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

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:

1. To be able to control the

Answer 1

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

Answer 2

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 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

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