte.size=1)
legend(x=1.5, y=1.1, c("typeA","typeB", "typeC"), pch=21,
col="#777777", pt.bg=colrs, pt.cex=2, cex=.8, bty="n", ncol=1)
The plot I got looks like below:
In the above figure there are 5 clusters. And it looks like all the clusters are very close.

How do I increase the space between the clusters? How to move them far?

How to name the clusters in the Figure?

How to bring the nodes typeC to the top?
Any help is appreciated. thanq.