Visualizing your Network

This page illustrates how to use visualize a network model using the tools in enaR and the network package.

The first step is to prepare the workspace.

rm(list = ls())
library(enaR)
library(network)

Then we can load the library of models and select one to use for this illustration.

# load data
data(enaModels)        # load library of Ecosystem Networks
names(enaModels)       # view model names
m <- enaModels[[9]]    # select the oyster model

Simple Plot

We can then create a simple plot of the model with the default graphics parameters as

# Set the random seed to control plot output
set.seed(2)  # this is only used to ensure our plots look the same. 

# Plot network data object (uses plot.network)
plot(m)

Fancy Plot

We can create a fancier plot by exerting more control on the plotting parameters. Here is an example.

## Set colors to use
my.col <- c('red','yellow',rgb(204,204,153,maxColorValue=255),'grey22')
## Extract flow information for later use.
F <- as.matrix(m,attrname='flow')
## Get indices of positive flows
f <- which(F!=0, arr.ind=T)
opar <- par(las=1,bg=my.col[4],xpd=TRUE,mai=c(1.02, 0.62, 0.82, 0.42))
## Set the random seed to control plot output
set.seed(2)
plot(m,
## Scale nodes with storage
     vertex.cex=log(m%v%'storage'),
## Add node labels
     label= m%v%'vertex.names',
     boxed.labels=FALSE,
     label.cex=0.65,
## Make rounded nodes
     vertex.sides=45,
## Scale arrows to flow magnitude
     edge.lwd=log10(abs(F[f])),
     edge.col=my.col[3],
     vertex.col=my.col[1],
     label.col='white',
     vertex.border = my.col[3],
     vertex.lty = 1,
     xlim=c(-4,1),ylim=c(-2,-2))
## Lastly, remove changes to the plotting parameters
rm(opar)