Draw Network in R (control edge thickness plus non-overlapping edges) - r

Question

I need to draw a network with 5 nodes and 20 directed edges (an edge connecting each 2 nodes) using R, but I need two features to exist:
To be able to control the thickness of each edge.
The edges not to be overlapping (i.e.,the edge form A to B is not drawn over the edge from B to A)
I've spent hours looking for a solution, and tried many packages, but there's always a problem.
Can anybody suggest a solution please and provide a complete example as possible?
Many Thanks in advance.

Answer 1

If it is ok for the lines to be curved then I know two ways. First I create an edgelist:
Edges <- data.frame(
from = rep(1:5,each=5),
to = rep(1:5,times=5),
thickness = abs(rnorm(25)))
Edges <- subset(Edges,from!=to)
This contains the node of origin at the first column, node of destination at the second and weight at the third. You can use my pacake qgraph to plot a weighted graph using this. By default the edges are curved if there are multiple edges between two nodes:
library("qgraph")
qgraph(Edges,esize=5,gray=TRUE)
However this package is not really intended for this purpose and you can't change the edge colors (yet, working on it:) ). You can only make all edges black with a small trick:
qgraph(Edges,esize=5,gray=TRUE,minimum=0,cut=.Machine$double.xmin)
For more control you can use the igraph package. First we make the graph:
library("igraph")
g <- graph.edgelist(as.matrix(Edges[,-3]))
Note the conversion to matrix and subtracting one because the first node is 0. Next we define the layout:
l <- layout.fruchterman.reingold(g)
Now we can change some of the edge parameters with the E()function:
# Define edge widths:
E(g)$width <- Edges$thickness * 5
# Define arrow widths:
E(g)$arrow.width <- Edges$thickness * 5
# Make edges curved:
E(g)$curved <- 0.2
And finally plot the graph:
plot(g,layout=l)

Answer 2

While not an R answer specifically, I would recommend using Cytoscape to generate the network.
You can automate it using a RCytoscape.
http://bioconductor.org/packages/release/bioc/html/RCytoscape.html

Answer 3

The package informatively named 'network' can draw directed networks fairly well, and handle your issues.
ex.net <- rbind(c(0, 1, 1, 1), c(1, 0, 0, 1), c(0, 0, 0, 1), c(1, 0, 1, 0))
plot(network(ex.net), usecurve = T, edge.curve = 0.00001,
edge.lwd = c(4, rep(1, 7)))
The edge.curve argument, if set very low and combined with usecurve=T, separates the edges, although there might be a more direct way of doing this, and edge.lwd can take a vector as its argument for different sizes.
It's not always the prettiest result, I admit. But it's fairly easy to get decent looking network plots that can be customized in a number of different ways (see ?network.plot).

Answer 4

The 'non overlapping' constraint on edges is the big problem here. First, your network has to be 'planar' otherwise it's impossible in 2-dimensions (you cant connect three houses to gas, electric, phone company buildings without crossovers).
I think an algorithm for planar graph layout essentially solves the 4-colour problem. Have fun with that. Heuristics exist, search for planar graph layout, and force-directed, and read Planar Graph Layouts